{"text_format":"2","workbook":"xlsx","n_sheets":8,"sheets":["Raw","gDNA Qubit ","Primer-test","Test PCR","Exp PCR","Experiment2016-09-09","Experiment2016-09-19","ScoreTable2016-09-23"],"not_rendered":{"charts":0,"images":0,"macros":0,"external_links":0,"defined_names":0,"comments":0,"pivot_tables":0},"unopened":[],"bounds":{"document_bytes":16777216,"sheet_cells":100000,"run_cost":"one","rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0,"cell_chars":16384,"cell_head_chars":4096},"cells_cut":0,"cells_raw":0,"read":"whole","date_system":"1900"}

{"sheet":"Raw","index":0,"n_rows":10,"n_cols":17,"rows_kept":10,"cut":false,"hidden":false,"merged":[]}
["type","transl","gene","desc","group","start","stop","strand","chr","cM","fw","check1","rev","check2","check3","fragment_length"]
["known","4AL_5AL","TRIAE_CS42_5AL_TGACv1_375821_AA1227550.1:group17899:46367:51595","NADH-ubiquinone_oxidoreductase_B18_subunit,_Uncharacterized_protein","group17899",46367,51595,"-","5A",82.2857,"GTTGATGTAGTAGTGCCTCTGTTAT","PASS","TGGCCACGATAACCTCACAA","PASS",{"$f":"TRUE()","v":1},78,"memo: since frag size is small, we need to ask to run 3% agarose gel, 50 bp ladder and additional no template control to distinguish primer-dimers from PCR product."]
["known","4AL_5AL","TRIAE_CS42_5AL_TGACv1_375102_AA1216090.1:group17588:72632:76155","UDP-galactose_transporter_2","group17588",72632,76155,"-","5A",94.846,"GATGGAGATGATCACAGATGGATTA","PASS","ACGGAGACCTAAGGCAAAAGG","PASS",{"$f":"TRUE()","v":1},57]
["known","7BS_4AL","TRIAE_CS42_4AL_TGACv1_288159_AA0938900.2:group1175:29540:34615","WRKY_transcription_factor_73","group1175",29540,34615,"-","4A",111.1788,"ACAACCACGTTTGCTATTAGCT","PASS","TCACACCCTAAATACGCCCA","PASS",{"$f":"TRUE()","v":1},58]
["novel","5BL_4BS","TRIAE_CS42_4BS_TGACv1_328754_AA1093140.1:group17187:56413:57306","Acetyltransferase,_GNAT_family_protein,_expressed,_protein,_Putative_acetyltransferase","group17187",56413,57306,"-","4B",50.376,"GGATACCATGTGCAATGTACGTAG","PASS","GGATCGGAGAAAGGGAGTAGT","PASS",{"$f":"TRUE()","v":1},101]
["novel","7AL_3AL","TRIAE_CS42_3AL_TGACv1_193998_AA0624240.1:group12953:15776:19955","Pre-mRNA-splicing_factor_SLU7","group12953",15776,19955,"-","3A",70.7247,"CGATAATGCTCGTATGCGGAATTAT","PASS","ACTCTCATATTCCCACCCACA","PASS",{"$f":"TRUE()","v":1},67]
["known","4AL_5AL","TRIAE_CS42_5AL_TGACv1_373985_AA1186550.1:group16803:245897:251356","Expressed_protein,_protein,_cDNA_clone:J013169H09,_full_insert_sequence","group16803",245897,251356,"-","5A",94.846,"TTGAAAGGTCCGTCATGCAC","PASS","AGAACGAGAACCGGAAACAT","PASS",{"$f":"TRUE()","v":1},118]
["known","5AL_4AL","TRIAE_CS42_4AL_TGACv1_288492_AA0950070.1:group3295:35327:36995","F-box_domain_containing_protein","group3295",35327,36995,"-","4A",76.49516667,"AGAATATGTTTTAACACGGTACAGC","PASS","CCCCCTCTATCACACACAACC","PASS",{"$f":"TRUE()","v":1},89]
["known","7BS_4AL","TRIAE_CS42_4AL_TGACv1_288446_AA0948840.1:group6850:140646:145980","Alpha/beta-hydrolase_superfamily_protein,_Uncharacterized_protein","group6850",140646,145980,"plus","4A",111.1788,"CGAGGCTTTTGTAAGAGCGAAC","PASS","CTCCCACCGCGCTTAAATG","PASS",{"$f":"TRUE()","v":1},69]
["novel","5AL_7BS","TRIAE_CS42_7BS_TGACv1_592267_AA1934680.2:group7391:27286:32606","Chloroplast_thylakoid_membrane,_putative_isoform_1","group7391",27286,32606,"+","7B",1.136333333,"GTAGTACTCCACAACACACGG","PASS","TTTGTTGAGGAAGGAGGCCC","PASS",{"$f":"TRUE()","v":1},50]

{"sheet":"gDNA Qubit ","index":1,"n_rows":12,"n_cols":5,"rows_kept":12,"cut":false,"hidden":false,"merged":[]}
["gDNA","Conc (ng/µl)","V for 30uL at 2ng/ul","H2O"]
["N1A-T1D",3.8,{"$f":"2*30/B2","v":15.7894736842105},{"$f":"30-C2","v":14.2105263157895}]
["N1D-T1A",4.04,{"$f":"2*30/B3","v":14.8514851485149},{"$f":"30-C3","v":15.1485148514851}]
["N2A-T2D",9.38,{"$f":"2*30/B4","v":6.39658848614072},{"$f":"30-C4","v":23.6034115138593}]
["N6D-T6A",5.78,{"$f":"2*30/B5","v":10.3806228373702},{"$f":"30-C5","v":19.6193771626298}]
["N1B-T1A",4.18,{"$f":"2*30/B6","v":14.3540669856459},{"$f":"30-C6","v":15.6459330143541}]
["N1D-T1B",10.4,{"$f":"2*30/B7","v":5.76923076923077},{"$f":"30-C7","v":24.2307692307692}]
["N2D-T2A",3.44,{"$f":"2*30/B8","v":17.4418604651163},{"$f":"30-C8","v":12.5581395348837}]
["N5D-T5A",16.3,{"$f":"2*30/B9","v":3.68098159509202},{"$f":"30-C9","v":26.319018404908}]
[null,null,"V for 30uL at 2ng/ul","V for 180uL at 2ng/ul","H20"]
["CS42",85.8,{"$f":"2*30/B11","v":0.699300699300699},{"$f":"2*180/B11","v":4.1958041958042},{"$f":"180-D11","v":175.804195804196}]
["CS42 1:10"]

{"sheet":"Primer-test","index":2,"n_rows":20,"n_cols":13,"rows_kept":20,"cut":false,"hidden":false,"merged":[]}
["sample","transl","chr","fw","rev","fw len","rev len","fw + rev","insert_length","fragment_length","20160902_CS42","20160902_H2O","20160905_HS-TapeStation_size"]
[1,"4AL_5AL","5A","GTTGATGTAGTAGTGCCTCTGTTAT","TGGCCACGATAACCTCACAA",{"$f":"LEN(D2)","v":25},{"$f":"LEN(E2)","v":20},{"$f":"F2+G2","v":45},{"$f":"J2-H2","v":33},78," +?","PD",83]
[2,"4AL_5AL","5A","GATGGAGATGATCACAGATGGATTA","ACGGAGACCTAAGGCAAAAGG",{"$f":"LEN(D3)","v":25},{"$f":"LEN(E3)","v":21},{"$f":"F3+G3","v":46},{"$f":"J3-H3","v":11},57," +"," -"]
[3,"7BS_4AL","4A","ACAACCACGTTTGCTATTAGCT","TCACACCCTAAATACGCCCA",{"$f":"LEN(D4)","v":22},{"$f":"LEN(E4)","v":20},{"$f":"F4+G4","v":42},{"$f":"J4-H4","v":16},58," +"," -"]
[4,"5BL_4BS","4B","GGATACCATGTGCAATGTACGTAG","GGATCGGAGAAAGGGAGTAGT",{"$f":"LEN(D5)","v":24},{"$f":"LEN(E5)","v":21},{"$f":"F5+G5","v":45},{"$f":"J5-H5","v":56},101,"NS"," -",117]
[5,"7AL_3AL","3A","CGATAATGCTCGTATGCGGAATTAT","ACTCTCATATTCCCACCCACA",{"$f":"LEN(D6)","v":25},{"$f":"LEN(E6)","v":21},{"$f":"F6+G6","v":46},{"$f":"J6-H6","v":21},67," -","PD?"]
[6,"4AL_5AL","5A","TTGAAAGGTCCGTCATGCAC","AGAACGAGAACCGGAAACAT",{"$f":"LEN(D7)","v":20},{"$f":"LEN(E7)","v":20},{"$f":"F7+G7","v":40},{"$f":"J7-H7","v":78},118,"NS"," -","131?"]
[7,"5AL_4AL","4A","AGAATATGTTTTAACACGGTACAGC","CCCCCTCTATCACACACAACC",{"$f":"LEN(D8)","v":25},{"$f":"LEN(E8)","v":21},{"$f":"F8+G8","v":46},{"$f":"J8-H8","v":43},89,"NS","PD",95]
[8,"7BS_4AL","4A","CGAGGCTTTTGTAAGAGCGAAC","CTCCCACCGCGCTTAAATG",{"$f":"LEN(D9)","v":22},{"$f":"LEN(E9)","v":19},{"$f":"F9+G9","v":41},{"$f":"J9-H9","v":28},69," +","PD",75]
[9,"5AL_7BS","7B","GTAGTACTCCACAACACACGG","TTTGTTGAGGAAGGAGGCCC",{"$f":"LEN(D10)","v":21},{"$f":"LEN(E10)","v":20},{"$f":"F10+G10","v":41},{"$f":"J10-H10","v":9},50,"NS","PD","61?"]
[]
[]
[{"$nulls":10},"CS42","H20"]
[{"$nulls":9},"No. of +",{"$f":"COUNTIF(K$2:K$10,\" +\")","v":3},{"$f":"COUNTIF(L$2:L$10,\" +\")","v":0}]
[{"$nulls":9},"No. of +?",{"$f":"COUNTIF(K$2:K$10,\" +?\")","v":1},{"$f":"COUNTIF(L$2:L$10,\" +?\")","v":0}]
[{"$nulls":9},"No. of -",{"$f":"COUNTIF(K$2:K$10,\" -\")","v":1},{"$f":"COUNTIF(L$2:L$10,\" -\")","v":4}]
[{"$nulls":9},"No. of NS",{"$f":"COUNTIF(K$2:K$10,\"NS\")","v":4},{"$f":"COUNTIF(L$2:L$10,\"NS\")","v":0}]
[{"$nulls":9},"No. of PD",{"$f":"COUNTIF(K$2:K$10,\"PD\")","v":0},{"$f":"COUNTIF(L$2:L$10,\"PD\")","v":4}]
[{"$nulls":9},"No. of PD?",{"$f":"COUNTIF(K$2:K$10,\"PD?\")","v":0},{"$f":"COUNTIF(L$2:L$10,\"PD?\")","v":1}]
[{"$nulls":9},"Total",{"$f":"SUM(K14:K19)","v":9},{"$f":"SUM(L14:L19)","v":9}]

{"sheet":"Test PCR","index":3,"n_rows":44,"n_cols":9,"rows_kept":44,"cut":false,"hidden":false,"merged":[[24,8,26,8],[27,8,29,8]]}
[null,null,18,18]
[null,"1x","x (with DNA)","x (without DNA)",null,null,"95°C","03:00:00"]
["Nuclease free water qsp 25uL",{"$f":"B10-SUM(B4:B9)","v":11.78},{"$f":"B3*$C$1","v":212.04},{"$f":"B3*$D$1+C8","v":214.2},null,null,"95°C","00:15:00","10 cycles"]
["5X GC buffer (with MgCl2)",5,{"$f":"B4*$C$1","v":90},{"$f":"B4*$D$1","v":90},null,null,"55°C","00:30:00"]
["Betaine 5M (1M final)",5,{"$f":"B5*$C$1","v":90},{"$f":"B5*$D$1","v":90},null,null,"72°C","00:10:00"]
["dNTPs",0.5,{"$f":"B6*$C$1","v":9},{"$f":"B6*$D$1","v":9},null,null,"95°C","00:15:00","20 cycles"]
["Mix For+Rev primer 5uM each",2.5," -"," -",null,null,"50°C","00:30:00"]
["CS42 DNA 10ng",0.12,{"$f":"B8*$C$1","v":2.16}," -",null,null,"72°C","00:10:00"]
["Kapa 2G robust polymerase",0.1,{"$f":"B9*$C$1","v":1.8},{"$f":"B9*$D$1","v":1.8},null,null,"72°C","01:00:00"]
[null,25,{"$nulls":4},"10°C","hold"]
[null,{"$f":"SUM(B3:B9)","v":25}]
[]
[null,"1x","x (with DNA)","x (without DNA)"]
["Nuclease free water qsp 25uL",{"$f":"B20-SUM(B15:B19)","v":16.78},{"$f":"B14*$C$1","v":302.04},{"$f":"B14*$D$1+C18","v":304.2}]
["5X GC buffer (with MgCl2)",5,{"$f":"B15*$C$1","v":90},{"$f":"B15*$D$1","v":90}]
["dNTPs",0.5,{"$f":"B16*$C$1","v":9},{"$f":"B16*$D$1","v":9}]
["Mix For+Rev primer 5uM each",2.5," -"]
["CS42 DNA 10ng",0.12,{"$f":"B18*$C$1","v":2.16}]
["Kapa 2G robust polymerase",0.1,{"$f":"B19*$C$1","v":1.8},{"$f":"B19*$D$1","v":1.8}]
[null,25]
[null,{"$f":"SUM(B14:B19)","v":25}]
[]
[]
[null,"1x",{"$nulls":4},"95°C","03:00:00"]
["Nuclease free water qsp 25uL",{"$f":"B11-SUM(B26:B30)","v":11.9},{"$nulls":4},"95°C","00:15:00","10 cycles\nramp \n -1C/cycle until 50C"]
["5X GC buffer (with MgCl2)",5,{"$nulls":4},"60°C","00:15:00"]
["dNTPs",0.5,{"$nulls":4},"72°C","00:15:00"]
["Mix For+Rev primer 5uM each",2.5,{"$nulls":4},"95°C","00:15:00","20 cycles"]
["CS42 DNA 2ng/uL",5,{"$nulls":4},"50°C","00:15:00"]
["Kapa 2G robust polymerase",0.1,{"$nulls":4},"72°C","00:15:00"]
[{"$nulls":6},"72°C","05:00:00"]
[{"$nulls":6},"10°C","hold"]
[]
[]
[null,"1x",35]
["Nuclease free water qsp 25uL",9.875,{"$f":"B36*$C$35","v":345.625},{"$f":"B36*2.2","v":21.725}]
["5X GC buffer",5,{"$f":"B37*$C$35","v":175}]
["MgCl2",2,{"$f":"B38*$C$35","v":70}]
["dNTPs 10mM, freshly prepared",0.5,{"$f":"B39*$C$35","v":17.5}]
["Forward primer 10uM",1.25]
["Reverse primer 10uM",1.25]
["DNA",5]
["HotStart GoTaq 5U/uL",0.125,{"$f":"B43*$C$35","v":4.375}]
[null,"25uL"]

{"sheet":"Exp PCR","index":4,"n_rows":14,"n_cols":10,"rows_kept":14,"cut":false,"hidden":false,"merged":[]}
[{"$nulls":7},"CS42 DNA (ng/uL)",85.8]
[null,null,"PPMM","SMM"]
[null,"1x","6x (with DNA)","61x"]
["Nuclease free water qsp 25uL",{"$f":"B10-SUM(B5:B9)","v":11.9},{"$f":"B4*6","v":71.4},{"$f":"B4*61","v":725.9},null,null,"PP= Primer pair"]
["5X GC buffer (with MgCl2)",5,{"$f":"B5*6","v":30},{"$f":"B5*61","v":305}]
["dNTPs",0.5,{"$f":"B6*6","v":3},{"$f":"B6*61","v":30.5},null,null,"PP1","PP2","PP3","PP4"]
["Mix For+Rev primer 5uM each",2.5,{"$f":"B7*6","v":15},null,null,null,"PP5","PP6","PP7","PP8"]
["DNA",5,{"$nulls":4},"PP9","PP10","PP11","PP12"]
["Kapa 2G robust polymerase",0.1,{"$f":"B9*6","v":0.6},{"$f":"B9*61","v":6.1},null,null,"PP13","PP14"]
[null,25]
[null,{"$f":"SUM(B4:B9)","v":25},{"$nulls":4},"PP16","PP17","PP18","PP19"]
[{"$nulls":6},"PP20","PP21","PP22","PP23"]
[null,null,{"$f":"C4+C5+C9+C6","v":105},{"$f":"SUM(D4:D10)","v":1067.5},null,null,"PP24","PP25","PP26","PP27"]
[null,{"$f":"B10-B8","v":20},{"$f":"B14*6","v":120}]

{"sheet":"Experiment2016-09-09","index":5,"n_rows":12,"n_cols":14,"rows_kept":12,"cut":false,"hidden":false,"merged":[]}
[{"$nulls":7},"touch-down PCR scores 09.09.2016"]
["gDNA",null,"Primer pair (PP)","transl","group","gDNA-dep","gDNA-arr","CS42 10ng","CS42 1ng","Nulli-dep 10ng","Nulli-arr 10ng","H20","option B when extra","Note"]
["N1A-T1D",null,1,"4AL_5AL","group17899","N4A-T4D","N5A-T5B"," +"," +"," +"," +"," +"]
["N1D-T1A",null,2,"4AL_5AL","group17588","N4A-T4D","N5A-T5B"," +"," -"," +"," -"," -"]
["N2A-T2D",null,3,"7BS_4AL","group1175","N7B-T7A","N4A-T4D"," ++"," +"," ++"," -"," -"]
["N6A-T6D",null,4,"5BL_4BS","group17187","N5B-T5D","N4B-T4A"," ++"," +"," ++"," -"," -",null,"lower unspecific band"]
["N7B-T7A",null,5,"7AL_3AL","group12953","N7A-T7D","N3A-T3D"," ++?"," ++?"," ++?"," ++?"," ++?",null,"contamination?"]
["N1B-T1A",null,6,"4AL_5AL","group16803","N4A-T4D","N5A-T5B"," ++"," +"," ++"," -"," -",null,"several extra bands"]
["N1D-T1B",null,7,"5AL_4AL","group3295","N5A-T5B","N4A-T4D"," +","PD?"," +","PD?","PD?",null,"several extra bands"]
["N2B-T2A",null,8,"7BS_4AL","group6850","N7B-T7A","N4A-T4D"," ++"," +"," ++"," ++"," -"]
["N5D-T5A",null,9,"5AL_7BS","group7391","N5A-T5B","N7B-T7A"," ++"," ++"," ++"," ++"," ++"]
["N7D-T7B"]

{"sheet":"Experiment2016-09-19","index":6,"n_rows":11,"n_cols":10,"rows_kept":11,"cut":false,"hidden":false,"merged":[]}
[{"$nulls":5},"PCR scores 19.09.2016"]
["Primer pair (PP)","transl","group","gDNA-dep","gDNA-arr","CS42 10ng","CS42 1ng","Nulli-dep 10ng","Nulli-arr 10ng","H20"]
[1,"4AL_5AL","group17899","N4A-T4D","N5A-T5B"," ++"," +"," ++"," -"," -"]
[2,"4AL_5AL","group17588","N4A-T4D","N5A-T5B"," ++"," +"," ++"," -"," -"]
[3,"7BS_4AL","group1175","N7B-T7A","N4A-T4D"," ++"," +"," ++"," -"," -"]
[4,"5BL_4BS","group17187","N5B-T5D","N4B-T4A"," +"," -"," +"," -"," -"]
[5,"7AL_3AL","group12953","N7A-T7D","N3A-T3D"," +"," ?"," -"," +"," -"]
[6,"4AL_5AL","group16803","N4A-T4D","N5A-T5B"," ++"," +"," ++"," ?"," -"]
[7,"5AL_4AL","group3295","N5A-T5B","N4A-T4D"," ++"," +"," ++"," +"," -"]
[8,"7BS_4AL","group6850","N7B-T7A","N4A-T4D"," ++"," +"," ++"," ++"," -"]
[9,"5AL_7BS","group7391","N5A-T5B","N7B-T7A"]

{"sheet":"ScoreTable2016-09-23","index":7,"n_rows":18,"n_cols":18,"rows_kept":18,"cut":false,"hidden":false,"merged":[]}
["Primer pair (PP)","transl","group","chr","cM","fragment_length","gDNA-dep","gDNA-arr","PCR date","Annealing temperature","Gel number","CS42 10ng","CS42 1ng","Nulli-dep 10ng","Nulli-arr 10ng","H20","Translocation"]
[1,"4AL_5AL","group17899","5A",82.2857,78,"N4A-T4D","N5A-T5B","19.09.2016",55,1," ++"," +"," ++"," -"," -",{"$f":"TRUE()","v":1}]
[2,"4AL_5AL","group17588","5A",94.846,57,"N4A-T4D","N5A-T5B","19.09.2016",55,1," ++"," +"," ++"," -"," -",{"$f":"TRUE()","v":1}]
[3,"7BS_4AL","group1175","4A",111.1788,58,"N7B-T7A","N4A-T4D","19.09.2016",55,1," ++"," +"," ++"," -"," -",{"$f":"TRUE()","v":1}]
[4,"5BL_4BS","group17187","4B",50.376,101,"N5B-T5D","N4B-T4A","20.09.2016",55,2," +"," -"," +"," -"," -",{"$f":"TRUE()","v":1}]
[5,"7AL_3AL","group12953","3A",70.7247,67,"N7A-T7D","N3A-T3D","20.09.2016",55,2," ++"," +"," -"," +"," -",{"$f":"FALSE()","v":0}]
[6,"5AL_4AL","group3295","4A",76.49516667,89,"N5A-T5B","N4A-T4D","21.09.2016",60,3," ++"," +"," ++"," -"," -",{"$f":"TRUE()","v":1}]
[7,"5AL_7BS","group7391","7B",1.136333333,50,"N5A-T5B","N7B-T7A","22.09.2016",60,3," +"," -"," +"," -"," -",{"$f":"TRUE()","v":1}]
[8,"4AL_5AL","group16803","5A",94.846,118,"N4A-T4D","N5A-T5B","23.09.2019",60,4," ++"," +"," ++"," -"," -",{"$f":"TRUE()","v":1}]
[9,"7BS_4AL","group6850","4A",111.1788,69,"N7B-T7A","N4A-T4D","22.09.2016",60,4," +"," -"," ++","? slightly higher band"," -","?","maybe false, slightly higher band with Nulli-arr"]
[]
[]
[{"$nulls":16},"?",1]
[{"$nulls":16},{"$f":"FALSE()","v":0},1]
[{"$nulls":16},{"$f":"TRUE()","v":1},7]
[{"$nulls":16},"TOTAL",9]
[]
[{"$nulls":17},{"$f":"R15/R16","v":0.777777777777778}]