Table 3. Summary of RNA-Seq raw data metrics.
| Sample ID | Genotype | Sample Code | Treatment Code | Replicate | Raw Read Pairs | Trimmed Read Pairs | Percentage | Insert_Size | StdDev |
|---|---|---|---|---|---|---|---|---|---|
| Read pair counts are shown per individual sample. The percentage of retained reads after trimming as well as insert size (st dev) per RNA sample and replica are shown. The sample ID consists of the genotype name -X, I or XI-; the environmental perturbation—FI: fish; TR: Triops; PA: P ramosa parasite; BX: toxic cyanobacteria strain; BN: non-toxic cyanobacteria strain; CR: crowding; CA: carbaryl; CD: cadmium; PB: lead; PH5; UV: UV exposure; NaCl: Sodium Chloride; CO: control-; replica-sample code for sequence submission. The protocols run on the three strains, their biological replicates and the associated NCBI Sequence Read Archive run accession numbers are listed in Supplementary Table 2. | |||||||||
| I_CO_r1_03 | I | Dman_03 | CO | r1 | 63,494,959.000 | 49,603,877.000 | 78.12% | 289 | 137 |
| I_CA_r1_05 | I | Dman_05 | CA | r1 | 62,993,811.000 | 49,028,587.000 | 77.83% | 311 | 188 |
| I_BX_r1_09 | I | Dman_09 | BX | r1 | 60,794,872.000 | 48,712,777.000 | 80.13% | 292 | 156 |
| I_TR_r1_13 | I | Dman_13 | TR | r1 | 55,021,109.000 | 43,773,368.000 | 79.56% | 319 | 173 |
| I_FI_r1_15 | I | Dman_15 | FI | r1 | 58,768,662.000 | 48,858,401.000 | 83.14% | 276 | 143 |
| I_BN_r1_21 | I | Dman_21 | BN | r1 | 68,881,858.000 | 55,980,417.000 | 81.27% | 272 | 116 |
| I_PA_r1_23 | I | Dman_23 | PA | r1 | 73,454,356.000 | 60,869,142.000 | 82.87% | 298 | 141 |
| I_CR_r1_27 | I | Dman_27 | CR | r1 | 64,360,226.000 | 53,858,355.000 | 83.68% | 287 | 90 |
| I_CO_r2_29 | I | Dman_29 | CO | r2 | 53,507,535.000 | 44,845,409.000 | 83.81% | 268 | 144 |
| I_CO_r3_31 | I | Dman_31 | CO | r3 | 50,103,302.000 | 44,154,666.000 | 88.13% | 277 | 151 |
| I_CA_r2_35 | I | Dman_35 | CA | r2 | 54,459,613.000 | 47,952,269.000 | 88.05% | 262 | 92 |
| I_BX_r2_36 | I | Dman_36 | BX | r2 | 58,852,394.000 | 51,366,050.000 | 87.28% | 289 | 139 |
| I_BX_r3_38 | I | Dman_38 | BX | r3 | 48,433,025.000 | 38,663,288.000 | 79.83% | 265 | 87 |
| I_FI_r2_39 | I | Dman_39 | FI | r2 | 51,705,574.000 | 41,476,171.000 | 80.22% | 269 | 153 |
| I_FI_r3_41 | I | Dman_41 | FI | r3 | 48,109,963.000 | 38,197,802.000 | 79.40% | 271 | 146 |
| I_CA_r3_44 | I | Dman_44 | CA | r3 | 56,372,343.000 | 45,134,149.000 | 80.06% | 255 | 89 |
| I_BN_r2_46 | I | Dman_46 | BN | r2 | 54,184,465.000 | 44,125,200.000 | 81.44% | 298 | 130 |
| I_BN_r3_47 | I | Dman_47 | BN | r3 | 47,781,030.000 | 39,153,548.000 | 81.94% | 304 | 195 |
| I_CR_r2_50 | I | Dman_50 | CR | r2 | 48,214,069.000 | 40,159,238.000 | 83.29% | 279 | 120 |
| I_CR_r3_52 | I | Dman_52 | CR | r3 | 51,730,328.000 | 42,678,747.000 | 82.50% | 283 | 121 |
| I_TR_r2_53 | I | Dman_53 | TR | r2 | 58,022,273.000 | 46,414,803.000 | 79.99% | 283 | 150 |
| I_TR_r3_54 | I | Dman_54 | TR | r3 | 82,196,854.000 | 70,756,025.000 | 86.08% | 295 | 120 |
| I_PA_r2_56 | I | Dman_56 | PA | r2 | 72,623,134.000 | 62,031,907.000 | 85.42% | 288 | 122 |
| I_PA_r3_58 | I | Dman_58 | PA | r3 | 62,249,354.000 | 51,270,680.000 | 82.36% | 292 | 88 |
| X_CO_r1_32 | X | Dman_32 | CO | r1 | 71,868,056.000 | 54,279,251.000 | 75.53% | 278 | 111 |
| X_CA_r1_33 | X | Dman_33 | CA | r1 | 52,241,312.000 | 39,732,399.000 | 76.06% | 286 | 152 |
| X_FI_r1_42 | X | Dman_42 | FI | r1 | 71,287,854.000 | 57,746,708.000 | 81.00% | 283 | 172 |
| X_BN_r1_45 | X | Dman_45 | BN | r1 | 61,527,322.000 | 49,445,396.000 | 80.36% | 280 | 132 |
| X_BX_r1_48 | X | Dman_48 | BX | r1 | 66,965,781.000 | 50,685,192.000 | 75.69% | 266 | 114 |
| X_CR_r1_51 | X | Dman_51 | CR | r1 | 76,818,434.000 | 59,552,351.000 | 77.52% | 246 | 87 |
| X_PA_r1_55 | X | Dman_55 | PA | r1 | 58,307,384.000 | 44,248,248.000 | 75.89% | 251 | 85 |
| X_CA_r2_60 | X | Dman_60 | CA | r2 | 65,880,062.000 | 50,044,254.000 | 75.96% | 237 | 81 |
| X_CA_r3_61 | X | Dman_61 | CA | r3 | 66,867,949.000 | 50,405,221.000 | 75.38% | 232 | 83 |
| X_CO_r2_62 | X | Dman_62 | CO | r2 | 67,659,124.000 | 51,393,424.000 | 75.96% | 241 | 125 |
| X_FI_r2_64 | X | Dman_64 | FI | r2 | 70,280,087.000 | 54,395,752.000 | 77.40% | 243 | 85 |
| X_FI_r3_65 | X | Dman_65 | FI | r3 | 66,226,108.000 | 50,516,556.000 | 76.28% | 255 | 116 |
| X_BX_r2_67 | X | Dman_67 | BX | r2 | 67,379,171.000 | 51,252,578.000 | 76.07% | 286 | 145 |
| X_BX_r3_68 | X | Dman_68 | BX | r3 | 81,455,682.000 | 67,969,702.000 | 83.44% | 291 | 111 |
| X_TR_r1_70 | X | Dman_70 | TR | r1 | 57,871,883.000 | 48,655,208.000 | 84.07% | 279 | 163 |
| X_TR_r2_73 | X | Dman_73 | TR | r2 | 58,433,654.000 | 49,868,737.000 | 85.34% | 281 | 144 |
| X_BN_r2_74 | X | Dman_74 | BN | r2 | 75,608,849.000 | 57,220,416.000 | 75.68% | 287 | 134 |
| X_PA_r2_75 | X | Dman_75 | PA | r2 | 63,636,165.000 | 51,803,268.000 | 81.41% | 261 | 104 |
| X_CO_r3_76 | X | Dman_76 | CO | r3 | 90,321,814.000 | 73,595,073.000 | 81.48% | 271 | 101 |
| X_CO_r4_77 | X | Dman_77 | CO | r4 | 118,207,131.000 | 87,998,612.000 | 74.44% | 278 | 154 |
| X_CR_r2_78 | X | Dman_78 | CR | r2 | 62,101,323.000 | 54,966,131.000 | 88.51% | 287 | 139 |
| X_CR_r3_79 | X | Dman_79 | CR | r3 | 90,997,555.000 | 78,494,531.000 | 86.26% | 254 | 160 |
| X_PA_r3_80 | X | Dman_80 | PA | r3 | 58,790,865.000 | 50,985,812.000 | 86.72% | 43 | 112 |
| X_BN_r3_83 | X | Dman_83 | BN | r3 | 83,174,861.000 | 71,186,306.000 | 85.59% | 228 | 141 |
| X_TR_r3_84 | X | Dman_84 | TR | r3 | 46,523,201.000 | 33,845,684.000 | 72.75% | 226 | 117 |
| XI_CD_r1_01 | XI | XI_01 | CD | r1 | 35,429,813.000 | 35,359,972.000 | 99.80% | 166 | 53 |
| XI_CD_r2_02 | XI | XI_02 | CD | r2 | 58,550,652.000 | 58,459,895.000 | 99.84% | 166 | 54 |
| XI_CD_r3_03 | XI | XI_03 | CD | r3 | 16,981,329.000 | 16,957,777.000 | 99.86% | 164 | 53 |
| XI_CO_r1_04 | XI | XI_04 | CO | r1 | 17,549,155.000 | 17,526,674.000 | 99.87% | 173 | 98 |
| XI_CO_r2_05 | XI | XI_05 | CO | r2 | 12,968,443.000 | 12,951,973.000 | 99.87% | 161 | 52 |
| XI_CO_r3_06 | XI | XI_06 | CO | r3 | 22,191,696.000 | 22,165,545.000 | 99.88% | 166 | 150 |
| XI_PB_r1_07 | XI | XI_07 | PB | r1 | 13,209,418.000 | 13,022,646.000 | 98.59% | 160 | 49 |
| XI_PB_r2_08 | XI | XI_08 | PB | r2 | 25,098,583.000 | 25,063,912.000 | 99.86% | 168 | 121 |
| XI_PB_r3_09 | XI | XI_09 | PB | r3 | 20,147,612.000 | 20,119,479.000 | 99.86% | 164 | 53 |
| XI_PH5_r1_10 | XI | XI_10 | PH5 | r1 | 17,117,432.000 | 16,780,537.000 | 98.03% | 160 | 48 |
| XI_PH5_r2_11 | XI | XI_11 | PH5 | r2 | 23,043,903.000 | 22,676,257.000 | 98.40% | 158 | 49 |
| XI_PH5_r3_12 | XI | XI_12 | PH5 | r3 | 28,299,589.000 | 27,784,289.000 | 98.18% | 163 | 51 |
| XI_NaCl_r1_13 | XI | XI_13 | NaCl | r1 | 9,454,837.000 | 9,279,727.000 | 98.15% | 167 | 50 |
| XI_NaCl_r2_14 | XI | XI_14 | NaCl | r2 | 14,129,350.000 | 13,855,321.000 | 98.06% | 165 | 49 |
| XI_NaCl_r3_15 | XI | XI_15 | NaCl | r3 | 36,387,177.000 | 35,659,077.000 | 98.00% | 164 | 50 |
| XI_UV_r1_16 | XI | XI_16 | UV | r1 | 35,314,952.000 | 34,645,324.000 | 98.10% | 166 | 49 |
| XI_UV_r2_17 | XI | XI_17 | UV | r2 | 33,396,591.000 | 32,775,509.000 | 98.14% | 167 | 49 |
| XI_UV_r3_18 | XI | XI_18 | UV | r3 | 23,849,621.000 | 23,398,424.000 | 98.11% | 166 | 49 |