Supplemental Table S1. List of sRNA-seq libraries that were used as components in reference sets,,,,,,
prefix,genus_species,accession,description,aligned,unaligned,url
ath-b10,Arabidopsis thaliana,GSM2086247,Immature Inflorescence Tissue,5451665,8540,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR3222443_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,GSM2086248,Immature Inflorescence Tissue,5693019,6819,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR3222444_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,GSM2086249,Immature Inflorescence Tissue,8455006,8076,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR3222445_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,GSM2094956,Silique 5D ,4031145,4789,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR3269282_trimmed2Single.bam
ath-b10,Arabidopsis thaliana,GSM2094962,Hypocotyl,3703428,3274,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR3269288_trimmed2Single.bam
ath-b10,Arabidopsis thaliana,GSM2094974,Flower carpel ,3805464,3901,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR3269300_trimmed2Single.bam
ath-b10,Arabidopsis thaliana,GSM2094975,Bent Torpedo Embryo,3800376,5605,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR3269301_trimmed2Single.bam
ath-b10,Arabidopsis thaliana,GSM2094976,Green Leaf Embryo ,4493799,6276,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR3269302_trimmed2Single.bam
ath-b10,Arabidopsis thaliana,GSM2094977,Seedling,3001769,3270,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR3269303_trimmed2Single.bam
ath-b10,Arabidopsis thaliana,GSM2094978,Root,3907895,4245,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR3269304_trimmed2Single.bam
ath-b10,Arabidopsis thaliana,GSM2094979,Shoot Apical Meristem,3457681,3519,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR3269305_trimmed2Single.bam
ath-b10,Arabidopsis thaliana,GSM2300932,Seedling 2,34096301,25030,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR4115240_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,GSM2300933,Seedling 2,21495743,13141,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR4115241_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,GSM2300934,Seedling 2,24199825,13986,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR4115242_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,SRR5151108,Rosette from three week old plants,6023881,3094,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR5151108_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,SRR5151109,Rosette from three week old plants,6469078,3485,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR5151109_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,SRR5151110,Rosette from three week old plants,4962060,7480,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR5151110_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,SRR5151111,Rosette from three week old plants,5363514,8274,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR5151111_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,GSM2514737,21 day old plants,10692653,26417,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR5295846_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,GSM2514738,21 day old plants,11503954,30271,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR5295847_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,GSM2514739,21 day old plants,11391852,33753,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR5295848_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,GSM2825283,Inflorescence Tissues,9073977,13616,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR6192867_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,GSM2825284,Inflorescence Tissues,10719612,17057,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR6192868_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,GSM2825285,Inflorescence Tissues,7714710,11712,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR6192869_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,GSM2889189,Inflorescence Tissues,27329593,34839,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR6376831_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,GSM2889190,Inflorescence Tissues,23000982,25658,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR6376832_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,SRR6852083,2 weeks leaves,35023485,28829,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR6852083_trimmedSingle.bam
ath-b10,Arabidopsis thaliana,SRR6852084,2 weeks leaves,30020803,19780,http://plantsmallrnagenes.science.psu.edu/ath-b10/alignments/SRR6852084_trimmedSingle.bam
bna-b1,Brassica napus,GSM854154,silique (3 -- 7 -- 14 -- 21 days after flowering in Nanjing) -- control conditions,4904439,1434126,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/GSM854154.bam
bna-b1,Brassica napus,GSM854155,silique (3 -- 7 -- 14 -- 21 days after flowering in Nanjing) -- control conditions,5039197,1427733,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/GSM854155.bam
bna-b1,Brassica napus,GSM854157,silique (3 -- 7 -- 14 -- 21 days after flowering in Lhasa) -- control conditions,2874910,948700,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/GSM854157.bam
bna-b1,Brassica napus,GSM932400,seed (mature seed 50 days after flower opening) -- control conditions,12716945,3934763,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/GSM932400.bam
bna-b1,Brassica napus,GSM932401,seed (developing seed 7 -- 14 -- 21 -- 28 -- 42 days after flower opening) -- control conditions,15835641,2886439,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/GSM932401.bam
bna-b1,Brassica napus,SRR1363495,root (16-days-old plants) -- control conditions,9159199,7602785,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR1363495_3Q.bam
bna-b1,Brassica napus,SRR1363496,root (10-days-old plants) -- collected 6 days after infection with Verticillium longisporum VL43,7561784,9752188,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR1363496_3Q.bam
bna-b1,Brassica napus,SRR3539824,leaf -- mix of Sclerotinia sclerotiorum-inoculated (12 hours post-infection) and uninoculated leaves,6959062,3547922,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR3539824_3Q.bam
bna-b1,Brassica napus,SRR5331916,branch emergence site (at the bolting and or early flowering stages unknown) -- control conditions,5798591,3531703,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR5331916_3Q.bam
bna-b1,Brassica napus,SRR5332092,branch emergence site (at the bolting and or early flowering stages unknown) -- control conditions,6544417,4050400,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR5332092_3Q.bam
bna-b1,Brassica napus,SRR537600,seed cotyledon (45 days after flowering) -- control conditions,7006977,3042284,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR537600_3Q.bam
bna-b1,Brassica napus,SRR537601,seed coat (15 days after flowering) -- control conditions,8819119,3162655,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR537601_3Q.bam
bna-b1,Brassica napus,SRR537602,seed embryo (15 days after flowering) -- control conditions,4973799,4371425,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR537602_3Q.bam
bna-b1,Brassica napus,SRR537603,seed coat (35 days after flowering) -- control conditions,5262844,3365476,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR537603_3Q.bam
bna-b1,Brassica napus,SRR537604,seed embryo (35 days after flowering) -- control conditions,7094587,4887726,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR537604_3Q.bam
bna-b1,Brassica napus,SRR537605,seed endosperm (35 days after flowering) -- control conditions,3928002,5239101,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR537605_3Q.bam
bna-b1,Brassica napus,SRR537606,seed coat and endosperm (45 days after flowering) -- control conditions,4062145,4201541,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR537606_3Q.bam
bna-b1,Brassica napus,SRR537609,seed embryo (45 days after flowering) -- control conditions,5223488,4590574,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR537609_3Q.bam
bna-b1,Brassica napus,SRR537612,seed hypocotyl (45 days after flowering) -- control conditions,7970423,3528289,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR537612_3Q.bam
bna-b1,Brassica napus,SRR537633,seed radicle (45 days after flowering ) -- control conditions,9835544,4447518,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR537633_3Q.bam
bna-b1,Brassica napus,SRR537657,seed radicle (25 days after flowering ) -- control conditions,9341609,2513754,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR537657_3Q.bam
bna-b1,Brassica napus,SRR537857,seed hypocotyl (25 days after flowering) -- control conditions,7108165,3058299,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR537857_3Q.bam
bna-b1,Brassica napus,SRR538066,seed cotyledon (25 days after flowering) -- control conditions,5464097,3615586,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR538066_3Q.bam
bna-b1,Brassica napus,SRR538067,seed embryo (25 days after flowering) -- control conditions,4986597,2606016,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR538067_3Q.bam
bna-b1,Brassica napus,SRR538151,seed endosperm (25 days after flowering) -- control conditions,6691655,3438636,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR538151_3Q.bam
bna-b1,Brassica napus,SRR538225,seed coat (25 days after flowering) -- control conditions,5839495,1849499,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR538225_3Q.bam
bna-b1,Brassica napus,SRR538253,seed endosperm (15 days after flowering) -- control conditions,9702813,3910043,http://plantsmallrnagenes.science.psu.edu/bna-b1/alignments/SRR538253_3Q.bam
bol-b1.0,Brassica oleracea var. capitata,SRR799356,leaf (mature leaf) -- control conditions,19351393,5517000,http://plantsmallrnagenes.science.psu.edu/bol-b1.0/alignments/SRR799356_3Q.bam
bol-b1.0,Brassica oleracea var. capitata,SRR799357,leaf (mature leaf) -- control conditions,18681788,5074656,http://plantsmallrnagenes.science.psu.edu/bol-b1.0/alignments/SRR799357_3Q.bam
bol-b1.0,Brassica oleracea var. capitata,SRR799358,leaf (mature leaf) -- control conditions,20605768,5435329,http://plantsmallrnagenes.science.psu.edu/bol-b1.0/alignments/SRR799358_3Q.bam
bra-b1,Brassica rapa var. pekinensis,SRR2136646,flower bud (less than 6 mm length -- contain the entire developmental progress from anther generation to pollen abortion) -- control conditions,13000896,8629674,http://plantsmallrnagenes.science.psu.edu/bra-b1/alignments/SRR2136646_3Q.bam
bra-b1,Brassica rapa var. pekinensis,SRR2136647,flower bud (less than 6 mm length -- contain the entire developmental progress from anther generation to mature pollen) -- control conditions,15434200,8399156,http://plantsmallrnagenes.science.psu.edu/bra-b1/alignments/SRR2136647_3Q.bam
bra-b1,Brassica rapa var. pekinensis,SRR2912891,root -- control conditions,12337076,2146427,http://plantsmallrnagenes.science.psu.edu/bra-b1/alignments/SRR2912891_3Q.bam
bra-b1,Brassica rapa var. pekinensis,SRR2912893,stem -- control conditions,13582000,2192482,http://plantsmallrnagenes.science.psu.edu/bra-b1/alignments/SRR2912893_3Q.bam
bra-b1,Brassica rapa var. pekinensis,SRR2912894,leaf -- control conditions,10984722,6403987,http://plantsmallrnagenes.science.psu.edu/bra-b1/alignments/SRR2912894_3Q.bam
cpa-b0.4,Carica papaya,GSM712525,leaf (1-2-weeks-old plants) -- control conditions,3705338,959441,http://plantsmallrnagenes.science.psu.edu/cpa-b0.4/alignments/GSM712525.bam
cpa-b0.4,Carica papaya,GSM712526,flower (from female plants -- 1-3-weeks after flowering) -- control conditions,3478716,1179117,http://plantsmallrnagenes.science.psu.edu/cpa-b0.4/alignments/GSM712526.bam
cpa-b0.4,Carica papaya,GSM712527,leaf (2-3-weeks-old male plants) -- infected with ringspot virus,3004374,1500892,http://plantsmallrnagenes.science.psu.edu/cpa-b0.4/alignments/GSM712527.bam
cpa-b0.4,Carica papaya,SRR3538831,pistil (1.5cm long -- non-functional rudimentary pistils from normal male flowers) -- control conditions,18470721,2705394,http://plantsmallrnagenes.science.psu.edu/cpa-b0.4/alignments/SRR3538831_3Q.bam
cpa-b0.4,Carica papaya,SRR3538833,pistil (1.5cm long -- developed and functional pistils from male-to-hermaphrodite sex reversal flowers) -- sex change induced by low temperature,18315563,3685386,http://plantsmallrnagenes.science.psu.edu/cpa-b0.4/alignments/SRR3538833_3Q.bam
clt-b1,Citrullus lanatus,GSM936361,leaf and stem (3-weeks-old plants) -- fruit flesh -- rind and placenta (10 days after pollination) -- control conditions,5626276,1553055,http://plantsmallrnagenes.science.psu.edu/clt-b1/alignments/GSM936361.bam
clt-b1,Citrullus lanatus,SRR3318267,leaf (2-true-leaf stage) -- collected after 25 days post-inoculation with Cucumber Green Mottle Mosaic Virus ,11624171,14552656,http://plantsmallrnagenes.science.psu.edu/clt-b1/alignments/SRR3318267_3Q.bam
clt-b1,Citrullus lanatus,SRR3318270,leaf (2-true-leaf stage) -- collected after 25 days post-inoculation with mock solution,28408964,2045724,http://plantsmallrnagenes.science.psu.edu/clt-b1/alignments/SRR3318270_3Q.bam
clt-b1,Citrullus lanatus,SRR357407,part above cotyledons (2-true-leaf stage) -- control conditions,9627449,703168,http://plantsmallrnagenes.science.psu.edu/clt-b1/alignments/SRR357407_3Q.bam
clt-b1,Citrullus lanatus,SRR357408,part above cotyledons (2-true-leaf stage) -- control conditions,9648873,814367,http://plantsmallrnagenes.science.psu.edu/clt-b1/alignments/SRR357408_3Q.bam
clt-b1,Citrullus lanatus,SRR357409,part above cotyledons (2-true-leaf stage) -- control conditions,4864864,617022,http://plantsmallrnagenes.science.psu.edu/clt-b1/alignments/SRR357409_3Q.bam
clt-b1,Citrullus lanatus,SRR3823160,leaf (4-leaf stage) -- control conditions,8942805,498295,http://plantsmallrnagenes.science.psu.edu/clt-b1/alignments/SRR3823160_3Q.bam
clt-b1,Citrullus lanatus,SRR3823161,leaf (4-leaf stage) -- control conditions,9923954,600864,http://plantsmallrnagenes.science.psu.edu/clt-b1/alignments/SRR3823161_3Q.bam
clt-b1,Citrullus lanatus,SRR3823162,leaf (4-leaf stage) -- collected after 3-days melatonin treatment,9303635,550318,http://plantsmallrnagenes.science.psu.edu/clt-b1/alignments/SRR3823162_3Q.bam
clt-b1,Citrullus lanatus,SRR3823163,leaf (4-leaf stage) -- collected after 3-days melatonin treatment,11135304,766561,http://plantsmallrnagenes.science.psu.edu/clt-b1/alignments/SRR3823163_3Q.bam
clt-b1,Citrullus lanatus,SRR3823164,leaf (4-leaf stage) -- collected after 36h cold treatment,11723818,758583,http://plantsmallrnagenes.science.psu.edu/clt-b1/alignments/SRR3823164_3Q.bam
clt-b1,Citrullus lanatus,SRR3823165,leaf (4-leaf stage) -- collected after 36h cold treatment,8906356,553598,http://plantsmallrnagenes.science.psu.edu/clt-b1/alignments/SRR3823165_3Q.bam
clt-b1,Citrullus lanatus,SRR3823166,leaf (4-leaf stage) -- collected after 3-days melatonin treatment and subsequent 36h cold treatment,9014670,532648,http://plantsmallrnagenes.science.psu.edu/clt-b1/alignments/SRR3823166_3Q.bam
clt-b1,Citrullus lanatus,SRR3823167,leaf (4-leaf stage) -- collected after 3-days melatonin treatment and subsequent 36h cold treatment,10591560,608269,http://plantsmallrnagenes.science.psu.edu/clt-b1/alignments/SRR3823167_3Q.bam
csa-b2,Cucumis sativus,SRR1514098,leaf (6-weeks-old plants) -- collected 0 -- 0.5 -- 1 -- 3 and 7 days after treatment with mock solution,15884191,8571259,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR1514098_3Q.bam
csa-b2,Cucumis sativus,SRR1514099,leaf (6-weeks-old plants) -- collected 0 -- 0.5 -- 1 -- 3 and 7 days after treatment with Pseudoperonospora cubensis,13647166,7735176,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR1514099_3Q.bam
csa-b2,Cucumis sativus,SRR2045586,leaf -- 1 day post inoculation with Pseudoperonospora cubensis,7631133,4811714,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045586_3Q.bam
csa-b2,Cucumis sativus,SRR2045587,leaf -- 1 day post inoculation with Pseudoperonospora cubensis,4863441,3595863,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045587_3Q.bam
csa-b2,Cucumis sativus,SRR2045694,leaf -- 2 days post inoculation with Pseudoperonospora cubensis,5951664,4912050,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045694_3Q.bam
csa-b2,Cucumis sativus,SRR2045714,leaf -- 2 days post inoculation with Pseudoperonospora cubensis,4887673,1877047,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045714_3Q.bam
csa-b2,Cucumis sativus,SRR2045729,leaf -- 3 days post inoculation with Pseudoperonospora cubensis,6209947,4607959,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045729_3Q.bam
csa-b2,Cucumis sativus,SRR2045731,leaf -- 3 days post inoculation with Pseudoperonospora cubensis,8012941,2890108,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045731_3Q.bam
csa-b2,Cucumis sativus,SRR2045884,leaf -- 4 days post inoculation with Pseudoperonospora cubensis,4702801,2317209,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045884_3Q.bam
csa-b2,Cucumis sativus,SRR2045885,leaf -- 4 days post inoculation with Pseudoperonospora cubensis,6615548,2778114,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045885_3Q.bam
csa-b2,Cucumis sativus,SRR2045886,leaf -- 6 days post inoculation with Pseudoperonospora cubensis,4900254,1847349,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045886_3Q.bam
csa-b2,Cucumis sativus,SRR2045996,leaf -- 6 days post inoculation with Pseudoperonospora cubensis,6310506,2766149,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045996_3Q.bam
csa-b2,Cucumis sativus,SRR2045887,leaf -- mock-inoculated -- control conditions,7262203,2888641,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045887_3Q.bam
csa-b2,Cucumis sativus,SRR2045888,leaf -- mock-inoculated -- control conditions,6512358,2320776,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045888_3Q.bam
csa-b2,Cucumis sativus,SRR2045889,leaf -- 1 day post inoculation with Pseudoperonospora cubensis,4011929,2387564,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045889_3Q.bam
csa-b2,Cucumis sativus,SRR2045890,leaf -- 1 day post inoculation with Pseudoperonospora cubensis,5014967,3827485,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045890_3Q.bam
csa-b2,Cucumis sativus,SRR2045891,leaf -- 2 days post inoculation with Pseudoperonospora cubensis,5066066,2086441,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045891_3Q.bam
csa-b2,Cucumis sativus,SRR2045892,leaf -- 2 days post inoculation with Pseudoperonospora cubensis,6019976,2683513,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045892_3Q.bam
csa-b2,Cucumis sativus,SRR2045893,leaf -- 3 days post inoculation with Pseudoperonospora cubensis,6151773,1952963,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045893_3Q.bam
csa-b2,Cucumis sativus,SRR2045894,leaf -- 3 days post inoculation with Pseudoperonospora cubensis,6427208,2722306,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045894_3Q.bam
csa-b2,Cucumis sativus,SRR2045895,leaf -- 4 days post inoculation with Pseudoperonospora cubensis,3329944,981532,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045895_3Q.bam
csa-b2,Cucumis sativus,SRR2045896,leaf -- 4 days post inoculation with Pseudoperonospora cubensis,6613050,2857698,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045896_3Q.bam
csa-b2,Cucumis sativus,SRR2045897,leaf -- 6 days post inoculation with Pseudoperonospora cubensis,5700422,2083431,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045897_3Q.bam
csa-b2,Cucumis sativus,SRR2045898,leaf -- 6 days post inoculation with Pseudoperonospora cubensis,6656583,3144641,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045898_3Q.bam
csa-b2,Cucumis sativus,SRR2045900,leaf -- mock-inoculated -- control conditions,3024090,1092906,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045900_3Q.bam
csa-b2,Cucumis sativus,SRR2045901,leaf -- mock-inoculated -- control conditions,5710146,2262887,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR2045901_3Q.bam
csa-b2,Cucumis sativus,SRR3156435,internode vascular tissue (2-weeks-old plants) -- 12h of phosphate deficiency stress,3602578,326409,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156435_3Q.bam
csa-b2,Cucumis sativus,SRR3156436,internode vascular tissue (2-weeks-old plants) -- 12h of phosphate deficiency stress,3881752,447255,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156436_3Q.bam
csa-b2,Cucumis sativus,SRR3156437,internode vascular tissue (2-weeks-old plants) -- 12h of phosphate deficiency stress,8107442,1025925,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156437_3Q.bam
csa-b2,Cucumis sativus,SRR3156438,internode vascular tissue (2-weeks-old plants) -- control conditions,2596367,256207,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156438_3Q.bam
csa-b2,Cucumis sativus,SRR3156439,internode vascular tissue (2-weeks-old plants) -- control conditions,3502572,415111,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156439_3Q.bam
csa-b2,Cucumis sativus,SRR3156440,internode vascular tissue (2-weeks-old plants) -- control conditions,10081599,1033175,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156440_3Q.bam
csa-b2,Cucumis sativus,SRR3156441,lamina (2-weeks-old plants) -- 12h of phosphate deficiency stress,3734888,1101875,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156441_3Q.bam
csa-b2,Cucumis sativus,SRR3156442,lamina (2-weeks-old plants) -- 12h of phosphate deficiency stress,5437267,1084445,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156442_3Q.bam
csa-b2,Cucumis sativus,SRR3156443,lamina (2-weeks-old plants) -- 12h of phosphate deficiency stress,9051844,3624329,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156443_3Q.bam
csa-b2,Cucumis sativus,SRR3156444,lamina (2-weeks-old plants) -- control conditions,4539600,1173181,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156444_3Q.bam
csa-b2,Cucumis sativus,SRR3156445,lamina (2-weeks-old plants) -- control conditions,2889282,676806,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156445_3Q.bam
csa-b2,Cucumis sativus,SRR3156446,lamina (2-weeks-old plants) -- control conditions,8627426,2677557,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156446_3Q.bam
csa-b2,Cucumis sativus,SRR3156447,major vein (2-weeks-old plants) -- 12h of phosphate deficiency stress,4014893,616300,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156447_3Q.bam
csa-b2,Cucumis sativus,SRR3156448,major vein (2-weeks-old plants) -- 12h of phosphate deficiency stress,10512432,1243045,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156448_3Q.bam
csa-b2,Cucumis sativus,SRR3156449,major vein (2-weeks-old plants) -- 12h of phosphate deficiency stress,14924098,2059260,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156449_3Q.bam
csa-b2,Cucumis sativus,SRR3156450,major vein (2-weeks-old plants) -- control conditions,4588433,788406,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156450_3Q.bam
csa-b2,Cucumis sativus,SRR3156451,major vein (2-weeks-old plants) -- control conditions,3110730,487527,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156451_3Q.bam
csa-b2,Cucumis sativus,SRR3156452,major vein (2-weeks-old plants) -- control conditions,10365211,1901125,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156452_3Q.bam
csa-b2,Cucumis sativus,SRR3156453,pholem sap (2-weeks-old plants) -- 12h of phosphate deficiency stress,4661549,299649,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156453_3Q.bam
csa-b2,Cucumis sativus,SRR3156454,pholem sap (2-weeks-old plants) -- 12h of phosphate deficiency stress,3862431,241912,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156454_3Q.bam
csa-b2,Cucumis sativus,SRR3156455,pholem sap (2-weeks-old plants) -- 12h of phosphate deficiency stress,9909174,549060,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156455_3Q.bam
csa-b2,Cucumis sativus,SRR3156456,pholem sap (2-weeks-old plants) -- control conditions,2359180,145760,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156456_3Q.bam
csa-b2,Cucumis sativus,SRR3156457,pholem sap (2-weeks-old plants) -- control conditions,5549316,284734,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156457_3Q.bam
csa-b2,Cucumis sativus,SRR3156458,pholem sap (2-weeks-old plants) -- control conditions,8656886,474837,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156458_3Q.bam
csa-b2,Cucumis sativus,SRR3156459,petiole vascular tissue (2-weeks-old plants) -- 12h of phosphate deficiency stress,4043072,482519,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156459_3Q.bam
csa-b2,Cucumis sativus,SRR3156460,petiole vascular tissue (2-weeks-old plants) -- 12h of phosphate deficiency stress,15228325,2072598,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156460_3Q.bam
csa-b2,Cucumis sativus,SRR3156461,petiole vascular tissue (2-weeks-old plants) -- 12h of phosphate deficiency stress,8480226,1034892,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156461_3Q.bam
csa-b2,Cucumis sativus,SRR3156462,petiole vascular tissue (2-weeks-old plants) -- control conditions,4576884,500262,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156462_3Q.bam
csa-b2,Cucumis sativus,SRR3156463,petiole vascular tissue (2-weeks-old plants) -- control conditions,4582912,446425,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156463_3Q.bam
csa-b2,Cucumis sativus,SRR3156464,petiole vascular tissue (2-weeks-old plants) -- control conditions,10942758,1231969,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156464_3Q.bam
csa-b2,Cucumis sativus,SRR3156465,root (2-weeks-old plants) -- 12h of phosphate deficiency stress,3521769,504791,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156465_3Q.bam
csa-b2,Cucumis sativus,SRR3156466,root (2-weeks-old plants) -- 12h of phosphate deficiency stress,3366867,583956,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156466_3Q.bam
csa-b2,Cucumis sativus,SRR3156467,root (2-weeks-old plants) -- 12h of phosphate deficiency stress,20163734,3129119,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156467_3Q.bam
csa-b2,Cucumis sativus,SRR3156468,root (2-weeks-old plants) -- control conditions,3418329,564549,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156468_3Q.bam
csa-b2,Cucumis sativus,SRR3156469,root (2-weeks-old plants) -- control conditions,2918680,495759,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156469_3Q.bam
csa-b2,Cucumis sativus,SRR3156470,root (2-weeks-old plants) -- control conditions,10526130,1640193,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156470_3Q.bam
csa-b2,Cucumis sativus,SRR3156471,shoot apex (2-weeks-old plants) -- 12h of phosphate deficiency stress,3623871,445991,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156471_3Q.bam
csa-b2,Cucumis sativus,SRR3156472,shoot apex (2-weeks-old plants) -- 12h of phosphate deficiency stress,3514380,388100,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156472_3Q.bam
csa-b2,Cucumis sativus,SRR3156473,shoot apex (2-weeks-old plants) -- 12h of phosphate deficiency stress,7480410,736939,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156473_3Q.bam
csa-b2,Cucumis sativus,SRR3156474,shoot apex (2-weeks-old plants) -- control conditions,4414539,433644,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156474_3Q.bam
csa-b2,Cucumis sativus,SRR3156475,shoot apex (2-weeks-old plants) -- control conditions,6359919,807076,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156475_3Q.bam
csa-b2,Cucumis sativus,SRR3156476,shoot apex (2-weeks-old plants) -- control conditions,8233070,1072819,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRR3156476_3Q.bam
csa-b2,Cucumis sativus,SRX1656937,leaf -- control conditions,71959085,16371696,http://plantsmallrnagenes.science.psu.edu/csa-b2/alignments/SRX1656937_3Q.bam
car-b2.0,Cicer arietinum,SRR1005424,shoot (15-days-old plants) -- control conditions,9098091,591251,http://plantsmallrnagenes.science.psu.edu/car-b2.0/alignments/SRR1005424_3Q.bam
car-b2.0,Cicer arietinum,SRR1005425,root (15-days-old plants) -- control conditions,9299138,579897,http://plantsmallrnagenes.science.psu.edu/car-b2.0/alignments/SRR1005425_3Q.bam
car-b2.0,Cicer arietinum,SRR1005426,leaf (mature leaf from mature plants) -- control conditions,10981103,743553,http://plantsmallrnagenes.science.psu.edu/car-b2.0/alignments/SRR1005426_3Q.bam
car-b2.0,Cicer arietinum,SRR1005427,stem (mature plants) -- control conditions,10724996,645210,http://plantsmallrnagenes.science.psu.edu/car-b2.0/alignments/SRR1005427_3Q.bam
car-b2.0,Cicer arietinum,SRR1005428,flower bud (mature plants) -- control conditions,11161146,734843,http://plantsmallrnagenes.science.psu.edu/car-b2.0/alignments/SRR1005428_3Q.bam
car-b2.0,Cicer arietinum,SRR1005429,mature flower (mature plants) -- control conditions,14764796,1032941,http://plantsmallrnagenes.science.psu.edu/car-b2.0/alignments/SRR1005429_3Q.bam
car-b2.0,Cicer arietinum,SRR1005430,young pod (mature plants) -- control conditions,16069749,1014274,http://plantsmallrnagenes.science.psu.edu/car-b2.0/alignments/SRR1005430_3Q.bam
car-b2.0,Cicer arietinum,SRR1293689,seedling (14-days-old plants) -- control conditions,10767548,1412336,http://plantsmallrnagenes.science.psu.edu/car-b2.0/alignments/SRR1293689_3Q.bam
car-b2.0,Cicer arietinum,SRR1609731,flower (8 to 9 weeks-old plants) -- control conditions,8118437,28588655,http://plantsmallrnagenes.science.psu.edu/car-b2.0/alignments/SRR1609731_3Q.bam
car-b2.0,Cicer arietinum,SRR1609732,leaf (8 to 9 weeks-old plants) -- control conditions,12941790,31463830,http://plantsmallrnagenes.science.psu.edu/car-b2.0/alignments/SRR1609732_3Q.bam
gma-b1.0,Glycine max,SRR1197117,cotyledon (7-days-old plants) -- darkness,4224329,4381873,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1197117_3Q.bam
gma-b1.0,Glycine max,SRR1197118,hypocotyl (7-days-old plants) -- darkness,4261517,3231243,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1197118_3Q.bam
gma-b1.0,Glycine max,SRR1197119,apical hook concave (7-days-old plants) -- darkness,8877236,3820744,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1197119_3Q.bam
gma-b1.0,Glycine max,SRR1197120,apical hook convex (7-days-old plants) -- darkness,6715656,2667629,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1197120_3Q.bam
gma-b1.0,Glycine max,SRR1197121,cotyledon (7-days-old plants) -- far-red light,2270669,2300365,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1197121_3Q.bam
gma-b1.0,Glycine max,SRR1197122,hypocotyl (7-days-old plants) -- far-red light,6420054,4602550,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1197122_3Q.bam
gma-b1.0,Glycine max,SRR1197123,apical hook concave (7-days-old plants) -- far-red light,6013136,4283340,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1197123_3Q.bam
gma-b1.0,Glycine max,SRR1197124,apical hook convex (7-days-old plants) -- far-red light,6044825,3190689,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1197124_3Q.bam
gma-b1.0,Glycine max,SRR1292924,seed coat hilum (globular stage) -- control conditions,11098377,25317701,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1292924_3Q.bam
gma-b1.0,Glycine max,SRR1292925,seed coat hilum (globular stage) -- control conditions,7195374,16938105,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1292925_3Q.bam
gma-b1.0,Glycine max,SRR1292926,seed coat inner integument (globular stage) -- control conditions,9716219,21690746,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1292926_3Q.bam
gma-b1.0,Glycine max,SRX547547,seed coat inner integument (globular stage) -- control conditions,9768956,29365445,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX547547_3Q.bam
gma-b1.0,Glycine max,SRR1292928,seed coat outer integument (globular stage) -- control conditions,12151024,18942500,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1292928_3Q.bam
gma-b1.0,Glycine max,SRR1292929,seed coat outer integument (globular stage) -- control conditions,8308077,12951923,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1292929_3Q.bam
gma-b1.0,Glycine max,SRR1294476,embryo proper (heart stage) -- control conditions,9773509,17835318,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1294476_3Q.bam
gma-b1.0,Glycine max,SRR1294477,embryo proper (heart stage) -- control conditions,6539547,11669047,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1294477_3Q.bam
gma-b1.0,Glycine max,SRR1294478,endosperm (heart stage) -- control conditions,5710363,20369863,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1294478_3Q.bam
gma-b1.0,Glycine max,SRR1294479,endosperm (heart stage) -- control conditions,6227265,16049484,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1294479_3Q.bam
gma-b1.0,Glycine max,SRR1294483,seed coat inner integument (heart stage) -- control conditions,6791348,21060291,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1294483_3Q.bam
gma-b1.0,Glycine max,SRX549096,seed coat inner integument (heart stage) -- control conditions,7366576,22153281,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX549096_3Q.bam
gma-b1.0,Glycine max,SRR1294484,seed coat outer integument (heart stage) -- control conditions,6548746,20046186,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1294484_3Q.bam
gma-b1.0,Glycine max,SRR1294485,seed coat outer integument (heart stage) -- control conditions,9340910,21629445,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1294485_3Q.bam
gma-b1.0,Glycine max,SRR1295517,embryo proper (cotyledon stage) -- control conditions,11634308,34360696,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1295517_3Q.bam
gma-b1.0,Glycine max,SRX550093,embryo proper (cotyledon stage) -- control conditions,9063840,22078598,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX550093_3Q.bam
gma-b1.0,Glycine max,SRR1295519,embryo proper axis (cotyledon stage) -- control conditions,8668596,8289956,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1295519_3Q.bam
gma-b1.0,Glycine max,SRX550095,embryo proper axis (cotyledon stage) -- control conditions,3645292,3077810,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX550095_3Q.bam
gma-b1.0,Glycine max,SRR1295520,embryo proper cotyledon (cotyledon stage) -- control conditions,6086371,7411250,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1295520_3Q.bam
gma-b1.0,Glycine max,SRR1295521,embryo proper cotyledon (cotyledon stage) -- control conditions,7192253,14405632,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1295521_3Q.bam
gma-b1.0,Glycine max,SRR1295524,seed coat epidermis (cotyledon stage) -- control conditions,25167693,23339931,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1295524_3Q.bam
gma-b1.0,Glycine max,SRR1295525,seed coat epidermis (cotyledon stage) -- control conditions,20089111,11224190,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1295525_3Q.bam
gma-b1.0,Glycine max,SRR1295526,seed coat hilum (cotyledon stage) -- control conditions,8474407,18301718,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1295526_3Q.bam
gma-b1.0,Glycine max,SRR1295527,seed coat hilum (cotyledon stage) -- control conditions,4684922,5348839,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1295527_3Q.bam
gma-b1.0,Glycine max,SRR1295530,seed coat outer integument (cotyledon stage) -- control conditions,7267717,17332786,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1295530_3Q.bam
gma-b1.0,Glycine max,SRR1295531,seed coat outer integument (cotyledon stage) -- control conditions,12212587,18194059,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1295531_3Q.bam
gma-b1.0,Glycine max,SRR1296582,seed axis epidermis (early maturation stage) -- control conditions,6761954,7201370,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296582_3Q.bam
gma-b1.0,Glycine max,SRR1296583,seed axis epidermis (early maturation stage) -- control conditions,6122298,8896790,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296583_3Q.bam
gma-b1.0,Glycine max,SRR1296584,seed axis plumule (early maturation stage) -- control conditions,11544855,9437177,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296584_3Q.bam
gma-b1.0,Glycine max,SRR1296585,seed axis plumule (early maturation stage) -- control conditions,13548535,10626102,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296585_3Q.bam
gma-b1.0,Glycine max,SRR1296586,seed axis parenchyma (early maturation stage) -- control conditions,5695176,6308974,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296586_3Q.bam
gma-b1.0,Glycine max,SRX551005,seed axis parenchyma (early maturation stage) -- control conditions,5485628,5699300,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX551005_3Q_filtered.bam
gma-b1.0,Glycine max,SRR1296589,seed axis root tip (early maturation stage) -- control conditions,9962386,9981074,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296589_3Q.bam
gma-b1.0,Glycine max,SRX551006,seed axis root tip (early maturation stage) -- control conditions,9787181,40257202,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX551006_3Q_filtered.bam
gma-b1.0,Glycine max,SRR1296590,seed axis shoot apical meristem (early maturation stage) -- control conditions,11109860,17629007,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296590_3Q.bam
gma-b1.0,Glycine max,SRR1296591,seed axis shoot apical meristem (early maturation stage) -- control conditions,14001488,22648456,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296591_3Q.bam
gma-b1.0,Glycine max,SRR1296592,seed axis stele (early maturation stage) -- control conditions,8245099,10676912,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296592_3Q.bam
gma-b1.0,Glycine max,SRR1296593,seed axis stele (early maturation stage) -- control conditions,9432223,9470697,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296593_3Q.bam
gma-b1.0,Glycine max,SRR1296594,seed axis vasculature (early maturation stage) -- control conditions,18524405,31548950,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296594_3Q.bam
gma-b1.0,Glycine max,SRR1296595,seed axis vasculature (early maturation stage) -- control conditions,6479778,7727933,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296595_3Q.bam
gma-b1.0,Glycine max,SRR1296596,seed cotyledon abaxial epidermis (early maturation stage) -- control conditions,8312028,16378761,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296596_3Q.bam
gma-b1.0,Glycine max,SRR1296597,seed cotyledon abaxial epidermis (early maturation stage) -- control conditions,8838131,18173855,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296597_3Q.bam
gma-b1.0,Glycine max,SRR1296601,seed cotyledon adaxial epidermis (early maturation stage) -- control conditions,5798763,14168446,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296601_3Q.bam
gma-b1.0,Glycine max,SRX551018,seed cotyledon adaxial epidermis (early maturation stage) -- control conditions,8844027,20851379,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX551018_3Q.bam
gma-b1.0,Glycine max,SRR1296602,seed cotyledon adaxial parenchyma (early maturation stage) -- control conditions,5791722,13137364,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296602_3Q_filtered.bam
gma-b1.0,Glycine max,SRR1296603,seed cotyledon adaxial parenchyma (early maturation stage) -- control conditions,7803752,15789877,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296603_3Q_filtered.bam
gma-b1.0,Glycine max,SRR1296605,seed cotyledon vasculature (early maturation stage) -- control conditions,7011860,13582418,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296605_3Q.bam
gma-b1.0,Glycine max,SRX551022,seed cotyledon vasculature (early maturation stage) -- control conditions,14877487,36043451,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX551022_3Q.bam
gma-b1.0,Glycine max,SRR1296607,endosperm (early maturation stage) -- control conditions,14791530,35677959,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296607_3Q.bam
gma-b1.0,Glycine max,SRX551024,endosperm (early maturation stage) -- control conditions,10670913,39709499,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX551024_3Q.bam
gma-b1.0,Glycine max,SRR1296610,seed coat hilum (early maturation stage) -- control conditions,16605515,17144874,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296610_3Q.bam
gma-b1.0,Glycine max,SRR1296611,seed coat hilum (early maturation stage) -- control conditions,15767677,27423299,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296611_3Q.bam
gma-b1.0,Glycine max,SRR1296612,seed coat palisade (early maturation stage) -- control conditions,9805257,18620690,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296612_3Q.bam
gma-b1.0,Glycine max,SRR1296613,seed coat palisade (early maturation stage) -- control conditions,12976358,10633885,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296613_3Q.bam
gma-b1.0,Glycine max,SRR1296614,seed coat parenchyma (early maturation stage) -- control conditions,4358074,7088787,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296614_3Q.bam
gma-b1.0,Glycine max,SRR1296615,seed coat parenchyma (early maturation stage) -- control conditions,8117908,10219097,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1296615_3Q.bam
gma-b1.0,Glycine max,SRR1451604,anther (from unopened flowers) -- control conditions,9829942,33043650,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451604_3Q.bam
gma-b1.0,Glycine max,SRR1451605,anther (from unopened flowers) -- control conditions,17775412,24229776,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451605_3Q.bam
gma-b1.0,Glycine max,SRR1451606,ovary (from unopened flowers) -- control conditions,7489354,18259086,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451606_3Q.bam
gma-b1.0,Glycine max,SRR1451607,ovary (from unopened flowers) -- control conditions,23688420,28662562,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451607_3Q.bam
gma-b1.0,Glycine max,SRR1451608,unopened flower -- control conditions,8160810,33306177,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451608_3Q.bam
gma-b1.0,Glycine max,SRR1451609,unopened flower -- control conditions,27140013,21019994,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451609_3Q.bam
gma-b1.0,Glycine max,SRR1451610,open flower for 1 day -- control conditions,17287308,43169473,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451610_3Q.bam
gma-b1.0,Glycine max,SRR1451611,open flower for 1 day -- control conditions,22059708,26783507,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451611_3Q.bam
gma-b1.0,Glycine max,SRR1451624,leaf (V1 stage) -- treated with water for 30 min -- control,21260887,7257951,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451624_3Q.bam
gma-b1.0,Glycine max,SRR1451625,leaf (V1 stage) -- treated with water for 30 min -- control,14450743,5562179,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451625_3Q.bam
gma-b1.0,Glycine max,SRR1451626,leaf (V1 stage) -- treated with chitin octamer for 30 min,21353659,9330223,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451626_3Q.bam
gma-b1.0,Glycine max,SRR1451627,leaf (V1 stage) -- treated with chitin octamer for 30 min,14451695,5473358,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451627_3Q.bam
gma-b1.0,Glycine max,SRR1451636,leaf (V1 stage) -- treated with water for 30 min -- control,24140611,9404723,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451636_3Q.bam
gma-b1.0,Glycine max,SRR1451637,leaf (V1 stage) -- treated with water for 30 min -- control,15732179,4416206,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451637_3Q.bam
gma-b1.0,Glycine max,SRR1451638,leaf (V1 stage) -- treated with a conserved 22-amino acid peptide from bacterial flagellin 22 for 30 min,20972042,8541043,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451638_3Q.bam
gma-b1.0,Glycine max,SRR1451639,leaf (V1 stage) -- treated with a conserved 22-amino acid peptide from bacterial flagellin 22 for 30 min,17931977,5019872,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451639_3Q.bam
gma-b1.0,Glycine max,SRR2040133,embryo proper (globular stage) -- control conditions,7344552,19226529,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2040133_3Q.bam
gma-b1.0,Glycine max,SRR2040134,embryo proper (globular stage) -- control conditions,7540440,19777716,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2040134_3Q.bam
gma-b1.0,Glycine max,SRR2040167,seed coat hilum (heart stage) -- control conditions,12093273,28470940,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2040167_3Q.bam
gma-b1.0,Glycine max,SRX1038545,seed coat hilum (heart stage) -- control conditions,9967836,21928520,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX1038545_3Q.bam
gma-b1.0,Glycine max,SRR2340571,stem (trefoil stage) -- control conditions,3099242,2649114,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340571_3Q.bam
gma-b1.0,Glycine max,SRR2340572,old leaf (trefoil stage) -- control conditions,2551611,1676697,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340572_3Q.bam
gma-b1.0,Glycine max,SRR2340573,new leaf (trefoil stage) -- control conditions,2251266,2384448,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340573_3Q.bam
gma-b1.0,Glycine max,SRR2340574,old cotyledon (trefoil stage) -- control conditions,2822449,1994390,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340574_3Q.bam
gma-b1.0,Glycine max,SRR2340575,old leaf (stage of flower bud differentiation) -- control conditions,3168116,2104717,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340575_3Q.bam
gma-b1.0,Glycine max,SRR2340576,new leaf (stage of flower bud differentiation) -- control conditions,4225640,2482717,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340576_3Q.bam
gma-b1.0,Glycine max,SRR2340577,leaf bud (stage of flower bud differentiation) -- control conditions,2394455,1340879,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340577_3Q.bam
gma-b1.0,Glycine max,SRR2340578,flower bud (stage of flower bud differentiation) -- control conditions,3410792,1903953,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340578_3Q.bam
gma-b1.0,Glycine max,SRR2340579,developing seed (around 10-weeks-old plants) -- control conditions,2569767,1957863,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340579_3Q.bam
gma-b1.0,Glycine max,SRR2340581,developing seed (around 8-weeks-old plants) -- control conditions,2849097,1394999,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340581_3Q.bam
gma-b1.0,Glycine max,SRR2340582,developing seed (around 6-weeks-old plants) -- control conditions,3825870,1782381,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340582_3Q.bam
gma-b1.0,Glycine max,SRR2340583,pod (of 3 weeks) -- control conditions,2722706,2192132,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340583_3Q.bam
gma-b1.0,Glycine max,SRR2340584,pod (of 2 weeks) -- control conditions,3404014,2305882,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340584_3Q.bam
gma-b1.0,Glycine max,SRR2340585,pod (of 1 week) -- control conditions,3585865,2420158,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340585_3Q.bam
gma-b1.0,Glycine max,SRR2340586,stem (stage of germination) -- control conditions,3328931,2664803,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340586_3Q.bam
gma-b1.0,Glycine max,SRR2340588,cotyledon (stage of germination) -- control conditions,4057467,2803354,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340588_3Q.bam
gma-b1.0,Glycine max,SRR2340589,new leaf (stage of germination) -- control conditions,2219589,3579026,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340589_3Q.bam
gma-b1.0,Glycine max,SRR2340590,flower bud (before flowering ) -- control conditions,3398582,1951040,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340590_3Q.bam
gma-b1.0,Glycine max,SRR2340591,flower (stage of florescence) -- control conditions,2493110,1672339,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340591_3Q.bam
gma-b1.0,Glycine max,SRR2340592,old flower -- control conditions,2556097,1522192,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340592_3Q.bam
gma-b1.0,Glycine max,SRR2340593,flower (5 days after flowering) -- control conditions,3172678,2315376,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR2340593_3Q.bam
gma-b1.0,Glycine max,SRR3090714,leaf (10-days-old plants mock-inoculated for 14 days) -- control conditions,4036610,1716874,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR3090714_3Q.bam
gma-b1.0,Glycine max,SRR3090715,leaf (10-days-old plants inoculated for 14 days with Soybean mosaic virus-L ) -- SMV-L-infected,4299531,2332568,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR3090715_3Q.bam
gma-b1.0,Glycine max,SRR3090716,leaf (10-days-old plants inoculated for 14 days with Soybean mosaic virus-LRB) -- SMV-LRB-infected,3444099,1890392,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR3090716_3Q.bam
gma-b1.0,Glycine max,SRR3090717,leaf (10-days-old plants inoculated for 14 days with Soybean mosaic virus-G7) -- SMV-G7-infected,3407559,2919793,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR3090717_3Q.bam
gma-b1.0,Glycine max,SRR955300,seed coat (early maturation stage) -- control conditions,20458419,23430340,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR955300_3Q.bam
gma-b1.0,Glycine max,SRR955301,seed cotyledon (early maturation stage) -- control conditions,24017383,23395771,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR955301_3Q.bam
gma-b1.0,Glycine max,SRR955302,seed axis (early maturation stage) -- control conditions,22065914,25193266,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR955302_3Q.bam
gma-b1.0,Glycine max,SRX1038514,seed coat epidermis (globular stage) -- control conditions,7729276,16963791,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX1038514_3Q.bam
gma-b1.0,Glycine max,SRX1038515,seed coat epidermis (globular stage) -- control conditions,7235841,15881049,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX1038515_3Q.bam
gma-b1.0,Glycine max,SRX547542,endosperm (globular stage) -- control conditions,7209473,18178265,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX547542_3Q.bam
gma-b1.0,Glycine max,SRX547543,endosperm (globular stage) -- control conditions,3934882,20203843,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX547543_3Q_filtered.bam
gma-b1.0,Glycine max,SRX549088,seed endothelium (heart stage) -- control conditions,8717396,28443253,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX549088_3Q.bam
gma-b1.0,Glycine max,SRX549089,seed endothelium (heart stage) -- control conditions,10607561,39308263,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX549089_3Q.bam
gma-b1.0,Glycine max,SRX549094,seed coat epidermis (heart stage) -- control conditions,7375642,25229990,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX549094_3Q.bam
gma-b1.0,Glycine max,SRX549095,seed coat epidermis (heart stage) -- control conditions,7260721,26896933,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX549095_3Q.bam
gma-b1.0,Glycine max,SRX549100,seed suspensor (heart stage) -- control conditions,8191746,32651575,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX549100_3Q.bam
gma-b1.0,Glycine max,SRX549101,seed suspensor (heart stage) -- control conditions,6880071,25758599,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX549101_3Q.bam
gma-b1.0,Glycine max,SRX550099,endosperm (cotyledon stage) -- control conditions,9360678,37570956,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX550099_3Q_filtered.bam
gma-b1.0,Glycine max,SRX550100,endosperm (cotyledon stage) -- control conditions,7950525,40924614,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX550100_3Q.bam
gma-b1.0,Glycine max,SRX550105,seed coat inner integument (cotyledon stage) -- control conditions,13499339,51592098,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX550105_3Q.bam
gma-b1.0,Glycine max,SRX550106,seed coat inner integument (cotyledon stage) -- control conditions,11081905,31049602,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX550106_3Q.bam
gma-b1.0,Glycine max,SRX551016,seed cotyledon abaxial parenchyma (early maturation stage) -- control conditions,7174628,13726185,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX551016_3Q_filtered.bam
gma-b1.0,Glycine max,SRX551017,seed cotyledon abaxial parenchyma (early maturation stage) -- control conditions,7710413,13550571,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX551017_3Q_filtered.bam
gma-b1.0,Glycine max,SRX551026,seed coat hourglass (early maturation stage) -- control conditions,6478191,19839724,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX551026_3Q.bam
gma-b1.0,Glycine max,SRX551027,seed coat hourglass (early maturation stage) -- control conditions,6562236,19875428,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRX551027_3Q.bam
gma-b1.0,Glycine max,SRR1451650,nodule -- 10 days post-inoculation with Bradyrhizobium japonicum strain USDA110,14278718,27997754,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451650_3Q.bam
gma-b1.0,Glycine max,SRR1451651,nodule -- 10 days post-inoculation with Bradyrhizobium japonicum strain USDA110,9930073,29491558,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451651_3Q.bam
gma-b1.0,Glycine max,SRR1451652,nodule -- 10 days post-inoculation with Bradyrhizobium japonicum strain USDA110,14156341,24224330,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451652_3Q.bam
gma-b1.0,Glycine max,SRR1451653,nodule -- 15 days post-inoculation with Bradyrhizobium japonicum strain USDA110,15642784,29707850,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451653_3Q.bam
gma-b1.0,Glycine max,SRR1451654,nodule -- 15 days post-inoculation with Bradyrhizobium japonicum strain USDA110,16068910,25386516,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451654_3Q.bam
gma-b1.0,Glycine max,SRR1451655,nodule -- 15 days post-inoculation with Bradyrhizobium japonicum strain USDA110,16539630,17753900,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451655_3Q.bam
gma-b1.0,Glycine max,SRR1451656,nodule -- 20 days post-inoculation with Bradyrhizobium japonicum strain USDA110,13743710,31078789,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451656_3Q.bam
gma-b1.0,Glycine max,SRR1451657,nodule -- 20 days post-inoculation with Bradyrhizobium japonicum strain USDA110,10959832,19353191,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451657_3Q.bam
gma-b1.0,Glycine max,SRR1451658,nodule -- 20 days post-inoculation with Bradyrhizobium japonicum strain USDA110,13909663,18335258,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451658_3Q.bam
gma-b1.0,Glycine max,SRR1451659,nodule -- 25 days post-inoculation with Bradyrhizobium japonicum strain USDA110,12823890,25013428,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451659_3Q.bam
gma-b1.0,Glycine max,SRR1451660,nodule -- 25 days post-inoculation with Bradyrhizobium japonicum strain USDA110,15725697,21794610,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451660_3Q.bam
gma-b1.0,Glycine max,SRR1451661,nodule -- 25 days post-inoculation with Bradyrhizobium japonicum strain USDA110,11757374,14770612,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451661_3Q.bam
gma-b1.0,Glycine max,SRR1451662,nodule -- 30 days post-inoculation with Bradyrhizobium japonicum strain USDA110,12767640,20249704,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451662_3Q.bam
gma-b1.0,Glycine max,SRR1451663,nodule -- 30 days post-inoculation with Bradyrhizobium japonicum strain USDA110,12648891,23341505,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451663_3Q.bam
gma-b1.0,Glycine max,SRR1451664,nodule -- 30 days post-inoculation with Bradyrhizobium japonicum strain USDA110,12493142,23935519,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR1451664_3Q.bam
gma-b1.0,Glycine max,SRR835758,root (10-days-old plants) -- mix of short-term low nitrogen stress: 0.5 h -- 2 h -- 6 h --12 h,8481858,11179548,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR835758_3Q.bam
gma-b1.0,Glycine max,SRR835759,root (10-days-old plants) -- mix of short-term control conditions: 0.5 h -- 2 h -- 6 h --12 h,9820772,10964073,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR835759_3Q.bam
gma-b1.0,Glycine max,SRR835760,root (10-days-old plants) -- mix of long-term low nitrogen stress: 3d -- 6d -- 9d -- 12d,11108469,12838000,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR835760_3Q.bam
gma-b1.0,Glycine max,SRR835761,root (10-days-old plants) -- mix of long-term control conditions: 3d -- 6d -- 9d -- 12d,10399025,10403479,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR835761_3Q.bam
gma-b1.0,Glycine max,SRR835762,root (10-days-old plants) -- mix of short-term low nitrogen stress: 0.5 h -- 2 h -- 6 h --12 h,11766781,10299665,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR835762_3Q.bam
gma-b1.0,Glycine max,SRR835763,root (10-days-old plants) -- mix of short-term control conditions: 0.5 h -- 2 h -- 6 h --12 h,10572881,9992157,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR835763_3Q.bam
gma-b1.0,Glycine max,SRR835764,root (10-days-old plants) -- mix of long-term low nitrogen stress: 3d -- 6d -- 9d -- 12d,11959871,10296116,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR835764_3Q.bam
gma-b1.0,Glycine max,SRR835765,root (10-days-old plants) -- mix of long-term control conditions: 3d -- 6d -- 9d -- 12d,13886775,10291811,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR835765_3Q.bam
gma-b1.0,Glycine max,SRR835766,shoot (10-days-old plants) -- mix of short-term low nitrogen stress: 0.5 h -- 2 h -- 6 h --12 h,19258688,3234157,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR835766_3Q.bam
gma-b1.0,Glycine max,SRR835767,shoot (10-days-old plants) -- mix of short-term control conditions: 0.5 h -- 2 h -- 6 h --12 h,18670519,3797801,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR835767_3Q.bam
gma-b1.0,Glycine max,SRR835768,shoot (10-days-old plants) -- mix of long-term low nitrogen stress: 3d -- 6d -- 9d -- 12d,20438897,1401310,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR835768_3Q.bam
gma-b1.0,Glycine max,SRR835769,shoot (10-days-old plants) -- mix of short-term low nitrogen stress: 0.5 h -- 2 h -- 6 h --12 h,20780602,2547480,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR835769_3Q.bam
gma-b1.0,Glycine max,SRR835770,shoot (10-days-old plants) -- mix of long-term control conditions: 3d -- 6d -- 9d -- 12d,19549111,1226484,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR835770_3Q.bam
gma-b1.0,Glycine max,SRR835771,shoot (10-days-old plants) -- mix of short-term control conditions: 0.5 h -- 2 h -- 6 h --12 h,19799632,3632956,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR835771_3Q.bam
gma-b1.0,Glycine max,SRR835772,shoot (10-days-old plants) -- mix of long-term low nitrogen stress: 3d -- 6d -- 9d -- 12d,19503382,1677141,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR835772_3Q.bam
gma-b1.0,Glycine max,SRR835773,shoot (10-days-old plants) -- mix of long-term control conditions: 3d -- 6d -- 9d -- 12d,18748435,1023024,http://plantsmallrnagenes.science.psu.edu/gma-b1.0/alignments/SRR835773_3Q.bam
mtr-b4.0,Medicago truncatula,GSM1651990,flower (mixed stages) -- control conditions,39552743,8740563,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/GSM1651990_MTF_chopped.bam
mtr-b4.0,Medicago truncatula,GSM1651991,nodule (14-days-old plants) -- collected 14-days after inoculation with Sinorhizobium meliloti strain 2011,23167990,9832735,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/GSM1651991_14d_Nodule_chopped.bam
mtr-b4.0,Medicago truncatula,GSM1651992,denodule root (28-days-old plants) -- control conditions,16738234,5515077,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/GSM1651992_14d_DeNodRoot_chopped.bam
mtr-b4.0,Medicago truncatula,GSM1651993,nodule (14-days-old plants) -- collected 16-days after inoculation with Sinorhizobium meliloti strain 2011,15174893,9817685,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/GSM1651993_16d_Nodule_chopped.bam
mtr-b4.0,Medicago truncatula,GSM1651994,denodule root (30-days-old plants) -- control conditions,7947118,3267140,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/GSM1651994_16d_DeNodRoot_chopped.bam
mtr-b4.0,Medicago truncatula,GSM721574,shoot (4-5-weeks-old plants) -- control conditions,5516208,904026,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/GSM721574-4852.bam
mtr-b4.0,Medicago truncatula,GSM721575,shoot (4-5-weeks-old plants) -- drought stress,5765351,740614,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/GSM721575-4855.bam
mtr-b4.0,Medicago truncatula,SRR088874,mycorrhizal root (seedling stage) -- collected 3 weeks after inoculation with Glomus intraradices,4957411,1133865,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR088874_3Q.bam
mtr-b4.0,Medicago truncatula,SRR088875,root (seedling stage) -- collected 3 weeks after control conditions growth,5663026,1197776,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR088875_3Q.bam
mtr-b4.0,Medicago truncatula,SRR1954869,leaf (2-months-olds plants) -- control conditions,26506387,5133668,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR1954869_3Q.bam
mtr-b4.0,Medicago truncatula,SRR1954870,root (3-weeks-old plants) -- control conditions,16690323,8090235,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR1954870_3Q.bam
mtr-b4.0,Medicago truncatula,SRR1954871,seedling (2-days-old plants) -- control conditions,20825715,5941127,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR1954871_3Q.bam
mtr-b4.0,Medicago truncatula,SRR1954872,hairy root (miRNA overexpression control with empty vector) -- control conditions,28715651,7949287,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR1954872_3Q.bam
mtr-b4.0,Medicago truncatula,SRR1954873,hairy root (miRNA overexpression control with empty vector) -- control conditions,20929198,6242004,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR1954873_3Q.bam
mtr-b4.0,Medicago truncatula,SRR1954884,hairy root (target mimics control with empty vector) -- control conditions,31021910,7448207,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR1954884_3Q.bam
mtr-b4.0,Medicago truncatula,SRR1954885,hairy root (target mimics control with empty vector) -- control conditions,32156491,8865729,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR1954885_3Q.bam
mtr-b4.0,Medicago truncatula,SRR522482,root (4-days-old plants) -- control conditions,9420949,1889041,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR522482_3Q.bam
mtr-b4.0,Medicago truncatula,SRR522483,root (4-days-old plants) -- control conditions,10914054,1551103,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR522483_3Q.bam
mtr-b4.0,Medicago truncatula,SRR701982,nodule (22-days-old plants) -- collected 10-days after inoculation with Sinorhizobium meliloti 2011,13578444,3418597,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR701982_3Q.bam
mtr-b4.0,Medicago truncatula,SRR701983,nodule (22-days-old plants) -- collected 10-days after inoculation with Sinorhizobium meliloti 2011,10177913,3776823,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR701983_3Q.bam
mtr-b4.0,Medicago truncatula,SRR701984,nodule (22-days-old plants) -- collected 10-days after inoculation with Sinorhizobium meliloti 2011,9181045,3477990,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR701984_3Q.bam
mtr-b4.0,Medicago truncatula,SRR804912,callus (10-days-old leaf explant non root forming callus) -- treated with NAA/BAP,20125482,3234229,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR804912_3Q.bam
mtr-b4.0,Medicago truncatula,SRR804913,callus (10-days-old leaf explant root forming callus) -- treated with NAA,19923172,2636676,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR804913_3Q.bam
mtr-b4.0,Medicago truncatula,SRR804914,root (3-days-old seedling -- non-meristematic cells in elongation zone) -- control conditions,15595903,1921698,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR804914_3Q.bam
mtr-b4.0,Medicago truncatula,SRR804915,root (3-days-old seedling -- meristematic cells in tip) -- control conditions,21755483,2950453,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR804915_3Q.bam
mtr-b4.0,Medicago truncatula,SRX327823,root (tip) -- control conditions,5820682,1166001,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRX327823_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943036,root (tip) -- salt stress,3187922,505276,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943036_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943037,nodulated root (5-days-old plants) -- collected 5 days after inoculation with Sinorhizobium meliloti Sm2011,3525710,616303,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943037_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943038,root (5-days-old plants) -- collected 5 days after control conditions growth,2752258,682119,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943038_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943039,mycorrhizal root (7-weeks-old plants) -- inoculated with Rhizophagus irregularis,2976846,825564,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943039_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943040,root (7-weeks-old plants) -- control conditions,2721422,1008954,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943040_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943041,root -- infected with Ralstonia solanacearum GMI1000,2274660,618240,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943041_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943042,root -- control conditions,2617063,443741,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943042_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943043,root (10-days-old plants) -- infected with Verticillium albo-atrum V31.2,10458956,2452463,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943043_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943044,root (tip) -- control conditions,18735314,2531010,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943044_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943045,root (tip) -- salt stress,15872611,1668187,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943045_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943046,leaf -- control conditions,14233111,2018980,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943046_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943047,root (tip) -- control conditions,8217513,1555287,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943047_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943048,root (tip) -- salt stress,11782566,2247351,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943048_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943049,root (5-days-old plants) -- treated with Myc-LCO factor,14935215,7283207,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943049_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943050,root (5-days-old plants) -- treated with Myc-LCO factor,17203749,4977630,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943050_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943051,root (5-days-old plants) -- treated with Myc-LCO factor,16361768,4660472,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943051_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943052,root (5-days-old plants) -- treated with Nod factor,11111155,4820750,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943052_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943053,root (5-days-old plants) -- treated with Nod factor,16111290,5053869,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943053_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943054,root (5-days-old plants) -- treated with Nod factor,15493635,6910979,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943054_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943055,root (5-days-old plants) -- treated with Myc/Nod factor,14379313,6915250,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943055_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943056,root (5-days-old plants) -- treated with Myc/Nod factor,17893597,4946681,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943056_3Q.bam
mtr-b4.0,Medicago truncatula,SRR943057,root (5-days-old plants) -- treated with Myc/Nod factor,16868331,4700717,http://plantsmallrnagenes.science.psu.edu/mtr-b4.0/alignments/SRR943057_3Q.bam
pvu-b1.0,Phaseolus vulgaris,GSM769289,root (3-weeks-old plants) -- control conditions,2331097,1410017,http://plantsmallrnagenes.science.psu.edu/pvu-b1.0/alignments/GSM769289-30953.bam
pvu-b1.0,Phaseolus vulgaris,GSM769290,flower (mix of -1 -- 0 -- +1 days from tripping) -- control conditions,2171949,844838,http://plantsmallrnagenes.science.psu.edu/pvu-b1.0/alignments/GSM769290-30955.bam
pvu-b1.0,Phaseolus vulgaris,ERR701178,callus -- 6 days after inoculation of  Agrobacterium rhizogenes in the stem of seedlings,7888685,5792200,http://plantsmallrnagenes.science.psu.edu/pvu-b1.0/alignments/ERR701178_3Q.bam
pvu-b1.0,Phaseolus vulgaris,ERR701618,leaf,27438102,10835279,http://plantsmallrnagenes.science.psu.edu/pvu-b1.0/alignments/ERR701618_Q.bam
pvu-b1.0,Phaseolus vulgaris,SRR1946753,flower bud (35-40-days-old plants) -- control conditions,10902311,2484341,http://plantsmallrnagenes.science.psu.edu/pvu-b1.0/alignments/SRR1946753_3Q.bam
pvu-b1.0,Phaseolus vulgaris,SRR1946754,seedling (1- 4-days-old plants) -- control conditions,12376868,4635744,http://plantsmallrnagenes.science.psu.edu/pvu-b1.0/alignments/SRR1946754_3Q.bam
pvu-b1.0,Phaseolus vulgaris,SRR1946755,root (15-days-old plants) -- control conditions ,10535279,3168893,http://plantsmallrnagenes.science.psu.edu/pvu-b1.0/alignments/SRR1946755_3Q.bam
pvu-b1.0,Phaseolus vulgaris,SRR1946756,leaf (10- and 20-days-old plants) -- control conditions ,8942045,2906497,http://plantsmallrnagenes.science.psu.edu/pvu-b1.0/alignments/SRR1946756_3Q.bam
pvu-b1.0,Phaseolus vulgaris,SRR1946757,nodule (2-days-old plants) -- collected 18 and 27 days after inoculation with Rhizobium tropici in the roots,4418192,2288205,http://plantsmallrnagenes.science.psu.edu/pvu-b1.0/alignments/SRR1946757_3Q.bam
pvu-b1.0,Phaseolus vulgaris,SRR3479064,root hair (3-days-old plants) -- induced for 6 h at 30 C in the dark with pure Rhizobium etli nodulation factors,8164844,3129063,http://plantsmallrnagenes.science.psu.edu/pvu-b1.0/alignments/SRR3479064_Q.bam
pvu-b1.0,Phaseolus vulgaris,SRR3479065,root hair (3-days-old plants) -- induced for 6 h at 30 C in the dark with pure Rhizobium etli nodulation factors,8088255,2774061,http://plantsmallrnagenes.science.psu.edu/pvu-b1.0/alignments/SRR3479065_Q.bam
pvu-b1.0,Phaseolus vulgaris,SRR3479066,root hair (3-days-old plants) -- induced for 6 h at 30 C in the dark with pure Rhizobium etli nodulation factors,6758977,2182505,http://plantsmallrnagenes.science.psu.edu/pvu-b1.0/alignments/SRR3479066_Q.bam
pvu-b1.0,Phaseolus vulgaris,SRR3479067,root hair (3-days-old plants -- treated for 6 h at 30 C in the dark with mock solution) -- control conditions,6889332,2287842,http://plantsmallrnagenes.science.psu.edu/pvu-b1.0/alignments/SRR3479067_Q.bam
pvu-b1.0,Phaseolus vulgaris,SRR3479068,root hair (3-days-old plants -- treated for 6 h at 30 C in the dark with mock solution) -- control conditions,5967837,2748319,http://plantsmallrnagenes.science.psu.edu/pvu-b1.0/alignments/SRR3479068_Q.bam
pvu-b1.0,Phaseolus vulgaris,SRR3479069,root hair (3-days-old plants -- treated for 6 h at 30 C in the dark with mock solution) -- control conditions,7362352,3823328,http://plantsmallrnagenes.science.psu.edu/pvu-b1.0/alignments/SRR3479069_Q.bam
hbr-b0,Hevea brasiliensis,SRR2386003,latex -- control conditions,8529837,2407104,http://plantsmallrnagenes.science.psu.edu/hbr-b0/alignments/SRR2386003_Q.bam
hbr-b0,Hevea brasiliensis,SRR401320,leaf (mature) -- control conditions,37165624,4416364,http://plantsmallrnagenes.science.psu.edu/hbr-b0/alignments/SRR401320_53Q.bam
hbr-b0,Hevea brasiliensis,SRR401321,leaf (young) -- control conditions,18082013,3756362,http://plantsmallrnagenes.science.psu.edu/hbr-b0/alignments/SRR401321_53Q.bam
hbr-b0,Hevea brasiliensis,SRR401322,leaf (mature) -- control conditions,31749013,3755280,http://plantsmallrnagenes.science.psu.edu/hbr-b0/alignments/SRR401322_53Q.bam
hbr-b0,Hevea brasiliensis,SRR401323,leaf (young) -- control conditions,19151655,3831877,http://plantsmallrnagenes.science.psu.edu/hbr-b0/alignments/SRR401323_53Q.bam
mes-b6,Manihot esculenta,Cassa_Cal,callus -- control conditions,29609115,9460955,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/Cassa_Cal_3Q.bam
mes-b6,Manihot esculenta,Cassa_Lf,leaf -- control conditions,26395277,6775374,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/Cassa_Lf_3Q.bam
mes-b6,Manihot esculenta,Cassa_Ste,stem -- control conditions,32199113,8409661,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/Cassa_Ste_3Q.bam
mes-b6,Manihot esculenta,sm3684M,male flower -- control conditions,32068696,10426180,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/sm3684M_3Q.bam
mes-b6,Manihot esculenta,sm3684_13F,female flower -- control conditions,28563721,6946343,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/sm3684_13F_3Q.bam
mes-b6,Manihot esculenta,SRR1027040,leaf and root (2-months-old plants -- folded and fully expanded leaf) -- control conditions,4245440,1588644,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/SRR1027040_3Q.bam
mes-b6,Manihot esculenta,SRR1027041,leaf and root (2-months-old plants -- folded and fully expanded leaf) -- gradual cold acclimation,4048735,1550212,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/SRR1027041_3Q.bam
mes-b6,Manihot esculenta,SRR1027042,leaf and root (2-months-old plants -- folded and fully expanded leaf) -- cold shock,3752866,1513947,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/SRR1027042_3Q.bam
mes-b6,Manihot esculenta,SRR1027043,leaf and root (2-months-old plants -- folded and fully expanded leaf) -- cold stress after cold acclimation,4004060,1768525,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/SRR1027043_3Q.bam
mes-b6,Manihot esculenta,SRR1557206,leaf (150 days after planting -- fully expanded leaf) -- control conditions,15309332,2583657,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/SRR1557206_3Q.bam
mes-b6,Manihot esculenta,SRR1557207,storage root (150 days after planting) -- control conditions,17066266,4110477,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/SRR1557207_3Q.bam
mes-b6,Manihot esculenta,SRR1557208,leaf (150 days after planting -- fully expanded leaf) -- control conditions,19811686,5273944,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/SRR1557208_3Q.bam
mes-b6,Manihot esculenta,SRR1557209,storage root (150 days after planting) -- control conditions,17376444,7843493,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/SRR1557209_3Q.bam
mes-b6,Manihot esculenta,SRR1557210,leaf (150 days after planting -- fully expanded leaf) -- control conditions,13444803,4412857,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/SRR1557210_3Q.bam
mes-b6,Manihot esculenta,SRR1557211,storage root (150 days after planting) -- control conditions,11763188,7862293,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/SRR1557211_3Q.bam
mes-b6,Manihot esculenta,SRR210763,leaf and stem (6-weeks-old plants) -- control conditions,5283651,2811339,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/SRR210763_3Q.bam
mes-b6,Manihot esculenta,SRR3051996,leaf (10-days-old plants -- newly developing upper most leaves) -- collected 32 days after been transferred to Jiffy pellets,3242116,2401072,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/SRR3051996_3Q.bam
mes-b6,Manihot esculenta,SRR3052009,leaf (10-days-old plants -- newly developing upper most leaves) -- collected 67 days after been transferred to Jiffy pellets,5679469,3378945,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/SRR3052009_3Q.bam
mes-b6,Manihot esculenta,SRR3052015,leaf (10-days-old plants -- newly developing upper most leaves) -- collected 67 days after been transferred to Jiffy pellets,3572776,1861544,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/SRR3052015_3Q.bam
mes-b6,Manihot esculenta,SRR315731,leaf and stem (6-weeks-old plants) -- collected 0-6-24h and 2-5-7-15days post-inoculation with Xanthomonas axonopodis pv manihotis -- strain Xam CIO151,5932989,2864898,http://plantsmallrnagenes.science.psu.edu/mes-b6/alignments/SRR315731_3Q.bam
ptc-b3.0,Populus trichocarpa,GSM717875,leaf -- control conditions,3804781,668030,http://plantsmallrnagenes.science.psu.edu/ptc-b3.0/alignments/GSM717875.bam
ptc-b3.0,Populus trichocarpa,GSM717876,xylem -- control conditions,3676194,882428,http://plantsmallrnagenes.science.psu.edu/ptc-b3.0/alignments/GSM717876.bam
ptc-b3.0,Populus trichocarpa,GSM717877,xylem -- mechnically treated,3397328,575498,http://plantsmallrnagenes.science.psu.edu/ptc-b3.0/alignments/GSM717877.bam
ptc-b3.0,Populus trichocarpa,SRR4010495,unknown -- control conditions,25140590,1855164,http://plantsmallrnagenes.science.psu.edu/ptc-b3.0/alignments/SRR4010495_3Q.bam
ptc-b3.0,Populus trichocarpa,SRR4010496,unknown -- drought stress,28592769,1952088,http://plantsmallrnagenes.science.psu.edu/ptc-b3.0/alignments/SRR4010496_3Q.bam
ptc-b3.0,Populus trichocarpa,SRR926847,female flower bud -- control conditions,7866019,10862774,http://plantsmallrnagenes.science.psu.edu/ptc-b3.0/alignments/SRR926847_3Q.bam
ptc-b3.0,Populus trichocarpa,SRR926848,female flower bud -- control conditions,5767593,11241396,http://plantsmallrnagenes.science.psu.edu/ptc-b3.0/alignments/SRR926848_3Q.bam
gba-b1.0,Gossypium barbadense,GSM699076,root (seedlings with 2 fully expanded leaves) -- collected 12h and 24h after inoculation with water,5512052,10087273,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/GSM699076_Gb-mock.bam
gba-b1.0,Gossypium barbadense,GSM699077,root (seedlings with 2 fully expanded leaves) -- collected 12h and 24h after inoculation with Verticillium dahliae VJ37,4080811,9639487,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/GSM699077_Gb-inft.bam
gba-b1.0,Gossypium barbadense,SRR080703,fiber (10 days post-anthesis) -- control conditions,4418392,3330929,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR080703_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032467,shoot apex (seedling stage with 2 leaves) -- control conditions,7600390,4452863,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032467_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032468,shoot apex (seedling stage with 2 leaves) -- control conditions,6012217,5909319,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032468_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032469,shoot apex (seedling stage with 2 leaves) -- control conditions,7830980,4360391,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032469_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032470,shoot apex (seedling stage with 2 leaves) -- control conditions,4897392,6465860,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032470_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032471,shoot apex (seedling stage with 2 leaves) -- control conditions,5275940,5989316,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032471_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032472,shoot apex (seedling stage with 2 leaves) -- control conditions,5587911,6279907,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032472_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032473,shoot apex (pre-budding stage with about 8 leaves) -- control conditions,6073108,5239309,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032473_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032474,shoot apex (pre-budding stage with about 8 leaves) -- control conditions,6195204,4803953,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032474_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032475,shoot apex (pre-budding stage with about 8 leaves) -- control conditions,6441870,5098091,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032475_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032476,shoot apex (pre-budding stage with about 6 leaves) -- control conditions,5701245,6284823,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032476_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032477,shoot apex (pre-budding stage with about 6 leaves) -- control conditions,6150012,5287998,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032477_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032478,shoot apex (pre-budding stage with about 6 leaves) -- control conditions,6012049,5553434,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032478_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032479,shoot apex (budding stage with 11 leaves) -- control conditions,6989451,4818470,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032479_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032480,shoot apex (budding stage with 11 leaves) -- control conditions,6519899,4795446,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032480_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032481,shoot apex (budding stage with 11 leaves) -- control conditions,6615000,4532147,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032481_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032482,shoot apex (budding stage with 9 leaves) -- control conditions,6089786,5532763,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032482_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032483,shoot apex (budding stage with 9 leaves) -- control conditions,6433103,5400866,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032483_3Q.bam
gba-b1.0,Gossypium barbadense,SRR2032484,shoot apex (budding stage with 9 leaves) -- control conditions,6101372,5864762,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR2032484_3Q.bam
gba-b1.0,Gossypium barbadense,SRR3098990,ovule (0 days post-anthesis) -- control conditions,23310977,18430993,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR3098990_3Q.bam
gba-b1.0,Gossypium barbadense,SRR3098997,fiber (10 days post-anthesis) -- control conditions,22582747,18006586,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR3098997_3Q.bam
gba-b1.0,Gossypium barbadense,SRR3099003,fiber (20 days post-anthesis) -- control conditions,9413581,32817740,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR3099003_3Q.bam
gba-b1.0,Gossypium barbadense,SRR3099008,fiber (30 days post-anthesis) -- control conditions,7383159,44320562,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR3099008_3Q.bam
gba-b1.0,Gossypium barbadense,SRR5138524,unknown root -- stem -- leaf -- petal -- anther -- and stigma,3694840,7001484,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR5138524_Q.bam
gba-b1.0,Gossypium barbadense,SRR5138526,unknown root -- stem -- leaf -- petal -- anther -- and stigma,4054381,7148102,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR5138526_Q.bam
gba-b1.0,Gossypium barbadense,SRR5138528,unknown root -- stem -- leaf -- petal -- anther -- and stigma,5351831,5736808,http://plantsmallrnagenes.science.psu.edu/gba-b1.0/alignments/SRR5138528_Q.bam
ghr-b1.1,Gossypium hirsutum,GSM699074,root (seedlings with 2 fully expanded leaves) -- collected 12h and 24h after inoculation with water,8420059,7215061,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/GSM699074_Gh-mock.bam
ghr-b1.1,Gossypium hirsutum,GSM699075,root (seedlings with 2 fully expanded leaves) -- collected 12h and 24h after inoculation with Verticillium dahliae VJ37,8039778,7708130,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/GSM699075_Gh-inft.bam
ghr-b1.1,Gossypium hirsutum,SRR080704,fiber (10 days post-anthesis) -- control conditions,6418584,1500877,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR080704_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR1586235,leaf (young) -- control conditions,11884520,7569573,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR1586235_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR1586236,leaf (young) -- control conditions,13925654,9240791,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR1586236_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR1586237,leaf (young) -- control conditions,12363812,7910675,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR1586237_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR1586238,ovule (0 days post anthesis) -- control conditions,22274765,8152281,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR1586238_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR1586239,ovule (0 days post anthesis) -- control conditions,15583091,6014781,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR1586239_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR1586240,ovule (0 days post anthesis) -- control conditions,27769446,9785523,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR1586240_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR1586241,fiber (14 days post anthesis) -- control conditions,19976752,4334671,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR1586241_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR1586242,fiber (14 days post anthesis) -- control conditions,18556899,4730691,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR1586242_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR1586243,fiber (14 days post anthesis) -- control conditions,21437428,5462888,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR1586243_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032485,shoot apex (seedling stage with 2 leaves) -- control conditions,9434113,2393048,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032485_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032486,shoot apex (seedling stage with 2 leaves) -- control conditions,9267167,2334335,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032486_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032487,shoot apex (seedling stage with 2 leaves) -- control conditions,9195373,2394153,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032487_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032488,shoot apex (seedling stage with 2 leaves) -- control conditions,9668647,2388616,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032488_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032489,shoot apex (seedling stage with 2 leaves) -- control conditions,9480662,2716577,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032489_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032490,shoot apex (seedling stage with 2 leaves) -- control conditions,9536015,2263228,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032490_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032491,shoot apex (pre-budding stage with 6 leaves) -- control conditions,7799481,3909297,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032491_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032492,shoot apex (pre-budding stage with 6 leaves) -- control conditions,7996368,3851215,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032492_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032493,shoot apex (pre-budding stage with 6 leaves) -- control conditions,8313665,3686136,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032493_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032494,shoot apex (pre-budding stage with 5 leaves) -- control conditions,7459405,3528088,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032494_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032495,shoot apex (pre-budding stage with 5 leaves) -- control conditions,7996153,4009046,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032495_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032496,shoot apex (pre-budding stage with 5 leaves) -- control conditions,7556343,3597677,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032496_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032497,shoot apex (budding stage with 8 leaves) -- control conditions,9039627,2259692,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032497_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032498,shoot apex (budding stage with 8 leaves) -- control conditions,8557890,2589927,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032498_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032499,shoot apex (budding stage with 8 leaves) -- control conditions,9310693,2432269,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032499_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032500,shoot apex (budding stage with 12 leaves) -- control conditions,8121840,3122305,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032500_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032501,shoot apex (budding stage with 12 leaves) -- control conditions,9053602,3119341,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032501_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2032502,shoot apex (budding stage with 12 leaves) -- control conditions,7062664,4004050,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2032502_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2217931,ovule (-3 -- -1 -- 0 -- 1 -- 3 -- 5 -- 10 -- 20 and 25 days post anthesis) -- control conditions,13134803,2862675,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2217931_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR2217933,ovule (-3 -- -1 -- 0 -- 1 -- 3 -- 5 -- 10 -- 20 and 25 days post anthesis) -- control conditions,14239313,3149216,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR2217933_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149190,fiber (10 days post-anthesis) -- control conditions,5284191,2275450,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149190_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149194,fiber (10 days post-anthesis) -- control conditions,5408952,2870233,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149194_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149198,fiber (10 days post-anthesis) -- control conditions,3677420,1898157,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149198_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149191,fiber (15 days post-anthesis) -- control conditions,2965272,2097732,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149191_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149193,fiber (15 days post-anthesis) -- control conditions,3913764,4954776,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149193_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149197,fiber (15 days post-anthesis) -- control conditions,4222464,3416934,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149197_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149192,fiber (5 days post-anthesis) -- control conditions,4594403,3193655,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149192_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149195,fiber (5 days post-anthesis) -- control conditions,3039611,1572466,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149195_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149196,fiber (5 days post-anthesis) -- control conditions,5430720,3046107,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149196_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149203,fiber (15 days post-anthesis) -- control conditions,3900678,2825294,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149203_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149206,fiber (15 days post-anthesis) -- control conditions,2803574,1984560,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149206_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149207,fiber (15 days post-anthesis) -- control conditions,3755227,2609061,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149207_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149204,fiber (5 days post-anthesis) -- control conditions,3952266,2042718,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149204_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149205,fiber (5 days post-anthesis) -- control conditions,5505490,3365760,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149205_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149211,fiber (5 days post-anthesis) -- control conditions,6100848,3254078,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149211_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149208,fiber (10 days post-anthesis) -- control conditions,3751280,2371045,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149208_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149209,fiber (10 days post-anthesis) -- control conditions,4376135,2464649,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149209_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR5149210,fiber (10 days post-anthesis) -- control conditions,3497548,2072186,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR5149210_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR576119,hypocotyl (1-week-old plants -- 28 C in dark) -- control conditions,18987670,5655746,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR576119_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR576121,embryogenic callus (2 months after induction at 28 C in light) -- control conditions,20452171,5122678,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR576121_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR651105,anther (meiosis stage) -- control conditions,11051884,2995277,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR651105_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR651106,anther (tetrad stage) -- control conditions,13252582,3271420,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR651106_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR651107,anther (uninucleate stage) -- control conditions,10507168,2448674,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR651107_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR651108,anther (meiosis stage) -- control conditions,8669927,2091420,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR651108_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR651109,anther (tetrad stage) -- control conditions,10595657,2704544,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR651109_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR651110,anther (uninucleate stage) -- control conditions,10969088,2745537,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR651110_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRR959502,seedling (2-weeks-old plants post-emergence) -- control conditions,4245482,1379166,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRR959502_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRX1502642,cotyledon -- collected 24h after infestation with whitefly,17852577,15947478,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRX1502642_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRX1502643,cotyledon -- control conditions,15953458,12333501,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRX1502643_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRX1502644,cotyledon -- collected 24h after infestation with whitefly,15251786,11123679,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRX1502644_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRX2362115,cotyledon -- control conditions,34647033,12856381,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRX2362115_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRX611311,leaf (17-days-old plants) -- control conditions,2867912,3009922,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRX611311_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRX611312,leaf (17-days-old plants) -- collected 4h after salt stress,3074560,3405761,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRX611312_3Q.bam
ghr-b1.1,Gossypium hirsutum,SRX611313,leaf (17-days-old plants) -- collected 24h after salt stress,2969042,3717734,http://plantsmallrnagenes.science.psu.edu/ghr-b1.1/alignments/SRX611313_3Q.bam
tcc-b1.1,Theobroma cacao,GSM2805293,leaf (immature green leaf stage -- tip of the leaves) -- control conditions,1787932,329282,http://plantsmallrnagenes.science.psu.edu/tcc-b1.1/alignments/4_S4_R1_001_3Q.bam
fan-b1.0,Fragaria x ananassa,SRR1649251,receptacle (fruit treated with water 14 days after athesis) -- control conditions,4892057,1786252,http://plantsmallrnagenes.science.psu.edu/fan-b1.0/alignments/SRR1649251_3Q.bam
fan-b1.0,Fragaria x ananassa,SRR1649252,receptacle (fruit treated with water 19 days after athesis) -- control conditions,5241760,2362097,http://plantsmallrnagenes.science.psu.edu/fan-b1.0/alignments/SRR1649252_3Q.bam
fan-b1.0,Fragaria x ananassa,SRR1649253,receptacle (fruit treated with water 22 days after athesis) -- control conditions,6550486,2199245,http://plantsmallrnagenes.science.psu.edu/fan-b1.0/alignments/SRR1649253_3Q.bam
fan-b1.0,Fragaria x ananassa,SRR1649254,receptacle (19 days after athesis) -- collected 5 days later after treatment with ABA at 14 days after athesis,4503133,3629016,http://plantsmallrnagenes.science.psu.edu/fan-b1.0/alignments/SRR1649254_3Q.bam
fan-b1.0,Fragaria x ananassa,SRR1649255,receptacle (22 days after athesis) -- collected 8 days later after treatment with ABA at 14 days after athesis,6051980,3459741,http://plantsmallrnagenes.science.psu.edu/fan-b1.0/alignments/SRR1649255_3Q.bam
fan-b1.0,Fragaria x ananassa,SRR1649256,receptacle (19 days after athesis) -- collected 5 days later after treatment with ABA biosynthesis blocker nordihydroguaiaretic acid at 14 days after athesis,5640915,2217459,http://plantsmallrnagenes.science.psu.edu/fan-b1.0/alignments/SRR1649256_3Q.bam
fan-b1.0,Fragaria x ananassa,SRR1649257,receptacle (22 days after athesis) -- collected 8 days later after treatment with ABA biosynthesis blocker nordihydroguaiaretic acid at 14 days after athesis,4969491,2343251,http://plantsmallrnagenes.science.psu.edu/fan-b1.0/alignments/SRR1649257_3Q.bam
fan-b1.0,Fragaria x ananassa,SRR3680868,leaf,19536456,13923115,http://plantsmallrnagenes.science.psu.edu/fan-b1.0/alignments/SRR3680868_Q.bam
fan-b1.0,Fragaria x ananassa,SRR393996,fruit (mix of young green fruitlets -- big green fruits -- white fruits -- pink fruits and mature red fruits) -- control conditions,12545327,9927514,http://plantsmallrnagenes.science.psu.edu/fan-b1.0/alignments/SRR393996_3Q.bam
fan-b1.0,Fragaria x ananassa,SRR907583,fruit (at commercial maturity) -- control conditions,14670937,4492009,http://plantsmallrnagenes.science.psu.edu/fan-b1.0/alignments/SRR907583_3Q.bam
fan-b1.0,Fragaria x ananassa,SRR907584,fruit (at commercial maturity stored at 20 C for 24 h) -- control conditions,15784208,4895640,http://plantsmallrnagenes.science.psu.edu/fan-b1.0/alignments/SRR907584_3Q.bam
fve-b2.0,Fragaria vesca,SRR1586419,ovary wall (6-months-old plants -- 4 days post anthesis) -- control conditions,18016006,3359247,http://plantsmallrnagenes.science.psu.edu/fve-b2.0/alignments/SRR1586419_3Q.bam
fve-b2.0,Fragaria vesca,SRR1586420,ovary wall (6-months-old plants -- 10 days post anthesis) -- control conditions,15538677,2557063,http://plantsmallrnagenes.science.psu.edu/fve-b2.0/alignments/SRR1586420_3Q.bam
fve-b2.0,Fragaria vesca,SRR1586421,seed (6-months-old plants -- 4 days post anthesis) -- control conditions,7769972,1625703,http://plantsmallrnagenes.science.psu.edu/fve-b2.0/alignments/SRR1586421_3Q.bam
fve-b2.0,Fragaria vesca,SRR1586422,seed (6-months-old plants -- 10 days post anthesis) -- control conditions,29352714,5294166,http://plantsmallrnagenes.science.psu.edu/fve-b2.0/alignments/SRR1586422_3Q.bam
fve-b2.0,Fragaria vesca,SRR1586423,receptacle (6-months-old plants -- 10 days post anthesis) -- control conditions,27150885,5566005,http://plantsmallrnagenes.science.psu.edu/fve-b2.0/alignments/SRR1586423_3Q.bam
fve-b2.0,Fragaria vesca,SRR1586424,flower bud (6-months-old plants -- unopen flowers between stages 8 and 12) -- control conditions,34289931,6526186,http://plantsmallrnagenes.science.psu.edu/fve-b2.0/alignments/SRR1586424_3Q.bam
fve-b2.0,Fragaria vesca,SRR1586425,leaf (6-months-old plants -- unexpanded leaf) -- control conditions,30275548,4859950,http://plantsmallrnagenes.science.psu.edu/fve-b2.0/alignments/SRR1586425_3Q.bam
fve-b2.0,Fragaria vesca,SRR1586426,seedling (6-months-old plants -- the organ is 4-weeks-old) -- control conditions,37514197,7346773,http://plantsmallrnagenes.science.psu.edu/fve-b2.0/alignments/SRR1586426_3Q.bam
fve-b2.0,Fragaria vesca,SRR2003391,stolon (8-weeks-old plants -- mixture of developmental stages) -- control conditions,11314300,1350468,http://plantsmallrnagenes.science.psu.edu/fve-b2.0/alignments/SRR2003391_Q.bam
fve-b2.0,Fragaria vesca,SRR2003392,flower bud (8-weeks-old plants -- mixture of developmental stages) -- control conditions,12325901,1540276,http://plantsmallrnagenes.science.psu.edu/fve-b2.0/alignments/SRR2003392_Q.bam
fve-b2.0,Fragaria vesca,SRR2003393,flower (8-weeks-old plants -- open flower mixture of developmental stages) -- control conditions,14686920,2108787,http://plantsmallrnagenes.science.psu.edu/fve-b2.0/alignments/SRR2003393_Q.bam
fve-b2.0,Fragaria vesca,SRR2003394,fruit (8-weeks-old plants -- mixture of developmental stages) -- control conditions,12762516,1852796,http://plantsmallrnagenes.science.psu.edu/fve-b2.0/alignments/SRR2003394_Q.bam
fve-b2.0,Fragaria vesca,SRR2003396,leaf (8-weeks-old plants -- mixture of developmental stages) -- control conditions,13158915,1198091,http://plantsmallrnagenes.science.psu.edu/fve-b2.0/alignments/SRR2003396_Q.bam
fve-b2.0,Fragaria vesca,SRX248546,flower (1 day after opening) -- control conditions,37746256,5799607,http://plantsmallrnagenes.science.psu.edu/fve-b2.0/alignments/SRX248546_3Q.bam
mdm-b3.0,Malus x domestica,GSM880654,flower (2-years-old plants -- whole flower) -- control conditions,3801495,1639906,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/GSM880654_apple_flower_proc.bam
mdm-b3.0,Malus x domestica,GSM880655,fruit (2-years-old plants -- 15 and 120 days after anthesis) -- control conditions,6533221,2750672,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/GSM880655_apple_fruit_proc.bam
mdm-b3.0,Malus x domestica,SRR1136652,leaf (mature leaf) -- healthy or asymptomatic ASGV-infected unknown,8149553,2025865,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR1136652_15Q.bam
mdm-b3.0,Malus x domestica,SRR1136653,leaf (mature leaf) -- healthy or asymptomatic ASGV-infected unknown,11210545,2707078,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR1136653_15Q.bam
mdm-b3.0,Malus x domestica,SRR1136654,leaf (mature leaf) -- healthy or asymptomatic ASGV-infected unknown,6077708,1663152,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR1136654_15Q.bam
mdm-b3.0,Malus x domestica,SRR1136655,leaf (mature leaf) -- healthy or asymptomatic ASGV-infected unknown,11598177,2693471,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR1136655_15Q.bam
mdm-b3.0,Malus x domestica,SRR1136656,leaf (mature leaf) -- healthy or asymptomatic ASGV-infected unknown,11761320,2537411,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR1136656_15Q.bam
mdm-b3.0,Malus x domestica,SRR1136657,leaf (mature leaf) -- healthy or asymptomatic ASGV-infected unknown,12987884,2940389,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR1136657_15Q.bam
mdm-b3.0,Malus x domestica,SRR1260325,leaf (mature leaf) -- healthy or asymptomatic ASGV-infected unknown,8489484,4230603,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR1260325_15Q.bam
mdm-b3.0,Malus x domestica,SRR1260330,leaf (mature leaf) -- healthy or asymptomatic ASGV-infected unknown,5633548,2634091,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR1260330_15Q.bam
mdm-b3.0,Malus x domestica,SRR1260335,leaf (mature leaf) -- healthy or asymptomatic ASGV-infected unknown,6783247,3302624,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR1260335_15Q.bam
mdm-b3.0,Malus x domestica,SRR1260336,leaf (mature leaf) -- healthy or asymptomatic ASGV-infected unknown,7320677,3736997,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR1260336_15Q.bam
mdm-b3.0,Malus x domestica,SRR1260339,leaf (mature leaf) -- healthy or asymptomatic ASGV-infected unknown,6260204,3445946,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR1260339_15Q.bam
mdm-b3.0,Malus x domestica,SRR1260346,leaf (mature leaf) -- healthy or asymptomatic ASGV-infected unknown,6723911,3459269,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR1260346_15Q.bam
mdm-b3.0,Malus x domestica,SRR2182475,leaf (actively-growing leaf) -- control conditions,9110517,3393789,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR2182475_3Q.bam
mdm-b3.0,Malus x domestica,SRR2182488,leaf (actively-growing leaf) -- control conditions,12484410,3592220,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR2182488_3Q.bam
mdm-b3.0,Malus x domestica,SRR2182476,leaf (actively-growing leaf) -- control conditions,11375251,3404096,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR2182476_3Q.bam
mdm-b3.0,Malus x domestica,SRR2182489,leaf (actively-growing leaf) -- control conditions,10605744,2878085,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR2182489_3Q.bam
mdm-b3.0,Malus x domestica,SRR2182477,leaf (actively-growing leaf) -- control conditions,9466053,3207758,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR2182477_3Q.bam
mdm-b3.0,Malus x domestica,SRR2182487,leaf (actively-growing leaf) -- control conditions,10896313,3460459,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR2182487_3Q.bam
mdm-b3.0,Malus x domestica,SRR2182478,leaf (actively-growing leaf) -- control conditions,10074798,3489629,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR2182478_3Q.bam
mdm-b3.0,Malus x domestica,SRR2182479,leaf (actively-growing leaf) -- control conditions,10785420,4028010,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR2182479_3Q.bam
mdm-b3.0,Malus x domestica,SRR2182480,leaf (actively-growing leaf) -- control conditions,8177088,3023921,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR2182480_3Q.bam
mdm-b3.0,Malus x domestica,SRR413923,leaf (2-years-old plants -- mixed stages) -- control conditions,18207646,5598390,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR413923_3Q.bam
mdm-b3.0,Malus x domestica,SRR413924,root (2-years-old plants -- young root) -- control conditions,16118314,4428764,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR413924_3Q.bam
mdm-b3.0,Malus x domestica,SRR5448177,vegetative bud (16-years-old plants -- lateral buds from extension shoots) -- control conditions,2032233,2133001,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR5448177_3Q.bam
mdm-b3.0,Malus x domestica,SRR5448179,floral bud (16-years-old plants -- terminal buds from non-fruiting spurs) -- control conditions,2232363,2305493,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR5448179_3Q.bam
mdm-b3.0,Malus x domestica,SRR5448180,floral bud (16-years-old plants -- terminal buds from non-fruiting spurs) -- control conditions,2124170,2262730,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR5448180_3Q.bam
mdm-b3.0,Malus x domestica,SRR5448181,floral bud (16-years-old plants -- terminal buds from non-fruiting spurs) -- control conditions,2644805,2059977,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRR5448181_3Q.bam
mdm-b3.0,Malus x domestica,SRX653560,shoot tip (meristem -- stem and leaves but not including the first fully expanded leaf) -- control conditions,4999794,4191049,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRX653560_3r.bam
mdm-b3.0,Malus x domestica,SRX653561,shoot tip (meristem -- stem and leaves but not including the first fully expanded leaf) -- control conditions,5065906,4081244,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRX653561_3r.bam
mdm-b3.0,Malus x domestica,SRX653562,shoot tip (meristem -- stem and leaves but not including the first fully expanded leaf) -- control conditions,4158841,3235849,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRX653562_3r.bam
mdm-b3.0,Malus x domestica,SRX653563,shoot tip (meristem -- stem and leaves but not including the first fully expanded leaf) -- control conditions,5924301,4416530,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRX653563_3r.bam
mdm-b3.0,Malus x domestica,SRX653564,shoot tip (meristem -- stem and leaves but not including the first fully expanded leaf) -- control conditions,7973466,6097418,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRX653564_3r.bam
mdm-b3.0,Malus x domestica,SRX653565,shoot tip (meristem -- stem and leaves but not including the first fully expanded leaf) -- control conditions,4359699,3587895,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRX653565_3r.bam
mdm-b3.0,Malus x domestica,SRX653566,shoot tip (meristem -- stem and leaves but not including the first fully expanded leaf) -- control conditions,5673617,4560005,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRX653566_3r.bam
mdm-b3.0,Malus x domestica,SRX653567,shoot tip (meristem -- stem and leaves but not including the first fully expanded leaf) -- control conditions,5984247,4964567,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRX653567_3r.bam
mdm-b3.0,Malus x domestica,SRX653568,shoot tip (meristem -- stem and leaves but not including the first fully expanded leaf) -- control conditions,3995796,3164934,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRX653568_3r.bam
mdm-b3.0,Malus x domestica,SRX653569,shoot tip (meristem -- stem and leaves but not including the first fully expanded leaf) -- control conditions,4636645,4060593,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRX653569_3r.bam
mdm-b3.0,Malus x domestica,SRX653570,shoot tip (meristem -- stem and leaves but not including the first fully expanded leaf) -- control conditions,4607874,3386999,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRX653570_3r.bam
mdm-b3.0,Malus x domestica,SRX653571,shoot tip (meristem -- stem and leaves but not including the first fully expanded leaf) -- control conditions,5767919,4926562,http://plantsmallrnagenes.science.psu.edu/mdm-b3.0/alignments/SRX653571_3r.bam
ppe-b2.0,Prunus persica ,GSM944973,flower (whole flower) -- control conditions,3780046,1348782,http://plantsmallrnagenes.science.psu.edu/ppe-b2.0/alignments/GSM944973_peach_flower_proc.bam
ppe-b2.0,Prunus persica ,GSM944974,fruit (mixed stages: 19 -- 40 and 82 days after bloom) -- control conditions,3324333,1568010,http://plantsmallrnagenes.science.psu.edu/ppe-b2.0/alignments/GSM944974_peach_fruit_proc.bam
ppe-b2.0,Prunus persica ,SRR3647209,fruit (6-years-old plants -- 35 -- 55 -- 75 -- 90 -- 105 days after bloom -- yellow flesh) -- control conditions,12874062,4052883,http://plantsmallrnagenes.science.psu.edu/ppe-b2.0/alignments/SRR3647209_3Q.bam
ppe-b2.0,Prunus persica ,SRR504531,root (seedling stage) -- control conditions,20516657,2043670,http://plantsmallrnagenes.science.psu.edu/ppe-b2.0/alignments/SRR504531_3Q.bam
ppe-b2.0,Prunus persica ,SRR504532,leaf (emerging first leaves) -- control conditions,15853618,2457703,http://plantsmallrnagenes.science.psu.edu/ppe-b2.0/alignments/SRR504532_3Q.bam
ppe-b2.0,Prunus persica ,SRR948299,leaf -- stem -- flower bud (young emerging leaves -- young stems) -- control conditions,9679451,4859441,http://plantsmallrnagenes.science.psu.edu/ppe-b2.0/alignments/SRR948299_3Q.bam
ppe-b2.0,Prunus persica ,SRX016320,leaf -- from a peach latent mosaic viroid-infected tree,3609802,2022398,http://plantsmallrnagenes.science.psu.edu/ppe-b2.0/alignments/SRX016320_3Q.bam
ccl-b1,Citrus clementina,SRR2722829,ovule (3 days after flowering -- before nucellar embryo initiation stage -- hand-pollinated at anthesis with the pollen of Poncirus trifoliata) -- control conditions,10667893,1216652,http://plantsmallrnagenes.science.psu.edu/ccl-b1/alignments/SRR2722829_3Q.bam
ccl-b1,Citrus clementina,SRR2722830,ovule (3 days after flowering -- before nucellar embryo initiation stage -- hand-pollinated at anthesis with the pollen of Poncirus trifoliata) -- control conditions,8891457,884496,http://plantsmallrnagenes.science.psu.edu/ccl-b1/alignments/SRR2722830_3Q.bam
ccl-b1,Citrus clementina,SRR2722831,ovule (7 days after flowering -- at nucellar embryo initiation stage -- hand-pollinated at anthesis with the pollen of Poncirus trifoliata) -- control conditions,11743061,1495600,http://plantsmallrnagenes.science.psu.edu/ccl-b1/alignments/SRR2722831_3Q.bam
ccl-b1,Citrus clementina,SRX1353676,ovule (7 days after flowering -- at nucellar embryo initiation stage -- hand-pollinated at anthesis with the pollen of Poncirus trifoliata) -- control conditions,9213955,1033981,http://plantsmallrnagenes.science.psu.edu/ccl-b1/alignments/SRX1353676_3Q.bam
csi-b2,Citrus sinensis,GSM712528,leaf (young -- fully expanded) -- control conditions,2520313,620885,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/GSM712528-31236_5Q.bam
csi-b2,Citrus sinensis,GSM712529,flower (fully open) -- control conditions,2017205,707219,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/GSM712529-31238_5Q.bam
csi-b2,Citrus sinensis,SRR039884,fruit pulp (170 days after flowering) -- control conditions,3233338,1113131,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR039884_3Q.bam
csi-b2,Citrus sinensis,SRR039885,fruit pulp (170 days after flowering) -- control conditions,4586147,2234739,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR039885_3Q.bam
csi-b2,Citrus sinensis,SRR1044049,callus (nonembryogenic) -- control conditions,20388217,2657918,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR1044049_3Q.bam
csi-b2,Citrus sinensis,SRR1044050,callus (embryogenic) -- control conditions,21327176,2854644,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR1044050_3Q.bam
csi-b2,Citrus sinensis,SRR1044051,callus (embryogenic -- mix of calli exposed to somatic embryo induction for 1 -- 2 -- 3 -- 4 weeks) -- control conditions,20537513,3410761,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR1044051_3Q.bam
csi-b2,Citrus sinensis,SRR1259268,root (15-weeks-old plants irrigated with 0 microM H3BO3 for 15 weeks; about 5-mm-long root apex) -- boron-deficiency stress,19202971,2749327,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR1259268_3Q.bam
csi-b2,Citrus sinensis,SRR1259269,root (15-weeks-old plants irrigated with 10 microM H3BO3 for 15 weeks; about5-mm-long root apex) -- control conditions,19104573,3235635,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR1259269_3Q.bam
csi-b2,Citrus sinensis,SRR2166946,leaf (15-weeks-old plants irrigated with 0 microM H3BO3 for 15 weeks; fully-expanded leaf) -- boron-deficiency stress,15081791,2837025,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR2166946_3Q.bam
csi-b2,Citrus sinensis,SRR2166947,leaf (15-weeks-old plants irrigated with 10 microM H3BO3 for 15 weeks; fully-expanded leaf) -- control conditions,14912125,2794084,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR2166947_3Q.bam
csi-b2,Citrus sinensis,SRR2848261,leaf (11-weeks-old plants cultured with 400microM H3BO3 for 15 weeks; fully expanded leaf -- excised at one third the height of the plant) -- boron toxicity stress,8527712,1574327,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR2848261_3Q.bam
csi-b2,Citrus sinensis,SRR2848262,leaf (11-weeks-old plants cultured with 10microM H3BO3 for 15 weeks; fully expanded leaf -- excised at one third the height of the plant) -- control conditions,11384206,2177308,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR2848262_3Q.bam
csi-b2,Citrus sinensis,SRR2977531,leaf (15-weeks-old plants irrigated with 0 mM MgSO4 for 16 weeks; fully-expanded -- about 7-weeks-old leaf) -- magnesium-deficiency stress,17699534,2515387,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR2977531_3Q.bam
csi-b2,Citrus sinensis,SRR2977532,leaf (15-weeks-old plants irrigated with 1 mM MgSO4 for 16 weeks; fully-expanded -- about 7-weeks-old leaf) -- control conditions,19054186,3102367,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR2977532_3Q.bam
csi-b2,Citrus sinensis,SRR3457416,root (15-weeks-old plants -- cultivated in Mg-deficiency conditions for 16 weeks -- fully expanded root) -- magnesium-deficiency stress,17428347,2922729,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR3457416_3Q.bam
csi-b2,Citrus sinensis,SRR3457417,root (31-weeks-old plants -- fully expanded root) -- control conditions,18422206,3306847,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR3457417_3Q.bam
csi-b2,Citrus sinensis,SRR3774375,fruit pulp (170 days after flowering) -- control conditions,23128798,10818424,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR3774375_3Q.bam
csi-b2,Citrus sinensis,SRR3774376,fruit pulp (170 days after flowering) -- control conditions,21349592,10369319,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR3774376_3Q.bam
csi-b2,Citrus sinensis,SRR3774377,fruit pulp (170 days after flowering) -- control conditions,18861279,11762620,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR3774377_3Q.bam
csi-b2,Citrus sinensis,SRR3774378,fruit pulp (170 days after flowering) -- control conditions,13576213,9700361,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR3774378_3Q.bam
csi-b2,Citrus sinensis,SRR847765,leaf (young and mature stages) -- control conditions,11588991,3900594,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR847765_3Q.bam
csi-b2,Citrus sinensis,SRR847766,flower (early flower bud -- flower bud and mature flower) -- control conditions,9683709,4767057,http://plantsmallrnagenes.science.psu.edu/csi-b2/alignments/SRR847766_3Q.bam
dca-b2.0,Daucus carota,GSM2805297,root (6-weeks-old plants -- whole root) -- control conditions,4141074,1001229,http://plantsmallrnagenes.science.psu.edu/dca-b2.0/alignments/10_S10_R1_001_3Q.bam
dca-b2.0,Daucus carota,GSM2805296,leaf (5-weeks-old plants -- whole leaf) -- control conditions,10130766,1711361,http://plantsmallrnagenes.science.psu.edu/dca-b2.0/alignments/8_S8_R1_001_3Q.bam
lsa-b8,Lactuca sativa,SRR3836170,leaf -- collected 12h after inoculation with the fungus Bremia lactucae,32123140,5142093,http://plantsmallrnagenes.science.psu.edu/lsa-b8/alignments/SRR3836170_3Q.bam
lsa-b8,Lactuca sativa,SRR3836171,leaf -- collected 5 days after inoculation with the fungus Bremia lactucae,36990693,5718216,http://plantsmallrnagenes.science.psu.edu/lsa-b8/alignments/SRR3836171_3Q.bam
lsa-b8,Lactuca sativa,SRR3836172,leaf -- collected 12h after inoculation with mock solution,32309992,5351656,http://plantsmallrnagenes.science.psu.edu/lsa-b8/alignments/SRR3836172_3Q.bam
lsa-b8,Lactuca sativa,SRR3836173,leaf -- collected 5 days after inoculation with mock solution,31955582,5490743,http://plantsmallrnagenes.science.psu.edu/lsa-b8/alignments/SRR3836173_3Q.bam
lsa-b8,Lactuca sativa,SRR3836174,leaf -- collected 12h after inoculation with the fungus Bremia lactucae,33890532,5610512,http://plantsmallrnagenes.science.psu.edu/lsa-b8/alignments/SRR3836174_3Q.bam
lsa-b8,Lactuca sativa,SRR3836175,leaf -- collected 5 days after inoculation with the fungus Bremia lactucae,29116844,8904840,http://plantsmallrnagenes.science.psu.edu/lsa-b8/alignments/SRR3836175_3Q.bam
lsa-b8,Lactuca sativa,SRR3836176,leaf -- collected 12h after inoculation with mock solution,34816475,5991676,http://plantsmallrnagenes.science.psu.edu/lsa-b8/alignments/SRR3836176_3Q.bam
lsa-b8,Lactuca sativa,SRR3836177,leaf -- collected 5 days after inoculation with mock solution,34115307,6241881,http://plantsmallrnagenes.science.psu.edu/lsa-b8/alignments/SRR3836177_3Q.bam
lsa-b8,Lactuca sativa,SRR3836178,leaf -- collected 12h after inoculation with the fungus Bremia lactucae,32568447,4601592,http://plantsmallrnagenes.science.psu.edu/lsa-b8/alignments/SRR3836178_3Q.bam
lsa-b8,Lactuca sativa,SRR3836179,leaf -- collected 12h after inoculation with mock solution,33739349,3734109,http://plantsmallrnagenes.science.psu.edu/lsa-b8/alignments/SRR3836179_3Q.bam
oeu-b6,Olea europaea,SRR636243,fruit (unripe) -- control conditions,12039336,3067011,http://plantsmallrnagenes.science.psu.edu/oeu-b6/alignments/SRR636243_3Q.bam
oeu-b6,Olea europaea,SRR636244,fruit (ripe) -- control conditions,10910725,2741534,http://plantsmallrnagenes.science.psu.edu/oeu-b6/alignments/SRR636244_3Q.bam
oeu-b6,Olea europaea,SRR636245,leaf (juvenile leaves from on-year trees) -- control conditions,12829432,3935702,http://plantsmallrnagenes.science.psu.edu/oeu-b6/alignments/SRR636245_3Q.bam
oeu-b6,Olea europaea,SRR636246,leaf (mature leaves from on-year trees) -- control conditions,11664407,3391544,http://plantsmallrnagenes.science.psu.edu/oeu-b6/alignments/SRR636246_3Q.bam
oeu-b6,Olea europaea,SRR636247,leaf (juvenile leaves from off-year trees) -- control conditions,12431813,3368568,http://plantsmallrnagenes.science.psu.edu/oeu-b6/alignments/SRR636247_3Q.bam
oeu-b6,Olea europaea,SRR636248,leaf (mature leaves from off-year trees) -- control conditions,12235173,3341311,http://plantsmallrnagenes.science.psu.edu/oeu-b6/alignments/SRR636248_3Q.bam
ccm-b0.32,Cuscuta campestris,SRR3977128,Interface between C. campestris and A. thaliana,8696417,1253776,http://plantsmallrnagenes.science.psu.edu/ccm-b0.32/alignments/SRR3977128_ca.bam
ccm-b0.32,Cuscuta campestris,SRR3977129,Interface between C. campestris and A. thaliana,7659735,1076422,http://plantsmallrnagenes.science.psu.edu/ccm-b0.32/alignments/SRR3977129_ca.bam
ccm-b0.32,Cuscuta campestris,SRR3977130,C. campestris parasite stem,7030013,651242,http://plantsmallrnagenes.science.psu.edu/ccm-b0.32/alignments/SRR3977130_ca.bam
ccm-b0.32,Cuscuta campestris,SRR3977131,C. campestris parasite stem,7285398,820417,http://plantsmallrnagenes.science.psu.edu/ccm-b0.32/alignments/SRR3977131_ca.bam
ccm-b0.32,Cuscuta campestris,SRR6074034,Interface between C. campestris and A. thaliana,11331405,1392172,http://plantsmallrnagenes.science.psu.edu/ccm-b0.32/alignments/SRR6074034_ca.bam
ccm-b0.32,Cuscuta campestris,SRR6074035,Interface between C. campestris and A. thaliana,9749943,908267,http://plantsmallrnagenes.science.psu.edu/ccm-b0.32/alignments/SRR6074035_ca.bam
ccm-b0.32,Cuscuta campestris,SRR6074036,C. campestris parasite stem,10329024,1193682,http://plantsmallrnagenes.science.psu.edu/ccm-b0.32/alignments/SRR6074036_ca.bam
ccm-b0.32,Cuscuta campestris,SRR6074037,C. campestris parasite stem,11628851,1199639,http://plantsmallrnagenes.science.psu.edu/ccm-b0.32/alignments/SRR6074037_ca.bam
ccm-b0.1,Cuscuta campestris,SRR3977128,Interface between C. campestris and A. thaliana,8857526,1092667,http://plantsmallrnagenes.science.psu.edu/ccm-b0.1/alignments/SRR3977128_ca.bam
ccm-b0.1,Cuscuta campestris,SRR3977129,Interface between C. campestris and A. thaliana,7803701,932456,http://plantsmallrnagenes.science.psu.edu/ccm-b0.1/alignments/SRR3977129_ca.bam
ccm-b0.1,Cuscuta campestris,SRR3977130,C. campestris stem tissue above site of haustorium,7021495,659760,http://plantsmallrnagenes.science.psu.edu/ccm-b0.1/alignments/SRR3977130_ca.bam
ccm-b0.1,Cuscuta campestris,SRR3977131,C. campestris stem tissue above site of haustorium,7299852,805963,http://plantsmallrnagenes.science.psu.edu/ccm-b0.1/alignments/SRR3977131_ca.bam
ccm-b0.1,Cuscuta campestris,SRR6074034,Interface between C. campestris and A. thaliana,11337785,1385792,http://plantsmallrnagenes.science.psu.edu/ccm-b0.1/alignments/SRR6074034_ca.bam
ccm-b0.1,Cuscuta campestris,SRR6074035,Interface between C. campestris and A. thaliana,9753158,905052,http://plantsmallrnagenes.science.psu.edu/ccm-b0.1/alignments/SRR6074035_ca.bam
ccm-b0.1,Cuscuta campestris,SRR6074036,C. campestris stem tissue above site of haustorium,10170229,1352477,http://plantsmallrnagenes.science.psu.edu/ccm-b0.1/alignments/SRR6074036_ca.bam
ccm-b0.1,Cuscuta campestris,SRR6074037,C. campestris stem tissue above site of haustorium,11463965,1364525,http://plantsmallrnagenes.science.psu.edu/ccm-b0.1/alignments/SRR6074037_ca.bam
can-b1.6,Capsicum annuum,GSM712519,leaf (fully grown middle or upper) -- control conditions,3260408,1247814,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/GSM712519-30954_5.bam
can-b1.6,Capsicum annuum,GSM712520,flower (pre-anthesis) -- control conditions,3825639,1222030,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/GSM712520-30957_5.bam
can-b1.6,Capsicum annuum,GSM712521,fruit (exterior tissues: endocarp -- exocarp -- mesocarp) -- control conditions,4673657,1818468,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/GSM712521-30961_5.bam
can-b1.6,Capsicum annuum,SRR3620778,tissue not known -- Ca-C1 control,66070872,17818419,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR3620778_3Q.bam
can-b1.6,Capsicum annuum,SRR3620779,tissue not known -- Ca-T1 anthracnose pathogen Colletotrichum capsici,26966410,15355827,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR3620779_3Q.bam
can-b1.6,Capsicum annuum,SRR595046,flower -- control conditions,39344945,16901118,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR595046_3Q.bam
can-b1.6,Capsicum annuum,SRR595047,fruit (6 days after pollination) -- control conditions,42696052,13167032,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR595047_3Q.bam
can-b1.6,Capsicum annuum,SRR595048,fruit (16 days after pollination) -- control conditions,30859660,6409805,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR595048_3Q.bam
can-b1.6,Capsicum annuum,SRR595050,fruit (36 days after pollination -- mature green) -- control conditions,32046475,7822306,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR595050_3Q.bam
can-b1.6,Capsicum annuum,SRR595051,fruit (38 days after pollination) -- control conditions,35707727,7185166,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR595051_3Q.bam
can-b1.6,Capsicum annuum,SRR595052,fruit (43 days after pollination) -- control conditions,29498087,5298377,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR595052_3Q.bam
can-b1.6,Capsicum annuum,SRR595053,fruit (48 days after pollination) -- control conditions,39760083,6718928,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR595053_3Q.bam
can-b1.6,Capsicum annuum,SRR595054,leaf -- control conditions,40552914,22025696,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR595054_3Q.bam
can-b1.6,Capsicum annuum,SRR595055,root -- control conditions,34227040,9693388,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR595055_3Q.bam
can-b1.6,Capsicum annuum,SRR595056,stem -- control conditions,33429167,10592431,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR595056_3Q.bam
can-b1.6,Capsicum annuum,SRR616260,fruit (25 days after pollination) -- control conditions,34353731,7364882,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR616260_3Q.bam
can-b1.6,Capsicum annuum,SRR771957,leaf (mature leaves) -- control conditions,7948000,3189480,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR771957_3Q.bam
can-b1.6,Capsicum annuum,SRR771958,flower (fully open) -- control conditions,8325836,2461605,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR771958_3Q.bam
can-b1.6,Capsicum annuum,SRR771959,fruit (mature green) -- control conditions,8831690,2007414,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR771959_3Q.bam
can-b1.6,Capsicum annuum,SRR771960,root (developing roots) -- control conditions,11732738,5484867,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR771960_3Q.bam
can-b1.6,Capsicum annuum,SRR771961,stem (developing stem) -- control conditions,10506231,4052723,http://plantsmallrnagenes.science.psu.edu/can-b1.6/alignments/SRR771961_3Q.bam
nta-b0,Nicotiana tabacum,DRR014393,leaf -- control conditions,1907762,665122,http://plantsmallrnagenes.science.psu.edu/nta-b0/alignments/DRR014393_3Q.bam
nta-b0,Nicotiana tabacum,GSM717860,leaf (50-days-old plants -- fully grown middle or upper leaves) -- control conditions,1923018,703599,http://plantsmallrnagenes.science.psu.edu/nta-b0/alignments/GSM717860-42210_5.bam
nta-b0,Nicotiana tabacum,GSM717861,male flower (72-days-old plants -- pre-anthesis) -- control conditions,3009468,1185122,http://plantsmallrnagenes.science.psu.edu/nta-b0/alignments/GSM717861-42212_5.bam
nta-b0,Nicotiana tabacum,SRR1661412,leaf (6-weeks-old plants) -- control conditions,18525702,2404396,http://plantsmallrnagenes.science.psu.edu/nta-b0/alignments/SRR1661412_3Q.bam
nta-b0,Nicotiana tabacum,SRR1661413,leaf (5-weeks-old plants) -- collected 10 days after infection with satR Cucumber mosaic virus Shandong strain devoid of SD-satRNA,13521198,8948670,http://plantsmallrnagenes.science.psu.edu/nta-b0/alignments/SRR1661413_3Q.bam
nta-b0,Nicotiana tabacum,SRR360389,root -- control conditions,6402692,5413850,http://plantsmallrnagenes.science.psu.edu/nta-b0/alignments/SRR360389_3Q.bam
nta-b0,Nicotiana tabacum,SRR360390,root -- 24h after topping,6526486,5051220,http://plantsmallrnagenes.science.psu.edu/nta-b0/alignments/SRR360390_3Q.bam
nta-b0,Nicotiana tabacum,SRR3680865,leaf -- control conditions,11263337,25453006,http://plantsmallrnagenes.science.psu.edu/nta-b0/alignments/SRR3680865_Q.bam
nta-b0,Nicotiana tabacum,SRR4453462,tissue not known -- treated with 3-acetonyl-3-hydroxyoxindole,10676571,968501,http://plantsmallrnagenes.science.psu.edu/nta-b0/alignments/SRR4453462_3Q.bam
nta-b0,Nicotiana tabacum,SRR4453463,tissue not known -- treated with dimethyl sulfoxide,9458378,966226,http://plantsmallrnagenes.science.psu.edu/nta-b0/alignments/SRR4453463_3Q.bam
nta-b0,Nicotiana tabacum,SRR638993,root (seedlings with 6 leaves) -- control conditions,13219069,3445408,http://plantsmallrnagenes.science.psu.edu/nta-b0/alignments/SRR638993_3Q.bam
nta-b0,Nicotiana tabacum,SRR638994,root (seedlings with 6 leaves) -- collected 6h and 48h after PEG-induced drought stress,12898911,3555634,http://plantsmallrnagenes.science.psu.edu/nta-b0/alignments/SRR638994_3Q.bam
nta-b0,Nicotiana tabacum,SRR638995,stem (seedlings with 6 leaves) -- control conditions,14882282,3746114,http://plantsmallrnagenes.science.psu.edu/nta-b0/alignments/SRR638995_3Q.bam
nta-b0,Nicotiana tabacum,SRR638996,leaf (seedlings with 6 leaves) -- control conditions,11400186,2270543,http://plantsmallrnagenes.science.psu.edu/nta-b0/alignments/SRR638996_3Q.bam
sly-b2.5,Solanum lycopersicum,ERR493659,fruit (ripe) -- control conditions,6562679,3602419,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR493659_Q.bam
sly-b2.5,Solanum lycopersicum,ERR493660,fruit (ripe) -- control conditions,7622120,2978992,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR493660_Q.bam
sly-b2.5,Solanum lycopersicum,ERR493661,fruit (ripe) -- control conditions,14214920,4700402,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR493661_Q.bam
sly-b2.5,Solanum lycopersicum,ERR493662,fruit (ripe) -- control conditions,9777330,2845003,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR493662_Q.bam
sly-b2.5,Solanum lycopersicum,ERR493663,fruit (ripe) -- control conditions,5328111,2986386,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR493663_Q.bam
sly-b2.5,Solanum lycopersicum,ERR493664,fruit (ripe) -- control conditions,7948331,1069121,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR493664_Q.bam
sly-b2.5,Solanum lycopersicum,ERR493665,fruit (ripe) -- control conditions,8485387,1330814,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR493665_Q.bam
sly-b2.5,Solanum lycopersicum,ERR985504,pollen (mature -- flower buds >= 10 mm -- bicellular pollen) -- control conditions,3562284,487790,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985504_15Q.bam
sly-b2.5,Solanum lycopersicum,ERR985505,pollen (mature -- flower buds >= 10 mm -- bicellular pollen) -- control conditions,2375516,327746,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985505_15Q.bam
sly-b2.5,Solanum lycopersicum,ERR985506,pollen (mature -- flower buds >= 10 mm -- bicellular pollen) -- control conditions,2508926,334058,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985506_15Q.bam
sly-b2.5,Solanum lycopersicum,ERR985507,pollen (post-meiotic -- flower buds 6-8 mm -- microspores) -- control conditions,4455391,713643,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985507_15Q.bam
sly-b2.5,Solanum lycopersicum,ERR985508,pollen (post-meiotic -- flower buds 6-8 mm -- microspores) -- control conditions,4130060,633746,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985508_15Q.bam
sly-b2.5,Solanum lycopersicum,ERR985509,pollen (post-meiotic -- flower buds 6-8 mm -- microspores) -- control conditions,3902056,532895,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985509_15Q.bam
sly-b2.5,Solanum lycopersicum,ERR985510,pollen (tetrad -- flower buds 4-6 mm -- meiotic stage/microspore mother cell) -- control conditions,4508717,591569,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985510_15Q.bam
sly-b2.5,Solanum lycopersicum,ERR985511,pollen (tetrad -- flower buds 4-6 mm -- meiotic stage/microspore mother cell) -- control conditions,5393793,611724,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985511_15Q.bam
sly-b2.5,Solanum lycopersicum,ERR985512,pollen (tetrad -- flower buds 4-6 mm -- meiotic stage/microspore mother cell) -- control conditions,6059255,610645,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985512_15Q.bam
sly-b2.5,Solanum lycopersicum,ERR985514,pollen (mature -- flower buds >= 10 mm -- bicellular pollen) -- heat stress,2401346,269426,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985514_15Q.bam
sly-b2.5,Solanum lycopersicum,ERR985515,pollen (mature -- flower buds >= 10 mm -- bicellular pollen) -- heat stress,4116337,462338,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985515_15Q.bam
sly-b2.5,Solanum lycopersicum,ERR985516,pollen (post-meiotic -- flower buds 6-8 mm -- microspores) -- heat stress,2268116,546345,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985516_15Q.bam
sly-b2.5,Solanum lycopersicum,ERR985517,pollen (post-meiotic -- flower buds 6-8 mm -- microspores) -- heat stress,2027464,414355,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985517_15Q.bam
sly-b2.5,Solanum lycopersicum,ERR985518,pollen (post-meiotic -- flower buds 6-8 mm -- microspores) -- heat stress,3621879,583314,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985518_15Q.bam
sly-b2.5,Solanum lycopersicum,ERR985519,pollen (tetrad -- flower buds 4-6 mm -- meiotic stage/microspore mother cell) -- heat stress,3495240,419771,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985519_15Q.bam
sly-b2.5,Solanum lycopersicum,ERR985520,pollen (tetrad -- flower buds 4-6 mm -- meiotic stage/microspore mother cell) -- heat stress,3853974,403512,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985520_15Q.bam
sly-b2.5,Solanum lycopersicum,ERR985521,pollen (tetrad -- flower buds 4-6 mm -- meiotic stage/microspore mother cell) -- heat stress,3828118,391165,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/ERR985521_15Q.bam
sly-b2.5,Solanum lycopersicum,GSM803579,leaf (3-weeks-old plants) -- control conditions,4285839,403706,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/GSM803579-14152_5.bam
sly-b2.5,Solanum lycopersicum,GSM803580,flower (pre-anthesis) -- control conditions,4439622,517906,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/GSM803580-14154_5.bam
sly-b2.5,Solanum lycopersicum,GSM803581,fruit (breaker stage -- early ripening) -- control conditions,4440059,505416,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/GSM803581-14156_5.bam
sly-b2.5,Solanum lycopersicum,SRR039920,flower bud (closed -- before flower blooming) -- control conditions,3095208,401373,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR039920_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR039922,fruit (1-3mm diameter) -- control conditions,2076364,577833,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR039922_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR039924,fruit (11-14mm diameter) -- control conditions,2589066,691753,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR039924_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR039925,fruit (mature green) -- control conditions,3171923,419598,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR039925_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR039926,fruit (breaker stage) -- control conditions,3851003,585401,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR039926_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR039927,fruit (3 days post breaker stage) -- control conditions,3672202,444839,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR039927_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR039929,fruit (7 days post breaker stage) -- control conditions,2693214,329109,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR039929_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR065156,shoot (2-weeks-old plants) -- control conditions,2278087,369313,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR065156_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR065157,shoot (2-weeks-old plants) -- control conditions,4923482,574253,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR065157_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1022870,shoot (2-weeks-old plants) -- control conditions,5736556,783184,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1022870_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1022871,shoot (2-weeks-old plants) -- control conditions,6523549,930767,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1022871_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1028350,shoot (2-weeks-old plants) -- control conditions,13613597,1887855,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1028350_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1028351,shoot (2-weeks-old plants) -- control conditions,12110599,1919538,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1028351_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1061628,leaf (4-6 leaf stage) -- mock infiltration,4192124,2378026,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1061628_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1061629,leaf (4-6 leaf stage) -- infiltrated with A. tumefaciens EHA105 harboring plasmid constructs with dimers of the Tomato leaf curl New Delhi virus ToLCNDV-A [HQ264185.1] and ToLCNDV-B [HQ2641856.1] genome components,4148179,1206808,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1061629_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1258335,leaf (2-weeks-old plants -- upper systemic leaves) -- 20 days post inoculation with mock treatment,3702100,728667,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1258335_35Q.bam
sly-b2.5,Solanum lycopersicum,SRR1258336,leaf (2-weeks-old plants -- upper systemic leaves) -- 20 days post inoculation with Cucumber mosaic virus-Fny,3772176,1213951,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1258336_35Q.bam
sly-b2.5,Solanum lycopersicum,SRR1344486,fruit pericarp (37 days post-anthesis -- immature green) -- control conditions,19667605,2383776,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1344486_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1344487,fruit pericarp (37 days post-anthesis -- immature green) -- control conditions,18889363,2292327,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1344487_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1344488,fruit pericarp (46 days post-anthesis -- breaker stage) -- control conditions,20700773,1642296,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1344488_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1344489,fruit pericarp (46 days post-anthesis -- breaker stage) -- control conditions,18475951,1470936,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1344489_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1344490,fruit pericarp (51 days post-anthesis -- pink stage) -- control conditions,16746083,1791580,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1344490_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1344491,fruit pericarp (51 days post-anthesis -- pink stage) -- control conditions,19059238,2082276,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1344491_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1344492,fruit pericarp (56 days post-anthesis -- red ripe stage) -- control conditions,17551713,1938008,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1344492_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1344493,fruit pericarp (56 days post-anthesis -- red ripe stage) -- control conditions,14182318,1564258,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1344493_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1344494,fruit pericarp (37 days post-anthesis -- immature green) -- control conditions,17794687,1419209,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1344494_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1344495,fruit pericarp (37 days post-anthesis -- immature green) -- control conditions,20031720,1593361,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1344495_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1344496,fruit pericarp (46 days post-anthesis -- breaker stage) -- control conditions,18428513,1678797,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1344496_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1344497,fruit pericarp (46 days post-anthesis -- breaker stage) -- control conditions,19055486,1908180,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1344497_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1344499,fruit pericarp (56 days post-anthesis -- yellow ripe stage) -- control conditions,18224406,1536579,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1344499_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1344500,fruit pericarp (56 days post-anthesis -- yellow ripe stage) -- control conditions,17123670,1449018,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1344500_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1344501,fruit pericarp (51 days post-anthesis -- yellow stage) -- control conditions,18608501,1549988,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1344501_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1344502,fruit pericarp (51 days post-anthesis -- yellow stage) -- control conditions,19326582,1655886,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1344502_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1609934,leaf (45-days-old plants -- young leaves) -- control conditions,11296641,1202336,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1609934_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1795959,anther (mix pre-meiotic -- meiotic and post-meiotic anthers) -- control conditions,29676143,3496713,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1795959_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1795960,anther (mix pre-meiotic -- meiotic and post-meiotic anthers but microsporogenesis in 7B-1 breaks down prior to the meiosis in microspore mother cells) -- control conditions,18863859,2468364,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1795960_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1805790,seedling (2-weeks-old plants) -- mix of treatments: 10 microM ABA or 140 mM mannitol or 120 mM NaCl incubated for 0 -- 2 -- 4 -- 8 -- 12 -- and 24 h -- or cold treatment,29048176,2102891,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1805790_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR1805791,seedling (2-weeks-old plants) -- mix of treatments: 10 microM ABA or 140 mM mannitol or 120 mM NaCl incubated for 0 -- 2 -- 4 -- 8 -- 12 -- and 24 h -- or cold treatment,10075274,35086132,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR1805791_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR2039800,leaf -- 21-days post-inoculation with mock inoculation buffer,5332506,406176,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR2039800_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR2039801,leaf -- 21-days post-inoculation with Potato spindle tuber viroid mild,5378772,551162,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR2039801_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR2039802,leaf -- 21-days post-inoculation with Potato spindle tuber viroid intermediate,4662974,944613,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR2039802_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR2923817,leaf (4-weeks-old plants -- young leaf) -- control conditions,17085067,1324551,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR2923817_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR2923834,leaf (4-weeks-old plants -- young leaf) -- control conditions,19659667,1531113,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR2923834_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR2923841,leaf (4-weeks-old plants -- young green leaf) -- control conditions,20837839,1381062,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR2923841_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR2923842,leaf (4-weeks-old plants -- young green leaf) -- control conditions,19234220,1423059,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR2923842_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR2923843,leaf (4-weeks-old plants -- young yellow leaf) -- control conditions,21342680,1484233,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR2923843_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR2923844,leaf (4-weeks-old plants -- young yellow leaf) -- control conditions,14818417,969933,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR2923844_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR2989577,leaf -- 72 hours post infection with mock inoculation buffer,5420877,303831,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR2989577_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR2989578,leaf -- 72 hours post infection with mock inoculation buffer,7877445,365923,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR2989578_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR2989579,leaf -- 72 hours post infection with Alternaria,7006090,1103632,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR2989579_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR2989580,leaf -- 72 hours post infection with Alternaria,3063723,315288,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR2989580_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR350338,fruit (17 days post-anthesis immature and 52 days post-anthesis fully ripe) -- control conditions,13108656,6951766,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR350338_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR350339,fruit (39 days post-anthesis mature green 42 days post-anthesis breaker stage) -- control conditions,8737982,2883099,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR350339_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR4346447,root (5-weeks-old plants) -- control conditions,33902656,3272000,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR4346447_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR4346448,root (5-weeks-old plants) -- +1-2-3 days in control conditions,26139517,4492871,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR4346448_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR4346449,root (5-weeks-old plants) -- +1-2-3 days post infection with root-knot nematode Meloidogyne incognita,38200208,3931480,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR4346449_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR4346450,root (5-weeks-old plants) -- +5-6-7 days in control conditions,23890199,3393750,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR4346450_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR4346451,root (5-weeks-old plants) -- +5-6-7 days post infection with root-knot nematode Meloidogyne incognita,22382872,2818913,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR4346451_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR4346452,root (5-weeks-old plants) -- +13-14-15 days in control conditions,38261724,4451570,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR4346452_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR4346453,root (5-weeks-old plants) -- +13-14-15 days post infection with root-knot nematode Meloidogyne incognita,29045430,3968459,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR4346453_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR4346454,root (5-weeks-old plants) -- +18-19-20 days in control conditions,30951125,4496602,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR4346454_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR4346455,root (5-weeks-old plants) -- +18-19-20 days post infection with root-knot nematode Meloidogyne incognita,27870009,4291796,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR4346455_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR4346456,root (5-weeks-old plants) -- +26-27-28 days in control conditions,37674290,5985442,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR4346456_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR4346457,root (5-weeks-old plants) -- +26-27-28 days post infection with root-knot nematode Meloidogyne incognita,49690172,9710050,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR4346457_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR583817,shoot apex (including 3 to 5 primordial leaves -- the first 2 leaves were removed) -- control conditions,3052266,320058,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR583817_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR786979,leaf (6-weeks-old plants) -- control conditions,3407981,5094727,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR786979_3.bam
sly-b2.5,Solanum lycopersicum,SRR786980,fruit -- control conditions,4209924,5585477,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR786980_3.bam
sly-b2.5,Solanum lycopersicum,SRR786981,leaf (6-weeks-old plants) -- 24h post-inoculation with Botrytis cinerea,3805570,4467400,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR786981_3.bam
sly-b2.5,Solanum lycopersicum,SRR786982,leaf (6-weeks-old plants) -- 72h post-inoculation with Botrytis cinerea,3578802,4978576,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR786982_3.bam
sly-b2.5,Solanum lycopersicum,SRR786983,fruit -- 24h post-inoculation with Botrytis cinerea,4375582,6270086,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR786983_3.bam
sly-b2.5,Solanum lycopersicum,SRR786984,fruit -- 72h post-inoculation with Botrytis cinerea,3295794,5604393,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR786984_3.bam
sly-b2.5,Solanum lycopersicum,SRR955375,leaf (5-weeks-old plants -- 6-8 leaf stages) -- 21 days post-inoculation with control A. tumefaciens strain GV3101 containing pBinPLUS,14871429,1199809,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR955375_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR955376,leaf (5-weeks-old plants -- 6-8 leaf stages) -- 21 days post-inoculation with A. tumefaciens strain GV3101 containing pBinPLUS-SH2-1.4 with Tomato yellow leaf curl virus [CN:SH2],14358897,1839531,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR955376_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR955377,leaf (5-weeks-old plants -- 6-8 leaf stages) -- 30 days post-inoculation with A. tumefaciens strain GV3101 containing pBinPLUS-SH2-1.4 with Tomato yellow leaf curl virus [CN:SH2],10209452,1909559,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR955377_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR955378,leaf (5-weeks-old plants -- 6-8 leaf stages) -- 21 days post-inoculation with control A. tumefaciens strain GV3101 containing pBinPLUS,14644169,1408592,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR955378_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR955379,leaf (5-weeks-old plants -- 6-8 leaf stages) -- 21 days post-inoculation with A. tumefaciens strain GV3101 containing pBinPLUS-SH2-1.4 with Tomato yellow leaf curl virus [CN:SH2],15400102,1515145,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR955379_3Q.bam
sly-b2.5,Solanum lycopersicum,SRR955380,leaf (5-weeks-old plants -- 6-8 leaf stages) -- 30 days post-inoculation with A. tumefaciens strain GV3101 containing pBinPLUS-SH2-1.4 with Tomato yellow leaf curl virus [CN:SH2],8838237,1336894,http://plantsmallrnagenes.science.psu.edu/sly-b2.5/alignments/SRR955380_3Q.bam
stu-b4.04,Solanum tuberosum,GSM803582,leaf (72-days-old plants -- fully grown middle or upper leaf) -- control conditions,3085153,1018369,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/GSM803582-14161_5.bam
stu-b4.04,Solanum tuberosum,GSM803583,flower (72-days-old plants -- mature flower) -- control conditions,3266438,1214020,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/GSM803583-14163_5.bam
stu-b4.04,Solanum tuberosum,GSM803584,stolon (72-days-old plants -- stolon separated from tubers) -- control conditions,3043534,1080476,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/GSM803584-14166_5.bam
stu-b4.04,Solanum tuberosum,SRR1035225,leaf (45-days-old plants) -- control conditions,21623611,6184560,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR1035225_3Q.bam
stu-b4.04,Solanum tuberosum,SRR1035226,stem (45-days-old plants) -- control conditions,18811023,5572648,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR1035226_3Q.bam
stu-b4.04,Solanum tuberosum,SRR1035227,root (45-days-old plants) -- control conditions,18355350,6084370,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR1035227_3Q.bam
stu-b4.04,Solanum tuberosum,SRR1035228,tuber (45-days-old plants -- stage 0) -- control conditions,23870330,6972320,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR1035228_3Q.bam
stu-b4.04,Solanum tuberosum,SRR1035229,tuber (45-days-old plants -- stage 1) -- control conditions,23266101,6868207,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR1035229_3Q.bam
stu-b4.04,Solanum tuberosum,SRR1035230,tuber (45-days-old plants -- stage 2) -- control conditions,24513870,6533882,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR1035230_3Q.bam
stu-b4.04,Solanum tuberosum,SRR1035231,tuber (45-days-old plants -- stage 3) -- control conditions,23748300,6833699,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR1035231_3Q.bam
stu-b4.04,Solanum tuberosum,SRR1068585,leaf (50-days-old plants -- entire plant leaves) -- control conditions,8371916,8230686,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR1068585_35Q.bam
stu-b4.04,Solanum tuberosum,SRR1103932,leaf (30-days-old plants -- entire plant leaves) -- PEG-induced drought stress for 20 days,8335535,8016813,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR1103932_35Q.bam
stu-b4.04,Solanum tuberosum,SRR3341159,leaf (8-weeks-old plants) -- shifted to dark for 3 days,2885166,1559828,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR3341159_15Q.bam
stu-b4.04,Solanum tuberosum,SRR3341161,leaf (8-weeks-old plants) -- shifted to dark for 3 days and exposed to red light for 12 --24 --and 48 h,3085926,1961867,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR3341161_15Q.bam
stu-b4.04,Solanum tuberosum,SRR3341162,microtuber (8-weeks-old plants) -- dark conditions,4788687,854985,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR3341162_15Q.bam
stu-b4.04,Solanum tuberosum,SRR3341163,microtuber (8-weeks-old plants) -- exposed to red light for 12 -- 24 -- and 48 h,4240882,919425,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR3341163_15Q.bam
stu-b4.04,Solanum tuberosum,SRR4112323,leaf -- lineage source inoculum -- passage 0 of infection with Potato virus Y strain NTN isolate NIB V 151,5099836,10901395,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112323_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112334,leaf -- lineage source inoculum -- passage 0 of infection with Potato virus Y strain NTN isolate NIB V 151,3718549,8167342,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112334_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112324,leaf -- lineage D3 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151,2560955,5507715,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112324_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112328,leaf -- lineage D3 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151,4612742,8046678,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112328_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112329,leaf -- lineage Dn1 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151,2855546,6222781,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112329_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112332,leaf -- lineage Dn1 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151,4884646,9786845,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112332_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112333,leaf -- lineage Dn2 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151,2716160,7307036,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112333_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112337,leaf -- lineage Dn2 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151,5006327,7703222,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112337_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112338,leaf -- lineage Dn2 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151,6664031,10255152,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112338_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112342,leaf -- lineage Dn3 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151,8775819,8741545,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112342_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112345,leaf -- lineage D1 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151,2101789,5175810,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112345_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112356,leaf -- lineage D1 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151,4925229,10598138,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112356_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112346,leaf -- lineage DnxD1 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151,5019528,8004259,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112346_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112347,leaf -- lineage P1 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151,8304621,10984136,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112347_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112350,leaf -- lineage P2 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151,2932245,7042833,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112350_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112353,leaf -- lineage P2 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151,5997656,7909557,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112353_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112354,leaf -- lineage P3 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151,5324373,5905350,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112354_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112359,leaf -- lineage P3 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151,5360313,9490838,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112359_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112361,leaf -- lineage D2 -- passage 1 of infection with Potato virus Y strain NTN isolate NIB V 151,3026996,6641002,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112361_3Q.bam
stu-b4.04,Solanum tuberosum,SRR4112364,leaf -- lineage D2 -- passage 6 of infection with Potato virus Y strain NTN isolate NIB V 151,3493929,14725808,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR4112364_3Q.bam
stu-b4.04,Solanum tuberosum,SRR643260,tuber -- collected after 11 -- 12 -- 15 and 25 days at 20 C,14580981,5004047,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR643260_3Q.bam
stu-b4.04,Solanum tuberosum,SRR643261,tuber -- collected after 10 days at 20 C then 1 -- 2 -- 5 and 15 days at 4 C,19364666,5509588,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR643261_3Q.bam
stu-b4.04,Solanum tuberosum,SRR825901,leaf (4-weeks-old plants) -- collected after 8 days at long day,2103755,524791,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR825901_3Q.bam
stu-b4.04,Solanum tuberosum,SRR825902,leaf (4-weeks-old plants) -- collected after 8 days at long day,4359364,963633,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRR825902_3Q.bam
stu-b4.04,Solanum tuberosum,SRX159043,leaf (4-weeks-old plants) -- collected after 8 days at long day,2690968,652947,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRX159043_3Q.bam
stu-b4.04,Solanum tuberosum,SRX159038,leaf (4-weeks-old plants) -- collected after 8 days at short day,2942702,613974,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRX159038_3Q.bam
stu-b4.04,Solanum tuberosum,SRX159039,leaf (4-weeks-old plants) -- collected after 8 days at short day,2796389,655450,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRX159039_3Q.bam
stu-b4.04,Solanum tuberosum,SRX159040,leaf (4-weeks-old plants) -- collected after 8 days at short day,2803009,635224,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRX159040_3Q.bam
stu-b4.04,Solanum tuberosum,SRX159044,stolon (4-weeks-old plants) -- collected after 12-16 days at short day,3018978,925973,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRX159044_3Q.bam
stu-b4.04,Solanum tuberosum,SRX159045,stolon (4-weeks-old plants) -- collected after 12-16 days at short day,3842009,1167175,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRX159045_3Q.bam
stu-b4.04,Solanum tuberosum,SRX159046,stolon (4-weeks-old plants) -- collected after 12-16 days at short day,3239993,925112,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRX159046_3Q.bam
stu-b4.04,Solanum tuberosum,SRX159047,swollen stolon (4-weeks-old plants) -- collected after 12-16 days at short day,3449017,926589,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRX159047_3Q.bam
stu-b4.04,Solanum tuberosum,SRX159048,swollen stolon (4-weeks-old plants) -- collected after 12-16 days at short day,2568028,712622,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRX159048_3Q.bam
stu-b4.04,Solanum tuberosum,SRX159049,swollen stolon (4-weeks-old plants) -- collected after 12-16 days at short day,2820645,682371,http://plantsmallrnagenes.science.psu.edu/stu-b4.04/alignments/SRX159049_3Q.bam
bvu-b1.2.2,Beta vulgaris,SRR5951746,unknown,8306387,3459738,http://plantsmallrnagenes.science.psu.edu/bvu-b1.2.2/alignments/SRR5951746_3Q.bam
bvu-b1.2.2,Beta vulgaris,SRR5957120,unknown,8060200,3174626,http://plantsmallrnagenes.science.psu.edu/bvu-b1.2.2/alignments/SRR5957120_3Q.bam
bvu-b1.2.2,Beta vulgaris,SRR5957121,unknown,8756616,3462471,http://plantsmallrnagenes.science.psu.edu/bvu-b1.2.2/alignments/SRR5957121_3Q.bam
bvu-b1.2.2,Beta vulgaris,SRR5957122,unknown,7989544,3150317,http://plantsmallrnagenes.science.psu.edu/bvu-b1.2.2/alignments/SRR5957122_3Q.bam
bvu-b1.2.2,Beta vulgaris,SRR5957123,unknown,7428990,4148615,http://plantsmallrnagenes.science.psu.edu/bvu-b1.2.2/alignments/SRR5957123_3Q.bam
bvu-b1.2.2,Beta vulgaris,SRR5958550,unknown,12480215,2516089,http://plantsmallrnagenes.science.psu.edu/bvu-b1.2.2/alignments/SRR5958550.bam
bvu-b1.2.2,Beta vulgaris,SRR5958579,unknown,7582921,2041578,http://plantsmallrnagenes.science.psu.edu/bvu-b1.2.2/alignments/SRR5958579.bam
bvu-b1.2.2,Beta vulgaris,SRR5958580,unknown,11520683,2467785,http://plantsmallrnagenes.science.psu.edu/bvu-b1.2.2/alignments/SRR5958580.bam
bvu-b1.2.2,Beta vulgaris,SRR5958581,unknown,12159261,2756739,http://plantsmallrnagenes.science.psu.edu/bvu-b1.2.2/alignments/SRR5958581.bam
bvu-b1.2.2,Beta vulgaris,SRR5958588,unknown,11295901,2231447,http://plantsmallrnagenes.science.psu.edu/bvu-b1.2.2/alignments/SRR5958588.bam
bvu-b1.2.2,Beta vulgaris,SRX286928,leaf -- control conditions,7019124,1617002,http://plantsmallrnagenes.science.psu.edu/bvu-b1.2.2/alignments/SRX286928_3Q.bam
cqi-b1.0,Chenopodium quinoa,SRR4300230,root -- control conditions,4825199,17831610,http://plantsmallrnagenes.science.psu.edu/cqi-b1.0/alignments/SRR4300230_3Q.bam
cqi-b1.0,Chenopodium quinoa,SRR4300231,root -- control conditions,3508861,8662642,http://plantsmallrnagenes.science.psu.edu/cqi-b1.0/alignments/SRR4300231_3Q.bam
cqi-b1.0,Chenopodium quinoa,SRR4300232,root -- control conditions,3016872,9501569,http://plantsmallrnagenes.science.psu.edu/cqi-b1.0/alignments/SRR4300232_3Q.bam
cqi-b1.0,Chenopodium quinoa,SRR4300233,shoot -- control conditions,8628522,3281635,http://plantsmallrnagenes.science.psu.edu/cqi-b1.0/alignments/SRR4300233_3Q.bam
cqi-b1.0,Chenopodium quinoa,SRR4300234,shoot -- control conditions,6871046,5400083,http://plantsmallrnagenes.science.psu.edu/cqi-b1.0/alignments/SRR4300234_3Q.bam
cqi-b1.0,Chenopodium quinoa,SRR4300235,shoot -- control conditions,6925749,7193629,http://plantsmallrnagenes.science.psu.edu/cqi-b1.0/alignments/SRR4300235_3Q.bam
cqi-b1.0,Chenopodium quinoa,SRR4300237,root -- low phosphate stress,5743946,5837079,http://plantsmallrnagenes.science.psu.edu/cqi-b1.0/alignments/SRR4300237_3Q.bam
cqi-b1.0,Chenopodium quinoa,SRR4300239,shoot -- low phosphate stress,5379467,4524700,http://plantsmallrnagenes.science.psu.edu/cqi-b1.0/alignments/SRR4300239_3Q.bam
cqi-b1.0,Chenopodium quinoa,SRR4300240,shoot -- low phosphate stress,6041961,2453659,http://plantsmallrnagenes.science.psu.edu/cqi-b1.0/alignments/SRR4300240_3Q.bam
cqi-b1.0,Chenopodium quinoa,SRR4300241,shoot -- low phosphate stress,7222248,1969103,http://plantsmallrnagenes.science.psu.edu/cqi-b1.0/alignments/SRR4300241_3Q.bam
sol-b1,Spinacia oleracea,GSM2805294,leaf (5-weeks-old plants -- leaf tip) -- control conditions,10230534,3115499,http://plantsmallrnagenes.science.psu.edu/sol-b1/alignments/2_S2_R1_001_3Q.bam
sol-b1,Spinacia oleracea,GSM2805295,leaf (3-weeks-old plants -- leaf tip) -- control conditions,3184928,1188056,http://plantsmallrnagenes.science.psu.edu/sol-b1/alignments/6_S6_R1_001_3Q.bam
egu-b5.1,Elaeis guineensis,SRR3042542,fruit (30-60 days after pollination) -- control conditions,12660056,2220807,http://plantsmallrnagenes.science.psu.edu/egu-b5.1/alignments/SRR3042542_3Q.bam
egu-b5.1,Elaeis guineensis,SRR3042544,fruit (60-100 days after pollination) -- control conditions,11224439,1957483,http://plantsmallrnagenes.science.psu.edu/egu-b5.1/alignments/SRR3042544_3Q.bam
egu-b5.1,Elaeis guineensis,SRR3042545,fruit (100-120 days after pollination) -- control conditions,14210137,1143655,http://plantsmallrnagenes.science.psu.edu/egu-b5.1/alignments/SRR3042545_3Q.bam
egu-b5.1,Elaeis guineensis,SRR3042547,fruit (120-140 days after pollination) -- control conditions,11957732,835081,http://plantsmallrnagenes.science.psu.edu/egu-b5.1/alignments/SRR3042547_3Q.bam
egu-b5.1,Elaeis guineensis,SRR3042548,fruit (140-160 days after pollination) -- control conditions,13427220,979677,http://plantsmallrnagenes.science.psu.edu/egu-b5.1/alignments/SRR3042548_3Q.bam
egu-b5.1,Elaeis guineensis,SRR5189964,female inflorescence (+6 developing stage) -- control conditions,12890487,2395501,http://plantsmallrnagenes.science.psu.edu/egu-b5.1/alignments/SRR5189964_3Q.bam
egu-b5.1,Elaeis guineensis,SRR5189967,female inflorescence (+15 developing stage) -- control conditions,12904281,2422657,http://plantsmallrnagenes.science.psu.edu/egu-b5.1/alignments/SRR5189967_3Q.bam
bdi-b1.0,Brachypodium distachyon,GSM506621,panicle (6-weeks-old plants) -  control conditions,4360711,619694,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/GSM506621-23192_5.bam
bdi-b1.0,Brachypodium distachyon,GSM1266841,leaf (6-weeks-old plants -  first and second leaves -  top of the blades -  not including the leaf sheath) -  control conditions,4482330,637018,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/GSM1266841_BDI04_processed_5.bam
bdi-b1.0,Brachypodium distachyon,SRR1033810,leaf (6-weeks-old plants -  first and second leaves -  top of the blades -  not including the leaf sheath) -  control conditions,4427933,508904,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR1033810_35Q.bam
bdi-b1.0,Brachypodium distachyon,GSM1266843,stem (6-weeks-old plants -  just above the first top node to just below the second node -  including both nodes as well as the leaf sheath of the second leaf) -  control conditions,3600059,401580,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/GSM1266843_BDI06_processed_5.bam
bdi-b1.0,Brachypodium distachyon,GSM1266844,leaf and stem (6-weeks-old plants -  first and second leaves -  top of the blades -  not including the leaf sheath; just above the first top node to just below the second node -  including both nodes as well as the leaf sheath of the second leaf) -  contr,2765539,767726,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/GSM1266844_OBD02_processed_5.bam
bdi-b1.0,Brachypodium distachyon,GSM1266845,shoot (3-weeks-old plants) -  control conditions,2033182,357810,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/GSM1266845_BDI02_processed_5.bam
bdi-b1.0,Brachypodium distachyon,SRR1033809,root (3-weeks-old plants) -  control conditions,5737589,843306,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR1033809_35Q.bam
bdi-b1.0,Brachypodium distachyon,SRR1033811,shoot (3-week-old plants) -  salt stress,7140692,621113,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR1033811_35Q.bam
bdi-b1.0,Brachypodium distachyon,SRR1033812,shoot (3-week-old plants) -  heat stress,7201011,600025,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR1033812_35Q.bam
bdi-b1.0,Brachypodium distachyon,SRR1033813,shoot (3-week-old plants) -  submergence stress,7043697,702963,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR1033813_35Q.bam
bdi-b1.0,Brachypodium distachyon,SRR1033814,shoot (3-week-old plants) -  control conditions,9732384,1070527,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR1033814_35Q.bam
bdi-b1.0,Brachypodium distachyon,SRR1033815,shoot (3-week-old plants) -  phosphate-starvation stress,10282712,957367,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR1033815_35Q.bam
bdi-b1.0,Brachypodium distachyon,SRR522511,leaf (third leaf expansion zone 2-6mm) -  control conditions,17403120,1266692,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR522511_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR522512,leaf (third leaf expansion zone 2-6mm) -  control conditions,22351286,1773644,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR522512_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR522513,leaf (third leaf expansion zone 2-6mm) -  drought stress,20818040,1269175,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR522513_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR522514,leaf (third leaf expansion zone 2-6mm) -  drought stress,23020075,1296240,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR522514_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR522515,leaf (third leaf division zone first 2 mm from the leaf base) -  control conditions,21974830,1544665,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR522515_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR522516,leaf (third leaf division zone first 2 mm from the leaf base) -  control conditions,20401652,1184736,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR522516_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR522517,leaf (third leaf division zone first 2 mm from the leaf base) -  drought stress,14139802,891750,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR522517_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR522518,leaf (third leaf division zone first 2 mm from the leaf base) -  drought stress,22810737,1320502,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR522518_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR1174000,leaf -  control conditions,5937863,722903,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR1174000_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR1174001,leaf -  salt stress for 48h,3727851,345918,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR1174001_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR1174002,leaf -  cold stress for 6h,9740989,689452,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR1174002_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR1174003,leaf -  cold stress for 24h,9045684,659357,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR1174003_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR1174004,leaf -  heat stress by air incubation for 1h,9176226,819489,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR1174004_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR1174005,leaf -  heat stress by air incubation for 3h,10514708,786146,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR1174005_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR1174006,leaf -  heat stress by water immersion for 1h,7293681,653526,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR1174006_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR1174007,leaf -  heat stress by water immersion for 3h,2660644,259212,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR1174007_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR3114501,seedling (three leaves stage) -  treated with 20 mM H2O2 for 6 h in plastic containers and collected at 2 -  4 -  or 6 h mixed together,11311015,7572298,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR3114501_3Q.bam
bdi-b1.0,Brachypodium distachyon,SRR3114502,seedling (three leaves stage) -  control conditions,10736209,7065871,http://plantsmallrnagenes.science.psu.edu/bdi-b1.0/alignments/SRR3114502_3Q.bam
hvu-b1,Hordeum vulgare,GSM717573,leaf (7-days-old plants) -  control conditions,1959418,884090,http://plantsmallrnagenes.science.psu.edu/hvu-b1/alignments/GSM717573-42190_5.bam
hvu-b1,Hordeum vulgare,GSM717574,inflorescence (pre-anthesis -  green anthers but not dehisced) -  control conditions,2477389,792435,http://plantsmallrnagenes.science.psu.edu/hvu-b1/alignments/GSM717574-42192_5.bam
hvu-b1,Hordeum vulgare,GSM717575,leaf (7-days-old plants) -  infected with Blumeria,2145338,1061225,http://plantsmallrnagenes.science.psu.edu/hvu-b1/alignments/GSM717575-42194_5.bam
hvu-b1,Hordeum vulgare,SRR070296,leaf (3-weeks-old plants) -  drought stress for 5 days ,3812024,631600,http://plantsmallrnagenes.science.psu.edu/hvu-b1/alignments/SRR070296_35Q.bam
hvu-b1,Hordeum vulgare,SRR070297,leaf (3-weeks-old plants) -  control conditions,3944486,1001200,http://plantsmallrnagenes.science.psu.edu/hvu-b1/alignments/SRR070297_35Q.bam
hvu-b1,Hordeum vulgare,SRR070298,leaf (3-weeks-old plants) -  control conditions,2186501,481819,http://plantsmallrnagenes.science.psu.edu/hvu-b1/alignments/SRR070298_35Q.bam
hvu-b1,Hordeum vulgare,SRR2481851,seedling (3-leaf stage) -  control conditions after 27h,6278260,5559961,http://plantsmallrnagenes.science.psu.edu/hvu-b1/alignments/SRR2481851_Q15.bam
hvu-b1,Hordeum vulgare,SRR2481852,seedling (3-leaf stage) -  salt stress after 27h,8563530,9048770,http://plantsmallrnagenes.science.psu.edu/hvu-b1/alignments/SRR2481852_Q15.bam
hvu-b1,Hordeum vulgare,SRR2481853,seedling (3-leaf stage) -  control conditions after 3h,9866921,6885361,http://plantsmallrnagenes.science.psu.edu/hvu-b1/alignments/SRR2481853_Q15.bam
hvu-b1,Hordeum vulgare,SRR2481854,seedling (3-leaf stage) -  salt stress after 3h,8328583,7412164,http://plantsmallrnagenes.science.psu.edu/hvu-b1/alignments/SRR2481854_Q15.bam
hvu-b1,Hordeum vulgare,SRR2481855,seedling (3-leaf stage) -  control conditions after 8h,8243886,5809479,http://plantsmallrnagenes.science.psu.edu/hvu-b1/alignments/SRR2481855_Q15.bam
hvu-b1,Hordeum vulgare,SRR2481856,seedling (3-leaf stage) -  salt stress after 8h,6526000,5657154,http://plantsmallrnagenes.science.psu.edu/hvu-b1/alignments/SRR2481856_Q15.bam
hvu-b1,Hordeum vulgare,SRR513546,immature grain (1-5 days post anthesis -  from the middle six rows of the head) -  control conditions ,4136861,1081058,http://plantsmallrnagenes.science.psu.edu/hvu-b1/alignments/SRR513546_3Q.bam
hvu-b1,Hordeum vulgare,SRR513547,immature grain (6-10 days post anthesis -  from the middle six rows of the head) -  control conditions ,4237678,1179245,http://plantsmallrnagenes.science.psu.edu/hvu-b1/alignments/SRR513547_3Q.bam
hvu-b1,Hordeum vulgare,SRR513548,immature grain (11-15 days post anthesis -  from the middle six rows of the head) -  control conditions ,4275332,1282446,http://plantsmallrnagenes.science.psu.edu/hvu-b1/alignments/SRR513548_3Q.bam
osa-b1.0,Oryza sativa,ERR037689,leaf (14-days-old plants) - cold stress,14942641,4422750,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/ERR037689_3Q_F.bam
osa-b1.0,Oryza sativa,ERR037690,leaf (14-days-old plants) - drought stress,17842394,3559965,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/ERR037690_3Q_F.bam
osa-b1.0,Oryza sativa,ERR037691,leaf (14-days-old plants) - drought stress,16792369,3568167,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/ERR037691_3Q_F.bam
osa-b1.0,Oryza sativa,ERR037692,leaf (14-days-old plants) - salt stress,10693484,2841531,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/ERR037692_3Q_F.bam
osa-b1.0,Oryza sativa,ERR037693,leaf (14-days-old plants) - salt stress,11890645,3084875,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/ERR037693_3Q_F.bam
osa-b1.0,Oryza sativa,ERR037694,leaf (14-days-old plants) - control conditions,15070600,3249948,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/ERR037694_3Q_F.bam
osa-b1.0,Oryza sativa,ERR037695,leaf (14-days-old plants) - control conditions,16527354,3674454,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/ERR037695_3Q_F.bam
osa-b1.0,Oryza sativa,GSM1409671,leaf (40-days-old-plants - at 1 cm below the infected loci) - treated with water for 2 hours - control,10198311,3025481,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM1409671_F.bam
osa-b1.0,Oryza sativa,GSM1409672,leaf (40-days-old-plants - at 1 cm below the infected loci) - treated with water for 6 hours - control,6975097,2383961,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM1409672_F.bam
osa-b1.0,Oryza sativa,GSM1409673,leaf (40-days-old-plants - at 1 cm below the infected loci) - treated with water for 12 hours - control,8391607,2209298,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM1409673_F.bam
osa-b1.0,Oryza sativa,GSM1409674,leaf (40-days-old-plants - at 1 cm below the infected loci) - treated with water for 24 hours - control,7642213,1816856,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM1409674_F.bam
osa-b1.0,Oryza sativa,GSM1409675,leaf (40-days-old-plants - at 1 cm below the infected loci) - treated with Xanthomonas oryzae pv. oryzae (Xoo) virulent strain PXO99 for 2 hours,7369268,2335299,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM1409675_F.bam
osa-b1.0,Oryza sativa,GSM1409676,leaf (40-days-old-plants - at 1 cm below the infected loci) - treated with Xanthomonas oryzae pv. oryzae (Xoo) virulent strain PXO99 for 6 hours,9858079,2892108,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM1409676_F.bam
osa-b1.0,Oryza sativa,GSM1409677,leaf (40-days-old-plants - at 1 cm below the infected loci) - treated with Xanthomonas oryzae pv. oryzae (Xoo) virulent strain PXO99 for 12 hours,9275620,2900903,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM1409677_F.bam
osa-b1.0,Oryza sativa,GSM1409678,leaf (40-days-old-plants - at 1 cm below the infected loci) - treated with Xanthomonas oryzae pv. oryzae (Xoo) virulent strain PXO99 for 24 hours,11597523,2813442,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM1409678_F.bam
osa-b1.0,Oryza sativa,GSM278571,grain (1-5 days after fetilization - developing grain) - control conditions,2311524,346527,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM278571_35_F.bam
osa-b1.0,Oryza sativa,GSM278572,grain (6-10 days after fetilization - developing grain) - control conditions,2248977,452012,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM278572_35_F.bam
osa-b1.0,Oryza sativa,GSM562947,panicle (young panicle - 4cm - mainly comprising the floral organs at differentiation stage In7) - control conditions,2443946,337901,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM562947_35_F.bam
osa-b1.0,Oryza sativa,GSM686039,undifferentiated callus - control conditions,10284328,2522387,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM686039_F.bam
osa-b1.0,Oryza sativa,GSM686040,differentiated callus - control conditions,10247095,3023880,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM686040_F.bam
osa-b1.0,Oryza sativa,GSM816693,seedling (2-weeks-old plants) - salt stress,2155671,653353,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816693_F.bam
osa-b1.0,Oryza sativa,GSM816694,seedling (2-weeks-old plants) - cold stress,2127468,640878,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816694_F.bam
osa-b1.0,Oryza sativa,GSM816705,root (endosperm was first removed from 9-days-old seedlings to avoid nutrient transport - sampled after 5 days) - control conditions,4147364,1329659,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816705_F.bam
osa-b1.0,Oryza sativa,GSM816707,root (endosperm was first removed from 9-days-old seedlings to avoid nutrient transport - sampled after 5 days) - KH2PO4 deficiency,4809967,1023317,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816707_F.bam
osa-b1.0,Oryza sativa,GSM816709,root (endosperm was first removed from 9-days-old seedlings to avoid nutrient transport - sampled after 5 days) - SO4 deficiency (substituted with Cl2),3881242,1284955,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816709_F.bam
osa-b1.0,Oryza sativa,GSM816711,root (endosperm was first removed from 9-days-old seedlings to avoid nutrient transport - sampled after 5 days) - NH4NO3 and KNO3 deficiency (KNO3 substituted with KCl) ,4543351,1180727,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816711_F.bam
osa-b1.0,Oryza sativa,GSM816713,root (endosperm was first removed from 9-days-old seedlings to avoid nutrient transport - sampled after 5 days) - KNO3 deficiency,4177200,1527185,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816713_F.bam
osa-b1.0,Oryza sativa,GSM816715,root (endosperm was first removed from 9-days-old seedlings to avoid nutrient transport - sampled after 5 days) - KNO3 deficiency and salt stress,2577348,1931384,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816715_F.bam
osa-b1.0,Oryza sativa,GSM816719,shoot (2-weeks-old plants) - control conditions,2295521,845855,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816719_F.bam
osa-b1.0,Oryza sativa,GSM816721,shoot (endosperm was first removed from 9-days-old seedlings to avoid nutrient transport - sampled after 5 days) - KH2PO4 deficiency,2334789,716327,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816721_F.bam
osa-b1.0,Oryza sativa,GSM816723,shoot (endosperm was first removed from 9-days-old seedlings to avoid nutrient transport - sampled after 5 days) - SO4 deficiency (substituted with Cl2),2037831,905087,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816723_F.bam
osa-b1.0,Oryza sativa,GSM816725,shoot (endosperm was first removed from 9-days-old seedlings to avoid nutrient transport - sampled after 5 days) - NH4NO3 and KNO3 deficiency (KNO3 substituted with KCl) ,2608741,600706,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816725_F.bam
osa-b1.0,Oryza sativa,GSM816727,shoot (endosperm was first removed from 9-days-old seedlings to avoid nutrient transport - sampled after 5 days) - KNO3 deficiency,3451074,602202,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816727_F.bam
osa-b1.0,Oryza sativa,GSM816729,shoot (endosperm was first removed from 9-days-old seedlings to avoid nutrient transport - sampled after 5 days) - KNO3 deficiency and salt stress,2577608,414442,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816729_F.bam
osa-b1.0,Oryza sativa,GSM816731,panicle (15 cm long and wrapped with panicle sheath) - control conditions,3600195,951516,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816731_F.bam
osa-b1.0,Oryza sativa,GSM816732,panicle (15 cm long and wrapped with panicle sheath) - control conditions,3363604,1080776,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816732_F.bam
osa-b1.0,Oryza sativa,GSM816734,panicle (15 cm long and wrapped with panicle sheath) - drought stress,3548705,881860,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816734_F.bam
osa-b1.0,Oryza sativa,GSM816735,panicle (15 cm long and wrapped with panicle sheath) - drought stress,3427274,827349,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816735_F.bam
osa-b1.0,Oryza sativa,GSM816737,panicle (15 cm long and wrapped with panicle sheath) - salt stress,3778388,1006970,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816737_F.bam
osa-b1.0,Oryza sativa,GSM816738,panicle (15 cm long and wrapped with panicle sheath) - salt stress,3442388,1076427,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816738_F.bam
osa-b1.0,Oryza sativa,GSM816740,panicle (15 cm long and wrapped with panicle sheath) - cold stress,2433826,631083,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/GSM816740_F.bam
osa-b1.0,Oryza sativa,SRR037238,seedling - control conditions,5469839,2247480,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR037238_3Q_F.bam
osa-b1.0,Oryza sativa,SRR089619,inflorescence (90-days-old plants - mature inflorescence - 14-17 cm long - stage In 9 - composed by rachis - branches and spikelets) - control conditions,6019614,1353969,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR089619_3Q_F.bam
osa-b1.0,Oryza sativa,SRR089620,inflorescence (90-days-old plants - mature inflorescence - 14-17 cm long - stage In 9 - composed by rachis - branches and spikelets) - drought stress,4679325,1348714,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR089620_3Q_F.bam
osa-b1.0,Oryza sativa,SRR089621,inflorescence (90-days-old plants - mature inflorescence - 14-17 cm long - stage In 9 - composed by rachis - branches and spikelets) - cold stress,3736975,1043579,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR089621_3Q_F.bam
osa-b1.0,Oryza sativa,SRR089622,inflorescence (90-days-old plants - mature inflorescence - 14-17 cm long - stage In 9 - composed by rachis - branches and spikelets) - salt stress,4304013,1159744,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR089622_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1036340,root (2-weeks-old plants) - phosphate deficiency for 21 days,5784821,9698427,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1036340_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1036341,shoot (2-weeks-old plants) - phosphate deficiency for 21 days,36298557,9913720,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1036341_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1036342,root (2-weeks-old plants) - phosphate deficiency for 21 days,5398202,7721889,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1036342_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1036343,shoot (2-weeks-old plants) - phosphate deficiency for 21 days,34503765,9276233,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1036343_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1036344,root (2-weeks-old plants) - phosphate deficiency for 21 days,2383491,3791052,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1036344_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1036345,shoot (2-weeks-old plants) - phosphate deficiency for 21 days,77840989,27384324,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1036345_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1036346,root (2-weeks-old plants) - control conditions for 21 days,4196125,6745407,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1036346_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1036347,shoot (2-weeks-old plants) - control conditions for 21 days,32192128,9803851,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1036347_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1036348,root (2-weeks-old plants) - control conditions for 21 days,3027457,5900888,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1036348_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1036349,shoot (2-weeks-old plants) - control conditions for 21 days,37067748,10733466,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1036349_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1036350,root (2-weeks-old plants) - control conditions for 21 days,2010078,4339800,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1036350_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1036351,shoot (2-weeks-old plants) - control conditions for 21 days,54891672,14799364,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1036351_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1555746,root (7-days-old plants) - control conditions,14399436,6722821,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1555746_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1555747,root (7-days-old plants) - cadmium stress,10959907,8703952,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1555747_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1555749,shoot (7-days-old plants) - cadmium stress,19634848,1933873,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1555749_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1555751,shoot (7-days-old plants) - control conditions,15818933,1505845,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1555751_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1556011,root - cadmium stress,10948141,10357936,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1556011_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1556014,root - control conditions,14399436,6722821,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1556014_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1556016,shoot - cadmium stress,19634848,1933873,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1556016_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1556018,shoot - control conditions,15818933,1505845,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1556018_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1556020,root - cadmium stress,10959907,8703952,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1556020_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1612403,leaf (fourth leaf at the four leaf stage) - control conditions,8165117,3977662,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1612403_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1612404,leaf (fourth leaf at the four leaf stage) - control conditions,5760687,3285347,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1612404_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1654490,leaf (40-days-old plants - five-leaf and six-leaf stages) - control conditions,9741557,1743560,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1654490_3Q_F.bam
osa-b1.0,Oryza sativa,SRR1654491,leaf (40-days-old plants - five-leaf and six-leaf stages) - control conditions,8593623,1766107,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR1654491_3Q_F.bam
osa-b1.0,Oryza sativa,SRR2544786,embryo (dry seed) - control conditions,14410219,7241055,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR2544786_Q_F.bam
osa-b1.0,Oryza sativa,SRR2544787,embryo (12-hours-imbibed seed) - control conditions,20325181,6242183,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR2544787_Q_F.bam
osa-b1.0,Oryza sativa,SRR2544788,embryo (24-hours-imbibed seed) - control conditions,16405607,4474791,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR2544788_Q_F.bam
osa-b1.0,Oryza sativa,SRR4279834,leaf (10-days-old plants) - treated 3 days with non-viruliferous SBPHs (Laodelphax striatellus Fallen),4356173,2080748,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR4279834_3Q_F.bam
osa-b1.0,Oryza sativa,SRR4279835,leaf (10-days-old plants) - treated 7 days with non-viruliferous SBPHs (Laodelphax striatellus Fallen),3151994,1352156,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR4279835_3Q_F.bam
osa-b1.0,Oryza sativa,SRR4279836,leaf (10-days-old plants) - treated 15 days with non-viruliferous SBPHs (Laodelphax striatellus Fallen),6677731,2150923,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR4279836_3Q_F.bam
osa-b1.0,Oryza sativa,SRR4279837,leaf (10-days-old plants) - treated 3 days with viruliferous SBPHs (Laodelphax striatellus Fallen) ,4247373,1363748,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR4279837_3Q_F.bam
osa-b1.0,Oryza sativa,SRR4279838,leaf (10-days-old plants) - treated 7 days with viruliferous SBPHs (Laodelphax striatellus Fallen) ,4343698,1622824,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR4279838_3Q_F.bam
osa-b1.0,Oryza sativa,SRR4279839,leaf (10-days-old plants) - treated 15 days with viruliferous SBPHs (Laodelphax striatellus Fallen) ,5949613,2638482,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR4279839_3Q_F.bam
osa-b1.0,Oryza sativa,SRR447127,root (14-days-old plants) - control conditions,3047182,2116978,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR447127_53Q_F.bam
osa-b1.0,Oryza sativa,SRR447128,root (14-days-old plants) - treated with 20microM sodium arsenite for 6 hours,3198940,2734942,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR447128_53Q_F.bam
osa-b1.0,Oryza sativa,SRR447129,root (14-days-old plants) - treated with 80microM sodium arsenite for 6 hours,2956765,1211562,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR447129_53Q_F.bam
osa-b1.0,Oryza sativa,SRR447130,root (14-days-old plants) - treated with 20microM sodium arsenite for 24 hours,3799239,2092331,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR447130_53Q_F.bam
osa-b1.0,Oryza sativa,SRR447131,root (14-days-old plants) - treated with 80microM sodium arsenite for 24 hours,4513307,1554863,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR447131_53Q_F.bam
osa-b1.0,Oryza sativa,SRR447132,shoot (14-days-old plants) - control conditions,3010013,1505091,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR447132_53Q_F.bam
osa-b1.0,Oryza sativa,SRR447133,shoot (14-days-old plants) - treated with 20microM sodium arsenite for 6 hours,3095513,1350161,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR447133_53Q_F.bam
osa-b1.0,Oryza sativa,SRR447134,shoot (14-days-old plants) - treated with 80microM sodium arsenite for 6 hours,3027835,2109599,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR447134_53Q_F.bam
osa-b1.0,Oryza sativa,SRR447135,shoot (14-days-old plants) - treated with 20microM sodium arsenite for 24 hours,4171832,1383704,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR447135_53Q_F.bam
osa-b1.0,Oryza sativa,SRR447136,shoot (14-days-old plants) - treated with 80microM sodium arsenite for 24 hours,2774378,1024543,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR447136_53Q_F.bam
osa-b1.0,Oryza sativa,SRR504360,leaf (6-weeks-old plants - fully expanded leaf) - control conditions,2573816,1462597,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR504360_3Q_F.bam
osa-b1.0,Oryza sativa,SRR643880,leaf (20-days-old plants) - mock inoculated with 0.2% gelatin - control,6673438,3369809,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR643880_3Q_F.bam
osa-b1.0,Oryza sativa,SRR643881,leaf (20-days-old plants) - inoculated with Magnaporthe oryzae 70-15 for 72 hours,5867905,2404732,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR643881_3Q_F.bam
osa-b1.0,Oryza sativa,SRR643882,leaf (20-days-old plants) - inoculated with Magnaporthe oryzae 70-15 for 96 hours,5992854,3648679,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR643882_3Q_F.bam
osa-b1.0,Oryza sativa,SRR711312,leaf (3-weeks-old plants - regenerated from tissue culture) - control conditions,18267006,8247885,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR711312_3Q_F.bam
osa-b1.0,Oryza sativa,SRR711313,leaf (3-weeks-old plants - regenerated from tissue culture) - control conditions,14379530,5498281,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR711313_3Q_F.bam
osa-b1.0,Oryza sativa,SRR711314,leaf (3-weeks-old plants - regenerated from tissue culture) - control conditions,12930426,5048584,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR711314_3Q_F.bam
osa-b1.0,Oryza sativa,SRR711315,leaf (3-weeks-old plants - regenerated from tissue culture) - control conditions,17948525,7230030,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR711315_3Q_F.bam
osa-b1.0,Oryza sativa,SRR711316,leaf (3-weeks-old plants - regenerated from tissue culture) - control conditions,15694357,6203793,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR711316_3Q_F.bam
osa-b1.0,Oryza sativa,SRR711317,leaf (3-weeks-old plants - regenerated from tissue culture) - control conditions,16096900,6878438,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR711317_3Q_F.bam
osa-b1.0,Oryza sativa,SRR711318,leaf (3-weeks-old plants - regenerated from tissue culture) - control conditions,19012422,7410228,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR711318_3Q_F.bam
osa-b1.0,Oryza sativa,SRR711319,leaf (3-weeks-old plants - regenerated from tissue culture) - control conditions,10418758,4572861,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR711319_3Q_F.bam
osa-b1.0,Oryza sativa,SRR711320,leaf (3-weeks-old plants - regenerated from tissue culture) - control conditions,12148764,7191645,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR711320_3Q_F.bam
osa-b1.0,Oryza sativa,SRR711321,leaf (3-weeks-old plants - regenerated from tissue culture) - control conditions,12014600,6998992,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR711321_3Q_F.bam
osa-b1.0,Oryza sativa,SRR771494,root (3-weeks-old plants) - control conditions,5873874,13928646,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR771494_3Q_F.bam
osa-b1.0,Oryza sativa,SRR771495,root (3-weeks-old plants) - control conditions,10438322,5867878,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR771495_3Q_F.bam
osa-b1.0,Oryza sativa,SRR771496,shoot (3-weeks-old plants) - control conditions,19442718,3648960,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR771496_3Q_F.bam
osa-b1.0,Oryza sativa,SRR771497,shoot (3-weeks-old plants) - control conditions,15738268,7905670,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR771497_3Q_F.bam
osa-b1.0,Oryza sativa,SRR771498,endosperm (7-8 days after fertilization - milky stage endosperm) - control conditions,15573620,3286232,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR771498_3Q_F.bam
osa-b1.0,Oryza sativa,SRR771499,embryo (7-8 days after fertilization) - control conditions,20413217,3438444,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR771499_3Q_F.bam
osa-b1.0,Oryza sativa,SRR976171,leaf lamina joint (of flag leaf) - control conditions,25633072,5286094,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR976171_3Q_F.bam
osa-b1.0,Oryza sativa,SRX016114,shoot (4-weeks-old plants - four-leaf stage) - control conditions,2522243,1287879,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRX016114_3Q_F.bam
osa-b1.0,Oryza sativa,SRR2154074,seed (husks removed) - control conditions,10676628,2884227,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR2154074_3Q.bam
osa-b1.0,Oryza sativa,SRR2154080,seedling (9-days-old plants) - control conditions,9663862,1640398,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR2154080_3Q.bam
osa-b1.0,Oryza sativa,SRR5049778,anther (floret length: 2.6-2.8mm - pre-meiotic interphase) - control conditions,7432942,1704660,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR5049778_3Q.bam
osa-b1.0,Oryza sativa,SRR5049779,anther (floret length: 3.8-4.0mm - meiosis) - control conditions,7094788,1828202,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR5049779_3Q.bam
osa-b1.0,Oryza sativa,SRR5049780,anther (floret length: 5.0-5.5mm - single microspore stage) - control conditions,8081030,2502478,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR5049780_3Q.bam
osa-b1.0,Oryza sativa,SRR5049781,anther (floret length: >6.5mm - bi-cellular pollen stage) - control conditions,5659828,2812028,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR5049781_3Q.bam
osa-b1.0,Oryza sativa,SRR5049786,ovary (floret length: 2.6-2.8mm - megasporocyte formation stage) - control conditions,7246086,1579856,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR5049786_3Q.bam
osa-b1.0,Oryza sativa,SRR5049787,ovary (floret length: 3.8-4.0mm - megasporocyte meiosis stage) - control conditions,6762456,2264835,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR5049787_3Q.bam
osa-b1.0,Oryza sativa,SRR5049788,ovary (floret length: 5.0-5.5mm - functional megaspore formation stage) - control conditions,8608349,1506988,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR5049788_3Q.bam
osa-b1.0,Oryza sativa,SRR5049789,ovary (floret length: >6.5mm - eight-nucleate embryo sac developing-stage) - control conditions,5960438,2000504,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR5049789_3Q.bam
osa-b1.0,Oryza sativa,SRR3234040,anther (floret length: 2.50-3.00mm - anther length: 0.75-0.85mm - pre-meiotic interphase) - control conditions,6944021,1198620,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR3234040_3Q.bam
osa-b1.0,Oryza sativa,SRR3234041,anther (floret length: 3.80-4.30mm - anther length: 1.00-1.35mm - meiosis) - control conditions,8583974,1797857,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR3234041_3Q.bam
osa-b1.0,Oryza sativa,SRR3234042,anther (floret length: 5.50-6.00mm - anther length: 1.40-1.55mm - single microspore stage) - control conditions,6466800,2622523,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/SRR3234042_3Q.bam
osa-b1.0,Oryza sativa,ERR035782,haploid uninucleate microspore (released from tetrades) - control conditions,2984135,2083669,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/ERR035782_3Q.bam
osa-b1.0,Oryza sativa,ERR035777,bicellular pollen (pollen grains before PMII and after PMI) - control conditions,6260495,3813197,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/ERR035777_3Q.bam
osa-b1.0,Oryza sativa,ERR035781,tricellular pollen (pollen grains after PMII but before dehydrated) - control conditions,6998610,4994884,http://plantsmallrnagenes.science.psu.edu/osa-b1.0/alignments/ERR035781_3Q.bam
sbi-b3.0,Sorghum bicolor,ERR266127,leaf (30-days-old plants -  fully opened uppermost leaves) -  drought stress,8147355,4020505,http://plantsmallrnagenes.science.psu.edu/sbi-b3.0/alignments/ERR266127_3Q.bam
sbi-b3.0,Sorghum bicolor,ERR266128,leaf (30-days-old plants -  fully opened uppermost leaves) -  control conditions,7747562,3855760,http://plantsmallrnagenes.science.psu.edu/sbi-b3.0/alignments/ERR266128_3Q.bam
sbi-b3.0,Sorghum bicolor,ERR266129,leaf (30-days-old plants -  fully opened uppermost leaves) -  drought stress,7827325,2982771,http://plantsmallrnagenes.science.psu.edu/sbi-b3.0/alignments/ERR266129_3Q.bam
sbi-b3.0,Sorghum bicolor,ERR266130,leaf (30-days-old plants -  fully opened uppermost leaves) -  control conditions,6753961,2224368,http://plantsmallrnagenes.science.psu.edu/sbi-b3.0/alignments/ERR266130_3Q.bam
sbi-b3.0,Sorghum bicolor,GSM803128,leaf (3-weeks-old plants) -  control conditions,3647265,2332731,http://plantsmallrnagenes.science.psu.edu/sbi-b3.0/alignments/GSM803128-10425.bam
sbi-b3.0,Sorghum bicolor,GSM803129,flower (~9-weeks-old-plants) -  control conditions,3385679,1240858,http://plantsmallrnagenes.science.psu.edu/sbi-b3.0/alignments/GSM803129-10427.bam
sbi-b3.0,Sorghum bicolor,GSM803130,young panicle in early grain fill,2921423,1171449,http://plantsmallrnagenes.science.psu.edu/sbi-b3.0/alignments/GSM803130-10429.bam
sbi-b3.0,Sorghum bicolor,SRR358899,seedling -  control conditions,16178902,2878502,http://plantsmallrnagenes.science.psu.edu/sbi-b3.0/alignments/SRR358899_3Q.bam
sbi-b3.0,Sorghum bicolor,SRR358900,seedling -  drought stress,16211695,3535475,http://plantsmallrnagenes.science.psu.edu/sbi-b3.0/alignments/SRR358900_3Q.bam
sbi-b3.0,Sorghum bicolor,SRR358901,seedling -  cold stress,15857529,2762566,http://plantsmallrnagenes.science.psu.edu/sbi-b3.0/alignments/SRR358901_3Q.bam
sbi-b3.0,Sorghum bicolor,SRR358902,seedling -  salt stress,15836610,3024030,http://plantsmallrnagenes.science.psu.edu/sbi-b3.0/alignments/SRR358902_3Q.bam
sit-b2,Setaria italica,ERR1292961,leaf (2-weeks-old plants) -  control conditions,16674287,885379,http://plantsmallrnagenes.science.psu.edu/sit-b2/alignments/ERR1292961_3Q.bam
sit-b2,Setaria italica,ERR1292962,leaf (2-weeks-old plants) -  moderate drought stress,13340952,1128935,http://plantsmallrnagenes.science.psu.edu/sit-b2/alignments/ERR1292962_3Q.bam
sit-b2,Setaria italica,GSM803573,leaf (5-6-weeks-old plants) -  control conditions,4203206,592534,http://plantsmallrnagenes.science.psu.edu/sit-b2/alignments/GSM803573.bam
sit-b2,Setaria italica,GSM803574,flower spike (2 pre-anthesis stages) -  control conditions,4809152,688682,http://plantsmallrnagenes.science.psu.edu/sit-b2/alignments/GSM803574.bam
sit-b2,Setaria italica,GSM803575,root -  control conditions,3696938,695099,http://plantsmallrnagenes.science.psu.edu/sit-b2/alignments/GSM803575.bam
sit-b2,Setaria italica,SRR630983,shoot (2-weeks-old plants) -  control conditions,16987601,3963497,http://plantsmallrnagenes.science.psu.edu/sit-b2/alignments/SRR630983_3Q.bam
sit-b2,Setaria italica,SRR631007,shoot (2-weeks-old plants) -  control conditions,15403398,3710086,http://plantsmallrnagenes.science.psu.edu/sit-b2/alignments/SRR631007_3Q.bam
sit-b2,Setaria italica,SRR631008,shoot (2-weeks-old plants) -  PEG-simulated drought stress,14117009,3888173,http://plantsmallrnagenes.science.psu.edu/sit-b2/alignments/SRR631008_3Q.bam
sit-b2,Setaria italica,SRR631010,shoot (2-weeks-old plants) -  PEG-simulated drought stress,14908321,4012177,http://plantsmallrnagenes.science.psu.edu/sit-b2/alignments/SRR631010_3Q.bam
tae-b1,Triticum aestivum,GSM803792,leaf (7-days-old plants) -  control conditions,2078106,1445907,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/GSM803792-14595_5.bam
tae-b1,Triticum aestivum,SRR1195024,dry grain -  control conditions,4184843,5448856,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1195024_3Q.bam
tae-b1,Triticum aestivum,SRR1195025,embryo of germinating seed (3-days-old plants -  leaves at the coleoptile tip) -  control conditions,5203392,4805372,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1195025_3Q.bam
tae-b1,Triticum aestivum,SRR1195279,shoot (3-days-old plants -  leaves at the coleoptile tip) -  control conditions,3861452,2167322,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1195279_3Q.bam
tae-b1,Triticum aestivum,SRR1195281,root (when the third leaf is at least 50% emerged) -  control conditions,4239884,5601191,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1195281_3Q.bam
tae-b1,Triticum aestivum,SRR1195282,stem (jointing stage) -  control conditions,8441544,3254700,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1195282_3Q.bam
tae-b1,Triticum aestivum,SRR1195944,young spikelet (0-5 mm) -  control conditions,7098863,7400640,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1195944_3Q.bam
tae-b1,Triticum aestivum,SRR1196022,young spikelet (10-15 mm) -  control conditions,10344252,5050150,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1196022_3Q.bam
tae-b1,Triticum aestivum,SRR1196023,flag leaf -  control conditions,6111782,3921443,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1196023_3Q.bam
tae-b1,Triticum aestivum,SRR1196029,grain (8 days after pollination) -  control conditions,7986472,6530275,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1196029_3Q.bam
tae-b1,Triticum aestivum,SRR1196045,grain (15 days after pollination) -  control conditions,9866781,4310769,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1196045_3Q.bam
tae-b1,Triticum aestivum,SRR1222483,spike (heading date stage) -  control conditions,10192973,2512677,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1222483_3Q.bam
tae-b1,Triticum aestivum,SRR1222484,spike (heading date stage) -  control conditions,9565163,2266124,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1222484_3Q.bam
tae-b1,Triticum aestivum,SRR1222485,seed (11 days after flowering) -  control conditions,7673421,3251922,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1222485_3Q.bam
tae-b1,Triticum aestivum,SRR1796319,grain (7 days post anthesis) -  control conditions,12964954,9025607,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1796319_3Q.bam
tae-b1,Triticum aestivum,SRR1796320,grain (14 days post anthesis) -  control conditions,8556473,9422207,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1796320_3Q.bam
tae-b1,Triticum aestivum,SRR1796321,grain (21 days post anthesis) -  control conditions,18547219,18569989,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1796321_3Q.bam
tae-b1,Triticum aestivum,SRR1796322,grain (28 days post anthesis) -  control conditions,5176365,7674642,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR1796322_3Q.bam
tae-b1,Triticum aestivum,SRR2586131,microspore (late vacuolated uninucleate stage) -  control conditions,2606525,8756580,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR2586131_Q.bam
tae-b1,Triticum aestivum,SRR2586136,microspore (late vacuolated uninucleate stage) -  control conditions,3225648,8038145,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR2586136_Q.bam
tae-b1,Triticum aestivum,SRR2586137,microspore (late vacuolated uninucleate stage) -  control conditions,5188750,5595007,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR2586137_Q.bam
tae-b1,Triticum aestivum,SRR2586138,microspore (slightly enlarged -  with a star-like structure) -  10-days cold pre-treatment of the spikes,4075464,7665334,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR2586138_Q.bam
tae-b1,Triticum aestivum,SRR2586139,microspore (slightly enlarged -  with a star-like structure) -  10-days cold pre-treatment of the spikes,3459280,7185004,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR2586139_Q.bam
tae-b1,Triticum aestivum,SRR2586140,microspore (slightly enlarged -  with a star-like structure) -  10-days cold pre-treatment of the spikes,4212242,6929010,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR2586140_Q.bam
tae-b1,Triticum aestivum,SRR2586141,microspore (enlarged -  showing first visible karyokinesis -  from in-vitro anther culture) -  control conditions,5884563,5906569,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR2586141_Q.bam
tae-b1,Triticum aestivum,SRR2586142,microspore (enlarged -  showing first visible karyokinesis -  from in-vitro anther culture) -  control conditions,5907982,5720345,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR2586142_Q.bam
tae-b1,Triticum aestivum,SRR2586143,microspore (enlarged -  showing first visible karyokinesis -  from in-vitro anther culture) -  control conditions,4824380,6153800,http://plantsmallrnagenes.science.psu.edu/tae-b1/alignments/SRR2586143_Q.bam
zma-b4,Zea mays,SRR3151733,leaf n.5 (V5 stage) -  control conditions,7670748,2311954,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/MaizeV4stageLeaves1_R1_35Q.bam
zma-b4,Zea mays,SRR3151734,leaf n.5 (V5 stage) -  control conditions,6597980,1780399,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/MaizeV4stageLeaves2_R1_35Q.bam
zma-b4,Zea mays,SRR3151735,leaf n.5 (V5 stage) -  control conditions,5761906,2438116,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/MaizeV4stageLeaves3_R1_35Q.bam
zma-b4,Zea mays,SRR3151736,wrapped leaf n.6 (V5 stage) -  control conditions,5342690,2238149,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/MaizeV4stageWhorls1_R1_35Q.bam
zma-b4,Zea mays,SRR3151737,wrapped leaf n.6 (V5 stage) -  control conditions,7775160,2893432,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/MaizeV4stageWhorls2_R1_35Q.bam
zma-b4,Zea mays,SRX1564781,wrapped leaf n.6 (V5 stage) -  control conditions,17549822,5593630,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/MaizeV4stageWhorls3_35Q.bam
zma-b4,Zea mays,SRR3151741,mature pollen -  control conditions,5775149,4703030,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/MaizePollen1_R1_35Q.bam
zma-b4,Zea mays,SRR3151742,mature pollen -  control conditions,6309688,4041456,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/MaizePollen2_R1_35Q.bam
zma-b4,Zea mays,SRR3151743,mature pollen -  control conditions,7633750,4645993,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/MaizePollen3_R1_35Q.bam
zma-b4,Zea mays,SRR3151744,embryo -  21-27 DAP -  control conditions,3494494,2527866,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/MaizeEmbryo_R1_35Q.bam
zma-b4,Zea mays,SRR2947005,shoot apical meristematic area -  meristem and a few surrounding developing leaves (V6/V7 stage) -  control conditions,21523155,5544111,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/13-varotto-140905_ep_CATGGC_L002_R1_001_35Q.bam
zma-b4,Zea mays,SRR2947006,shoot apical meristematic area -  meristem and a few surrounding developing leaves (V6/V7 stage) -  control conditions,24034859,6487959,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/14-varotto-140905_ep_CTAGCT_L002_R1_001_35Q.bam
zma-b4,Zea mays,SRR2947007,shoot apical meristematic area -  meristem and a few surrounding developing leaves (V6/V7 stage) -  drought stress,28321795,6937383,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/15-varotto-140905_ep_CTCAGA_L002_R1_001_35Q.bam
zma-b4,Zea mays,SRR2947008,shoot apical meristematic area -  meristem and a few surrounding developing leaves (V6/V7 stage) -  drought stress,21235969,6857387,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/16-varotto-140905_ep_TCGGCA_L002_R1_001_35Q.bam
zma-b4,Zea mays,SRR2086100,last visible wrapped leaf -  n.9-10 (V6/V7 stage) -  control conditions,8334250,3339737,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/1-r1_B73_C1_T0_35Q.bam
zma-b4,Zea mays,SRR2086116,last visible wrapped leaf -  n.9-10 (V6/V7 stage) -  control conditions,4179930,1773985,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/1-r2_B73_C1_T0_35Q.bam
zma-b4,Zea mays,SRR2086132,last visible wrapped leaf -  n.9-10 (V6/V7 stage) -  control conditions,5445651,2269212,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/1-r3_B73_C1_T0_35Q.bam
zma-b4,Zea mays,SRR2086101,last visible wrapped leaf -  n.9-10 (V6/V7 stage) -  drought stress,8943262,3149331,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/2-r1_B73_C2_T0_35Q.bam
zma-b4,Zea mays,SRR2086117,last visible wrapped leaf -  n.9-10 (V6/V7 stage) -  drought stress,3441098,1715287,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/2-r2_B73_C2_T0_35Q.bam
zma-b4,Zea mays,SRR2086133,last visible wrapped leaf -  n.9-10 (V6/V7 stage) -  drought stress,3874732,1510271,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/2-r3_B73_C2_T0_35Q.bam
zma-b4,Zea mays,SRR2086102,last visible wrapped leaf -  n.9-10 (V6/V7 stage) -  salt stress,5589198,2721102,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/3-r1_B73_C3_T0_35Q.bam
zma-b4,Zea mays,SRR2086118,last visible wrapped leaf -  n.9-10 (V6/V7 stage) -  salt stress,6367154,2483344,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/3-r2_B73_C3_T0_35Q.bam
zma-b4,Zea mays,SRR2086134,last visible wrapped leaf -  n.9-10 (V6/V7 stage) -  salt stress,5247709,2194136,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/3-r3_B73_C3_T0_35Q.bam
zma-b4,Zea mays,SRR2086103,last visible wrapped leaf -  n.9-10 (V6/V7 stage) -  drought + salt stress,8958312,3708544,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/4-r1_B73_C4_T0_35Q.bam
zma-b4,Zea mays,SRR2086119,last visible wrapped leaf -  n.9-10 (V6/V7 stage) -  drought + salt stress,4814991,1982421,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/4-r2_B73_C4_T0_35Q.bam
zma-b4,Zea mays,SRR2086135,last visible wrapped leaf -  n.9-10 (V6/V7 stage) -  drought + salt stress,4366936,1832688,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/4-r3_B73_C4_T0_35Q.bam
zma-b4,Zea mays,SRR2086104,last visible wrapped leaf -  n.11 (V8 stage) -  control conditions,7136128,3483584,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/5-r1_B73_C1_T7_35Q.bam
zma-b4,Zea mays,SRR2086120,last visible wrapped leaf -  n.11 (V8 stage) -  control conditions,3328805,1740648,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/5-r2_B73_C1_T7_35Q.bam
zma-b4,Zea mays,SRR2086136,last visible wrapped leaf -  n.11 (V8 stage) -  control conditions,4369414,1901395,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/5-r3_B73_C1_T7_35Q.bam
zma-b4,Zea mays,GSM381716,seedling shoot (14-days-old plants) -  control conditions,2229184,2097890,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/GSM381716-5792_AL_tr_name_35.bam
zma-b4,Zea mays,SRR032087,immature ear (size 0.5 _ 2cm) -  control conditions,3263789,1100766,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR032087_3Q.bam
zma-b4,Zea mays,SRR032088,pollen -  control conditions,5085175,3557592,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR032088_3Q.bam
zma-b4,Zea mays,SRR032089,root (3-days-old plants) -  control conditions,5297112,2520219,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR032089_3Q.bam
zma-b4,Zea mays,SRR032090,seedling (7-days-old plants) -  control conditions,5320929,2841088,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR032090_3Q.bam
zma-b4,Zea mays,SRR032091,immature tassel (size 0.5_2.5cm) -  control conditions,5918320,2440050,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR032091_3Q.bam
zma-b4,Zea mays,SRR034096,young leaf (6-weeks-old plants) -  control conditions,2198408,1028781,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR034096_35Q.bam
zma-b4,Zea mays,SRR034097,ear (10-11-weeks-old plants; post-meiotic stage; 3-5 cm long with silks about 1-4 cm long) -  control conditions,2235078,1032516,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR034097_35Q.bam
zma-b4,Zea mays,SRR034098,tassel (8-weeks-old plants; pre-meiotic stage; ranged in length between 2-4 cm long) -  control conditions,2407468,902835,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR034098_35Q.bam
zma-b4,Zea mays,SRR1583944,developing ear (4-6 cm stage) -  control conditions,11405510,4427204,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1583944_35Q.bam
zma-b4,Zea mays,SRR1917157,embryo (24 hr imbibed seeds) -  control conditions,8229000,11047863,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1917157_3Q.bam
zma-b4,Zea mays,SRR1917158,embryo (24 hr imbibed seeds) -  control conditions,6657010,8751331,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1917158_3Q.bam
zma-b4,Zea mays,SRR1660512,leaf n. 3 (7-day-old plants cultured in dark) mix of 8 samples: before illumination -  0.5 -  1 -  3 -  6 -  12 and 24 h after illumination and control 16h light/8-h night cycle,61053907,22503568,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1660512_3Q.bam
zma-b4,Zea mays,SRR3684389,endosperm (10 days after pollination) -  immersed in 1/2 MS with sucrose,8972018,4398559,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR3684389_3Q.bam
zma-b4,Zea mays,SRR3684242,endosperm (10 days after pollination) -  immersed in 1/2 MS with mannose -  an osmotic control,7363505,5864862,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR3684242_3Q.bam
zma-b4,Zea mays,SRR2155397,aboveground seedling (14-days-old plants) -  control conditions,50569545,14206876,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR2155397_Q.bam
zma-b4,Zea mays,SRR2155403,root (14-days-old plants) -  control conditions,25521097,7222498,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR2155403_Q.bam
zma-b4,Zea mays,SRR357417,seedling (14-days-old plants) -  control conditions,9545118,3185167,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR357417_3Q.bam
zma-b4,Zea mays,SRR357418,seedling (14-days-old plants) -  drought stress,7732528,3078479,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR357418_3Q.bam
zma-b4,Zea mays,SRR357419,seedling (14-days-old plants) -  cold stress,7950048,3617577,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR357419_3Q.bam
zma-b4,Zea mays,SRR357420,seedling (14-days-old plants) -  salt stress,8336887,2716883,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR357420_3Q.bam
zma-b4,Zea mays,SRR408793,unfertilized ears harvested after silks had emerged -  control conditions,40134516,13472952,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR408793_35Q.bam
zma-b4,Zea mays,SRR488774,shoot apical meristematic area (11-days-old plants) -  control conditions,23282797,8863717,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR488774_3Q.bam
zma-b4,Zea mays,SRR488776,top developing ear (V12 stage -  at the time when the 12th leaf had fully expanded) -  control conditions,3282720,998734,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR488776_3Q.bam
zma-b4,Zea mays,SRR488779,top developing ear (V12 stage -  at the time when the 12th leaf had fully expanded) -  low nitrogen,2535870,786131,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR488779_3Q.bam
zma-b4,Zea mays,SRR490839,leaf (3-weeks-old plants) -  control conditions,7410936,2706296,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR490839_3QF.bam
zma-b4,Zea mays,SRR490840,mix of immature seeds at 10 -  15 -  20 -  25 and 30 DAP -  control conditions,6713479,3566071,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR490840_3QF.bam
zma-b4,Zea mays,SRR521124,shoot (5-days-old plants) -  control conditions,12753902,8011860,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR521124_3Q.bam
zma-b4,Zea mays,SRR521125,shoot (5-days-old plants) -  control conditions,9237880,6168539,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR521125_3QF.bam
zma-b4,Zea mays,SRX159595,shoot (5-days-old plants) -  control conditions,10360933,3717744,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRX159595_Q.bam
zma-b4,Zea mays,SRR640303,seedling shoot (14-days-old plants) -  control conditions,3717390,3076851,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR640303_3QF.bam
zma-b4,Zea mays,SRR640304,seedling root (14-days-old plants) -  control conditions,3212841,4231350,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR640304_3QF.bam
zma-b4,Zea mays,SRR768248,mature pollen -  control conditions,2812814,3250601,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR768248_3Q.bam
zma-b4,Zea mays,SRR768249,in-vitro germinated pollen (after culturing mature pollen for 30 min in liquid medium) -  control conditions,5233173,5621540,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR768249_3Q.bam
zma-b4,Zea mays,SRR768250,mature silk (extending approximately 5 cm beyond the bracts) -  control conditions,6452843,2387895,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR768250_3Q.bam
zma-b4,Zea mays,SRR768251,pollinated silk -  control conditions,6215721,1784715,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR768251_3Q.bam
zma-b4,Zea mays,SRR768485,root (15-days-old plants) -  control conditions,8812014,5398167,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR768485_3Q.bam
zma-b4,Zea mays,SRR768487,root (15-days-old plants) -  low nitrate,8805429,3993599,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR768487_3Q.bam
zma-b4,Zea mays,SRR768489,shoot (15-days-old plants) -  low nitrate,9680090,3289442,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR768489_3Q.bam
zma-b4,Zea mays,SRR768492,shoot (15-days-old plants) -  control conditions,7986387,2803975,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR768492_3Q.bam
zma-b4,Zea mays,SRR895785,mixed ears at the growth point elongation -  spikelet differentiation -  floret primordium differentiation and floret organ differentiation phase -  control conditions,6476995,4896773,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR895785_3Q.bam
zma-b4,Zea mays,SRR924284,seedling leaf -  control conditions,34032219,14283328,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR924284_3Q.bam
zma-b4,Zea mays,SRR962471,shoot apical meristematic area (2-week-old plants) -  control conditions,8867950,4259813,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR962471_3Q.bam
zma-b4,Zea mays,SRR962473,shoot apical meristematic area (2-week-old plants) -  control conditions,4156421,2709530,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR962473_3Q.bam
zma-b4,Zea mays,SRR962475,shoot apical meristematic area (2-week-old plants) -  control conditions,3801499,2216114,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR962475_3Q.bam
zma-b4,Zea mays,SRR1028945,anther (0.2mm) -  control conditions,5896004,7462205,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028945_3Q.bam
zma-b4,Zea mays,SRR1028956,anther (0.2mm) -  control conditions,9918979,12470364,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028956_3Q.bam
zma-b4,Zea mays,SRR1028946,anther (0.4mm) -  control conditions,20252848,17957594,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028946_3Q.bam
zma-b4,Zea mays,SRR1028957,anther (0.4mm) -  control conditions,22360453,18418589,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028957_3Q.bam
zma-b4,Zea mays,SRR1028967,anther (0.4mm) -  control conditions,16519026,8862681,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028967_3Q.bam
zma-b4,Zea mays,SRR1028947,anther (0.7mm) -  control conditions,12898071,22218896,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028947_3Q.bam
zma-b4,Zea mays,SRR1028958,anther (0.7mm) -  control conditions,25739428,19798084,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028958_3Q.bam
zma-b4,Zea mays,SRR1028968,anther (0.7mm) -  control conditions,14611550,7366811,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028968_3Q.bam
zma-b4,Zea mays,SRR1028948,anther (1mm) -  control conditions,14939961,26305074,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028948_3Q.bam
zma-b4,Zea mays,SRR1028959,anther (1mm) -  control conditions,16443293,23594693,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028959_3Q.bam
zma-b4,Zea mays,SRR1028969,anther (1mm) -  control conditions,20480887,10700391,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028969_3Q.bam
zma-b4,Zea mays,SRR1028949,anther (1.5mm) -  control conditions,17783808,19392031,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028949_3Q.bam
zma-b4,Zea mays,SRR1028960,anther (1.5mm) -  control conditions,15612095,14678848,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028960_3Q.bam
zma-b4,Zea mays,SRR1028970,anther (1.5mm) -  control conditions,19347287,7804242,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028970_3Q.bam
zma-b4,Zea mays,SRR1028950,anther (2mm) -  control conditions,21554463,18446517,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028950_3Q.bam
zma-b4,Zea mays,SRR1028961,anther (2mm) -  control conditions,24051461,29492293,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028961_3Q.bam
zma-b4,Zea mays,SRR1028971,anther (2mm) -  control conditions,20447085,12957835,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028971_3Q.bam
zma-b4,Zea mays,SRR1028951,anther (2.5mm) -  control conditions,25956169,37838978,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028951_3Q.bam
zma-b4,Zea mays,SRR1028962,anther (2.5mm) -  control conditions,24468322,27891524,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028962_3Q.bam
zma-b4,Zea mays,SRR1028972,anther (2.5mm) -  control conditions,19245640,16120743,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028972_3Q.bam
zma-b4,Zea mays,SRR1028952,anther (3mm) -  control conditions,11742184,20770744,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028952_3Q.bam
zma-b4,Zea mays,SRR1028963,anther (3mm) -  control conditions,11246250,18074000,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028963_3Q.bam
zma-b4,Zea mays,SRR1028973,anther (3mm) -  control conditions,13677544,20341239,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028973_3Q.bam
zma-b4,Zea mays,SRR1028953,anther (4mm) -  control conditions,15276377,31770882,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028953_3Q.bam
zma-b4,Zea mays,SRR1028964,anther (4mm) -  control conditions,11273139,18538360,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028964_3Q.bam
zma-b4,Zea mays,SRR1028974,anther (4mm) -  control conditions,14836709,19025128,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028974_3Q.bam
zma-b4,Zea mays,SRR1028954,anther (5mm) -  control conditions,11419905,20583732,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028954_3Q.bam
zma-b4,Zea mays,SRR1028965,anther (5mm) -  control conditions,7086483,23335007,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028965_3Q.bam
zma-b4,Zea mays,SRR1028975,anther (5mm) -  control conditions,9722569,23650914,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028975_3Q.bam
zma-b4,Zea mays,SRR1028955,anther (mature pollen) -  control conditions,9460428,24723547,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028955_3Q.bam
zma-b4,Zea mays,SRR1028966,anther (mature pollen) -  control conditions,8951138,30599791,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028966_3Q.bam
zma-b4,Zea mays,SRR1028976,anther (mature pollen) -  control conditions,6258069,23575562,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1028976_3Q.bam
zma-b4,Zea mays,SRR1041542,tassel primordia (0.5-1 cm) -  control conditions,15608141,10919027,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1041542_3Q.bam
zma-b4,Zea mays,SRR1041543,tassel primordia (0.5-1 cm) -  control conditions,16242099,24501910,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1041543_3Q.bam
zma-b4,Zea mays,SRR1041544,tassel primordia (0.5-1 cm) -  control conditions,13563299,19217882,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1041544_3Q.bam
zma-b4,Zea mays,SRR899547,seedling (7-days-old plants) -  after 7 days inoculation with the diazotrophic bacterium H. seropedicae (HRC54),2001458,3138382,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR899547_3Q.bam
zma-b4,Zea mays,SRR1199373,seedling (7-days-old plants) -  after 7 days inoculation with the diazotrophic bacterium H. seropedicae (HRC54),2644233,3964565,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1199373_3Q.bam
zma-b4,Zea mays,SRR1199372,seedling (7-days-old plants) -  after 7 days in control conditions,10449947,16613110,http://plantsmallrnagenes.science.psu.edu/zma-b4/alignments/SRR1199372_Q.bam
mac-b2,Musa acuminata,GSM717699,leaf -- control conditions,2035263,892968,http://plantsmallrnagenes.science.psu.edu/mac-b2/alignments/GSM717699-42204_5.bam
mac-b2,Musa acuminata,GSM717700,male flower -- control conditions,2957305,1310858,http://plantsmallrnagenes.science.psu.edu/mac-b2/alignments/GSM717700-42205_5.bam
mac-b2,Musa acuminata,GSM717701,fruit (immature fruit 2 weeks after flowering) -- control conditions,2792923,2038803,http://plantsmallrnagenes.science.psu.edu/mac-b2/alignments/GSM717701-42207_5.bam
mac-b2,Musa acuminata,SRR1340394,root (6-8cm plants) -- treated with 100 mM NaCl ,9689306,4204402,http://plantsmallrnagenes.science.psu.edu/mac-b2/alignments/SRR1340394_Q.bam
mac-b2,Musa acuminata,SRR1524838,root (6-8cm plants) -- control conditions,11627857,3141164,http://plantsmallrnagenes.science.psu.edu/mac-b2/alignments/SRR1524838_3Q.bam
mac-b2,Musa acuminata,SRR1524839,root (6-8cm plants) -- treated with 300 mM NaCl ,13638866,1107725,http://plantsmallrnagenes.science.psu.edu/mac-b2/alignments/SRR1524839_3Q.bam
mac-b2,Musa acuminata,SRR2373957,fruit (75-80 perc plump stage) -- stored for 3 days after treated with 1-Methylcyclopropene 1-MCP,2087862,561681,http://plantsmallrnagenes.science.psu.edu/mac-b2/alignments/SRR2373957_3Q.bam
mac-b2,Musa acuminata,SRR2647084,leaf and root (full-spread leaves and one tip) -- control conditions,3273651,14571741,http://plantsmallrnagenes.science.psu.edu/mac-b2/alignments/SRR2647084_3Q.bam
mac-b2,Musa acuminata,SRR5192537,fruit (70-80 perc maturation -- 70-75 days after flowering) -- selected at 5 hours of storage and sealed with 5microL per L ethylene for 12 hours at 25 C -- unripened,2079014,1146625,http://plantsmallrnagenes.science.psu.edu/mac-b2/alignments/SRR5192537_3Q.bam
mac-b2,Musa acuminata,SRR5196702/SRR5194992,fruit (70-80 perc maturation -- 70-75 days after flowering) -- selected at 5 hours of storage and sealed with air or 0microL per L ethylene for 12 hours at 25 C -- unripened,7159375,2715345,http://plantsmallrnagenes.science.psu.edu/mac-b2/alignments/SRR5196702_SRR5194992_3Q.bam
atr-b1,Amborella trichopoda,GSM712477,leaves,3616907,520167,http://plantsmallrnagenes.science.psu.edu/atr-b1/alignments/GSM712477.bam
atr-b1,Amborella trichopoda,SRR606852,female flower,21244471,2156573,http://plantsmallrnagenes.science.psu.edu/atr-b1/alignments/SRR606852_trimmed.bam
atr-b1,Amborella trichopoda,SRR606853,leaf,16014391,3428330,http://plantsmallrnagenes.science.psu.edu/atr-b1/alignments/SRR606853_trimmed.bam
pab-b1.0c,Picea abies,ERR260430,Male flower,6945787,8099229,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260430_1_ca.bam
pab-b1.0c,Picea abies,ERR260431,Vegetative shoots,7200142,5647634,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260431_1_ca.bam
pab-b1.0c,Picea abies,ERR260432,Needles,8630131,5912560,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260432_1_ca.bam
pab-b1.0c,Picea abies,ERR260433,Needles,6065371,5066895,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260433_1_ca.bam
pab-b1.0c,Picea abies,ERR260434,Infected Needles,2826977,4126687,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260434_1_ca.bam
pab-b1.0c,Picea abies,ERR260435,Vegetative shoots,5656755,4606667,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260435_1_ca.bam
pab-b1.0c,Picea abies,ERR260436,Pineapple Galls,6589481,5802217,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260436_1_ca.bam
pab-b1.0c,Picea abies,ERR260437,Buds,3366114,4445238,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260437_1_ca.bam
pab-b1.0c,Picea abies,ERR260438,Female flower,8010722,5437537,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260438_1_ca.bam
pab-b1.0c,Picea abies,ERR260439,Vegetative shoots needles,6224475,5042082,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260439_1_ca.bam
pab-b1.0c,Picea abies,ERR260440,Wood,3352576,4473235,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260440_1_ca.bam
pab-b1.0c,Picea abies,ERR260441,Vegetative shoots needles,4763675,4032230,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260441_1_ca.bam
pab-b1.0c,Picea abies,ERR260442,Buds,4176876,4718332,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260442_1_ca.bam
pab-b1.0c,Picea abies,ERR260443,Dried twig needles,4454255,4571320,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260443_1_ca.bam
pab-b1.0c,Picea abies,ERR260444,Girdled twig needles,4219942,3965993,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260444_1_ca.bam
pab-b1.0c,Picea abies,ERR260445,Girdled twig stem,3708117,4465051,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260445_1_ca.bam
pab-b1.0c,Picea abies,ERR260446,Dawn needles,4277736,5826910,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260446_1_ca.bam
pab-b1.0c,Picea abies,ERR260447,Mid day needles,4123729,3536727,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260447_1_ca.bam
pab-b1.0c,Picea abies,ERR260448,Late afternoon needles,5194176,5906976,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260448_1_ca.bam
pab-b1.0c,Picea abies,ERR260449,Night needles,4479095,5000816,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260449_1_ca.bam
pab-b1.0c,Picea abies,ERR260450,Wood,2948555,2360885,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260450_1_ca.bam
pab-b1.0c,Picea abies,ERR260451,Wood,3716540,3773966,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260451_1_ca.bam
pab-b1.0c,Picea abies,ERR260452,Male flower,7001042,8154236,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260452_1_ca.bam
pab-b1.0c,Picea abies,ERR260453,Vegetative shoots,7251876,5706273,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260453_1_ca.bam
pab-b1.0c,Picea abies,ERR260454,Needles,8706804,5965648,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260454_1_ca.bam
pab-b1.0c,Picea abies,ERR260455,Needles,6110628,5106289,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260455_1_ca.bam
pab-b1.0c,Picea abies,ERR260456,Infected Needles,2849604,4149469,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260456_1_ca.bam
pab-b1.0c,Picea abies,ERR260457,Vegetative shoots,5709137,4657086,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260457_1_ca.bam
pab-b1.0c,Picea abies,ERR260458,Pineapple Galls,6650986,5866588,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260458_1_ca.bam
pab-b1.0c,Picea abies,ERR260459,Buds,3394039,4480092,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260459_1_ca.bam
pab-b1.0c,Picea abies,ERR260460,Female flower,8050053,5495058,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260460_1_ca.bam
pab-b1.0c,Picea abies,ERR260461,Vegetative shoots needles,6282219,5094543,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260461_1_ca.bam
pab-b1.0c,Picea abies,ERR260462,Wood,3381658,4495172,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260462_1_ca.bam
pab-b1.0c,Picea abies,ERR260463,Vegetative shoots needles,4798283,4066530,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260463_1_ca.bam
pab-b1.0c,Picea abies,ERR260464,Buds,4212388,4753353,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260464_1_ca.bam
pab-b1.0c,Picea abies,ERR260465,Dried twig needles,4484982,4598774,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260465_1_ca.bam
pab-b1.0c,Picea abies,ERR260466,Girdled twig needles,4253343,3993900,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260466_1_ca.bam
pab-b1.0c,Picea abies,ERR260467,Girdled twig stem,3743044,4494138,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260467_1_ca.bam
pab-b1.0c,Picea abies,ERR260468,Dawn needles,4326468,5865352,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260468_1_ca.bam
pab-b1.0c,Picea abies,ERR260469,Mid day needles,4162346,3561695,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260469_1_ca.bam
pab-b1.0c,Picea abies,ERR260470,Late afternoon needles,5249086,5934039,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260470_1_ca.bam
pab-b1.0c,Picea abies,ERR260471,Night needles,4537496,5039153,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260471_1_ca.bam
pab-b1.0c,Picea abies,ERR260472,Wood,2972748,2376368,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260472_1_ca.bam
pab-b1.0c,Picea abies,ERR260473,Wood,3749030,3799073,http://plantsmallrnagenes.science.psu.edu/pab-b1.0c/alignments/ERR260473_1_ca.bam
ppt-b3.0,Physcomitrella patens,SRR768442_SRR942518,wild-type protonemata (Gransden 2004),30266912,2713281,http://plantsmallrnagenes.science.psu.edu/ppt-b3.0/alignments/SRR768442_SRR942518_ca.bam
ppt-b3.0,Physcomitrella patens,SRR768443_SRR942519,wild-type protonemata (Gransden 2004),31991519,3067711,http://plantsmallrnagenes.science.psu.edu/ppt-b3.0/alignments/SRR768443_SRR942519_ca.bam
ppt-b3.0,Physcomitrella patens,SRR768444_SRR942520,wild-type protonemata (Gransden 2009),20203817,2289859,http://plantsmallrnagenes.science.psu.edu/ppt-b3.0/alignments/SRR768444_SRR942520_ca.bam
ppt-b3.0,Physcomitrella patens,SRR768445_SRR942521,wild-type protonemata (Gransden 2009),25472325,1997869,http://plantsmallrnagenes.science.psu.edu/ppt-b3.0/alignments/SRR768445_SRR942521_ca.bam
ppt-b3.0,Physcomitrella patens,SRR942522,wild-type protonemata (Gransden 2004),11102464,1272028,http://plantsmallrnagenes.science.psu.edu/ppt-b3.0/alignments/SRR942522_ca.bam
ppt-b3.0,Physcomitrella patens,SRR942523,wild-type protonemata (Gransden 2004),13557852,1887975,http://plantsmallrnagenes.science.psu.edu/ppt-b3.0/alignments/SRR942523_ca.bam
mpo-b3.0,Marchantia polymorpha,DRR042261_1,Mature thalli,7903189,2211142,http://plantsmallrnagenes.science.psu.edu/mpo-b3.0/alignments/DRR042261_1.bam
mpo-b3.0,Marchantia polymorpha,DRR042262_1,Antheridial heads with developing and mature antherida,4582523,1009763,http://plantsmallrnagenes.science.psu.edu/mpo-b3.0/alignments/DRR042262_1.bam
mpo-b3.0,Marchantia polymorpha,DRR042263_1,Archegonial heads before fertilization,4161286,1667271,http://plantsmallrnagenes.science.psu.edu/mpo-b3.0/alignments/DRR042263_1.bam
mpo-b3.0,Marchantia polymorpha,SRR2179617_1_ca,Thalli,9323961,1957424,http://plantsmallrnagenes.science.psu.edu/mpo-b3.0/alignments/SRR2179617_1_ca.bam