{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_selection = \"Oligo-dT\" and tissue_curation = \"Whole Organism\"", "rows": [[29718, "SRR27485663", "SRX23156886", "SRS20107307", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "4 cell R3", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: embryo 1 hpf  rep4", "EV06010", "EV06010", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV06010.R1.fastq.gz", "fastq", 620142356.0, 8227837.0, "EV06010.R1.fastq.gz", "0:75.37", "A:186029536;C:118842640;G:134072972;T:181171903;N:25305", 75, null, null, null, 186029536, 118842640, 134072972, 181171903, 25305, "SRX23156886", "SRS20107307", "SRA1783314", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.90656, null, 0.06918, null, 0.80192, null, 0.72472, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29721, "SRR27485666", "SRX23156883", "SRS20107304", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "24h R2", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: embryo 24 hpf  rep4", "EV06007", "EV06007", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV06007.R1.fastq.gz", "fastq", 758984715.0, 10062029.0, "EV06007.R1.fastq.gz", "0:75.43", "A:221215464;C:148997667;G:167225079;T:221520231;N:26274", 75, null, null, null, 221215464, 148997667, 167225079, 221520231, 26274, "SRX23156883", "SRS20107304", "SRA1783314", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.90914, null, 0.18457, null, 0.77782, null, 0.38818, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-11", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [29722, "SRR27485667", "SRX23156882", "SRS20107303", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Bud R2", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: embryo 10 hpf  rep4", "EV06006", "EV06006", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV06006.R1.fastq.gz", "fastq", 734373761.0, 9740919.0, "EV06006.R1.fastq.gz", "0:75.39", "A:217249501;C:141011173;G:161749180;T:214341396;N:22511", 75, null, null, null, 217249501, 141011173, 161749180, 214341396, 22511, "SRX23156882", "SRS20107303", "SRA1783314", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.902, null, 0.14583, null, 0.80937, null, 0.67478, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29723, "SRR27485668", "SRX23156881", "SRS20107302", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Dome R2", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: embryo 5 hpf  rep4", "EV06005", "EV06005", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV06005.R1.fastq.gz", "fastq", 776568876.0, 10317721.0, "EV06005.R1.fastq.gz", "0:75.27", "A:238745211;C:151859247;G:171793387;T:214113382;N:57649", 75, null, null, null, 238745211, 151859247, 171793387, 214113382, 57649, "SRX23156881", "SRS20107302", "SRA1783314", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.87227, null, 0.14085, null, 0.81797, null, 0.72906, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29724, "SRR27485669", "SRX23156880", "SRS20107301", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "1K cell R2", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: embryo 3 hpf  rep4", "EV06004", "EV06004", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV06004.R1.fastq.gz", "fastq", 682509965.0, 9050328.0, "EV06004.R1.fastq.gz", "0:75.41", "A:196111480;C:138950038;G:156032208;T:191368964;N:47275", 75, null, null, null, 196111480, 138950038, 156032208, 191368964, 47275, "SRX23156880", "SRS20107301", "SRA1783314", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.91494, null, 0.12926, null, 0.80044, null, 0.71156, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29725, "SRR27485670", "SRX23156879", "SRS20107300", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "4 cell R2", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: embryo 1 hpf  rep4", "EV06003", "EV06003", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV06003.R1.fastq.gz", "fastq", 706095550.0, 9366364.0, "EV06003.R1.fastq.gz", "0:75.39", "A:204324355;C:140058731;G:159377323;T:202282197;N:52944", 75, null, null, null, 204324355, 140058731, 159377323, 202282197, 52944, "SRX23156879", "SRS20107300", "SRA1783314", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.90788, null, 0.10297, null, 0.80168, null, 0.71073, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29726, "SRR27485671", "SRX23156878", "SRS20107299", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "24h R3", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: embryo 24 hpf  rep4", "EV06014", "EV06014", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV06014.R1.fastq.gz", "fastq", 708984998.0, 9425445.0, "EV06014.R1.fastq.gz", "0:75.22", "A:219626080;C:141270902;G:161722995;T:186246245;N:118776", 75, null, null, null, 219626080, 141270902, 161722995, 186246245, 118776, "SRX23156878", "SRS20107299", "SRA1783314", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.84881, null, 0.17975, null, 0.79693, null, 0.44149, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-11", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [29727, "SRR27485672", "SRX23156877", "SRS20107298", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Bud R3", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: embryo 10 hpf  rep4", "EV06013", "EV06013", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV06013.R1.fastq.gz", "fastq", 569494672.0, 7557761.0, "EV06013.R1.fastq.gz", "0:75.35", "A:170266388;C:110739260;G:124536859;T:163915551;N:36614", 75, null, null, null, 170266388, 110739260, 124536859, 163915551, 36614, "SRX23156877", "SRS20107298", "SRA1783314", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.90037, null, 0.16195, null, 0.81308, null, 0.71641, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29728, "SRR27485673", "SRX23156876", "SRS20107297", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Dome R3", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: embryo 5 hpf  rep4", "EV06012", "EV06012", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV06012.R1.fastq.gz", "fastq", 612322255.0, 8128508.0, "EV06012.R1.fastq.gz", "0:75.33", "A:190142665;C:119966127;G:131824584;T:170353082;N:35797", 75, null, null, null, 190142665, 119966127, 131824584, 170353082, 35797, "SRX23156876", "SRS20107297", "SRA1783314", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.89638, null, 0.12215, null, 0.8196, null, 0.79176, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29729, "SRR27485674", "SRX23156875", "SRS20107296", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "1K cell R3", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: embryo 3 hpf  rep4", "EV06011", "EV06011", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV06011.R1.fastq.gz", "fastq", 516168257.0, 6849932.0, "EV06011.R1.fastq.gz", "0:75.35", "A:157131780;C:98595108;G:111327650;T:149089977;N:23742", 75, null, null, null, 157131780, 98595108, 111327650, 149089977, 23742, "SRX23156875", "SRS20107296", "SRA1783314", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.89456, null, 0.0693, null, 0.80306, null, 0.73611, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29732, "SRR27477292", "SRX23148655", "SRS20099371", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "24h R4", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: embryo 24 hpf  rep4", "EV09007", "EV09007", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV09007.R1.fastq.gz", "fastq", 693872355.0, 9217545.0, "EV09007.R1.fastq.gz", "0:75.28", "A:207207066;C:136288214;G:150585299;T:199742228;N:49548", 75, null, null, null, 207207066, 136288214, 150585299, 199742228, 49548, "SRX23148655", "SRS20099371", "SRA1782413", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.89376, null, 0.11471, null, 0.79192, null, 0.60125, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [29733, "SRR27477293", "SRX23148654", "SRS20099366", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Bud R4", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: embryo 10 hpf  rep4", "EV09006", "EV09006", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV09006.R1.fastq.gz", "fastq", 476216388.0, 6331468.0, "EV09006.R1.fastq.gz", "0:75.21", "A:146002765;C:93329508;G:104039751;T:132799091;N:45273", 75, null, null, null, 146002765, 93329508, 104039751, 132799091, 45273, "SRX23148654", "SRS20099366", "SRA1782413", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.88768, null, 0.12305, null, 0.82696, null, 0.67338, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-10", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29734, "SRR27477294", "SRX23148653", "SRS20099369", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Dome R4", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: embryo 5 hpf  rep4", "EV09005", "EV09005", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. 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Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV09004.R1.fastq.gz", "fastq", 471461315.0, 6271281.0, "EV09004.R1.fastq.gz", "0:75.18", "A:148103215;C:93173628;G:103496734;T:126647635;N:40103", 75, null, null, null, 148103215, 93173628, 103496734, 126647635, 40103, "SRX23148652", "SRS20099365", "SRA1782413", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.87715, null, 0.11105, null, 0.80606, null, 0.74204, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-10", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29736, "SRR27477296", "SRX23148651", "SRS20099370", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "4 cell R4", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: embryo 1 hpf  rep4", "EV09003", "EV09003", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV09003.R1.fastq.gz", "fastq", 438955973.0, 5837128.0, "EV09003.R1.fastq.gz", "0:75.20", "A:134628611;C:87460856;G:98199538;T:118638244;N:28724", 75, null, null, null, 134628611, 87460856, 98199538, 118638244, 28724, "SRX23148651", "SRS20099370", "SRA1782413", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.89029, null, 0.11994, null, 0.80833, null, 0.72581, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-10", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [60659, "SRR12474618", "SRX8968764", "SRS7224501", "SRP278034", "PRJNA657343", "Satb2 acts as a gatekeeper for gene 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interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.", null, null, null, "Quantseq 14som SATB2 MUT BR1", "Quantseq 14som SATB2 MUT Rep1", null, "strain:TU|isolate:Satb2 mutant|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 hpf|dev stage:14 somites|sex:not applicable|tissue:whole embryo|Replicate:replicate=14som SATB2 MUT Rep1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Quantseq 14som SATB2 MUT BR1", "Quantseq 14som SATB2 MUT Rep1", "Quantseq 14som SATB2 MUT Rep1", "3 mRNA  seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP278034", null, null, "Quantseq_14som_SATB2_MUT_Rep1.fastq.gz", "fastq", 714114566.0, 9480391.0, "Quantseq 14som SATB2 MUT Rep1.fastq.gz", "0:75.33 1:0", "A:214876091;C:138572440;G:176756219;T:183862261;N:47555", 75, 0, null, null, 214876091, 138572440, 176756219, 183862261, 47555, "SRX8968702", "SRS7224439", "SRA1114017", "IISER-PUNE|biology", "IISER-PUNE", 1, 0.53567, null, 0.06484, null, 0.84618, null, 0.64745, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "India", "2020-08-19", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [60679, "SRR12474681", "SRX8968701", "SRS7224438", "SRP278034", "PRJNA657343", "Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development", "PRJNA657343", "Other", "Comprehensive integration of transcriptome  genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.", null, null, null, "Quantseq 80epi WT BR2", "Quantseq 80epi WT Rep2", null, "strain:TU|isolate:wild type|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:8 hpf|dev stage:80% epiboly|sex:not applicable|tissue:whole embryo|Replicate:replicate=80epi WT Rep2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Quantseq 80epi WT BR2", "Quantseq 80epi WT Rep2", "Quantseq 80epi WT Rep2", "3 mRNA  seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP278034", null, null, "Quantseq_80epi_WT_Rep2.fastq.gz", "fastq", 834116747.0, 11071286.0, "Quantseq 80epi WT Rep2.fastq.gz", "0:75.34 1:0", "A:243775122;C:161987024;G:207222240;T:220993929;N:138432", 75, 0, null, null, 243775122, 161987024, 207222240, 220993929, 138432, "SRX8968701", "SRS7224438", "SRA1114017", "IISER-PUNE|biology", "IISER-PUNE", 1, 0.6061, null, 0.10365, null, 0.83721, null, 0.67496, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "India", "2020-08-19", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [60680, "SRR12474682", "SRX8968700", "SRS7224437", "SRP278034", "PRJNA657343", "Satb2 acts as a gatekeeper for gene regulatory transitions during early embryonic development", "PRJNA657343", "Other", "Comprehensive integration of transcriptome  genome wide occupancy and chromatin accessibility profiles in satb2 loss of function and gain of function systems to discover novel and evolutionary conserved molecular interplays between Satb2 and the genetic drivers of neurogenesis and neural crest development program.", null, null, null, "Quantseq 80epi WT BR1", "Quantseq 80epi WT Rep1", null, "strain:TU|isolate:wild type|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:8 hpf|dev stage:80% epiboly|sex:not applicable|tissue:whole embryo|Replicate:replicate=80epi WT Rep1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Quantseq 80epi WT BR1", "Quantseq 80epi WT Rep1", "Quantseq 80epi WT Rep1", "3 mRNA  seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP278034", null, null, "Quantseq_80epi_WT_Rep1.fastq.gz", "fastq", 793778602.0, 10547219.0, "Quantseq 80epi WT Rep1.fastq.gz", "0:75.26 1:0", "A:238127973;C:158344527;G:199756679;T:197315931;N:233492", 75, 0, null, null, 238127973, 158344527, 199756679, 197315931, 233492, "SRX8968700", "SRS7224437", "SRA1114017", "IISER-PUNE|biology", "IISER-PUNE", 1, 0.51289, null, 0.09167, null, 0.85466, null, 0.6674, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "India", "2020-08-19", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [67761, "SRR17267991", "SRX13446017", "SRS11345216", "SRP351480", "PRJNA790108", "Shutdown corner  a large deletion mutant isolated from a haploid mutagenesis screen in zebrafish", "PRJNA790108", "Other", "Morphogenesis  the formation of three dimensional organ structures  requires precise coupling of genetic regulation and complex cell behaviors. The genetic networks governing many morphogenetic systems  including that of the embryonic eye  are poorly understood. In zebrafish  several forward genetic screens have sought to identify factors regulating eye development. These screens often look for eye defects at stages post the optic cup is formed and when retinal neurogenesis is under way. This approach can make it difficult to identify mutants specific for morphogenesis  as opposed to neurogenesis. To this end  we carried out a forward genetic  small scale haploidmutagenesis screen in zebrafish Danio rerio to identify factors that govern optic cup morphogenesis. We screened 100 genomes and isolated shutdown corner sco  a mutant which exhibits multiple tissue defects and harbors a 10 Mb deletion that encompasses 89 annotated genes. Using a combination of live imaging and antibody staining  we found cell proliferation  cell death  and tissue patterning defects in the sco optic cup. We also observed other phenotypes  including paralysis  neuromuscular defects  and ocular vasculature defects. To date  the largest deletion mutants reported in zebrafish are engineered using CRISPR Cas9 and are less than 300 kb. Because of the number of genes within the deletion interval  shutdown corner DfChr05:scoz207 could be a useful resource to the zebrafish community  as it may be helpful for gene mapping  understanding genetic interactions  or for study of the many genes lost in the mutant.", null, null, null, null, "sco Mutant", null, "strain:AB|age:3 dpf|sex:pooled male and female|tissue:whole embryo|genotype:Homozygous Mutant|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Zebrafish Embryos: 3 dpf sco mutant", "8525X1", "8525X1", "Sequencing libraries 18 pM were chemically denatured and applied to an Illumina TruSeq v3 single read flowcell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina TruSeq SR Cluster Kit v3 cBot HS GD 401 3001.   Following transfer of the flowcell to an Illumina HiSeq 2500 instrument HCS v2.0.12 and RTA v1.17.21.3  a 50 cycle single read sequence run was performed using TruSeq SBS v3 sequencing reagents FC 401 3002.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP351480", null, null, "8525X1_111104_SN141_0409_BD0DR0ABXX_1.txt", "fastq", 2385441300.0, 47708826.0, "8525X1 111104 SN141 0409 BD0DR0ABXX 1.txt", "0:50", "A:625043248;C:578161916;G:551073234;T:630745508;N:417394", 50, null, null, null, 625043248, 578161916, 551073234, 630745508, 417394, "SRX13446017", "SRS11345216", "SRA1345457", "Brigham Young University|Physiology and Developmental Biology", "University of Utah", 1, 0.93674, null, 0.06315, null, 0.67919, null, 0.4512, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2021-12-18", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [67762, "SRR17267992", "SRX13446016", "SRS11345215", "SRP351480", "PRJNA790108", "Shutdown corner  a large deletion mutant isolated from a haploid mutagenesis screen in zebrafish", "PRJNA790108", "Other", "Morphogenesis  the formation of three dimensional organ structures  requires precise coupling of genetic regulation and complex cell behaviors. The genetic networks governing many morphogenetic systems  including that of the embryonic eye  are poorly understood. In zebrafish  several forward genetic screens have sought to identify factors regulating eye development. These screens often look for eye defects at stages post the optic cup is formed and when retinal neurogenesis is under way. This approach can make it difficult to identify mutants specific for morphogenesis  as opposed to neurogenesis. To this end  we carried out a forward genetic  small scale haploidmutagenesis screen in zebrafish Danio rerio to identify factors that govern optic cup morphogenesis. We screened 100 genomes and isolated shutdown corner sco  a mutant which exhibits multiple tissue defects and harbors a 10 Mb deletion that encompasses 89 annotated genes. Using a combination of live imaging and antibody staining  we found cell proliferation  cell death  and tissue patterning defects in the sco optic cup. We also observed other phenotypes  including paralysis  neuromuscular defects  and ocular vasculature defects. To date  the largest deletion mutants reported in zebrafish are engineered using CRISPR Cas9 and are less than 300 kb. Because of the number of genes within the deletion interval  shutdown corner DfChr05:scoz207 could be a useful resource to the zebrafish community  as it may be helpful for gene mapping  understanding genetic interactions  or for study of the many genes lost in the mutant.", null, null, null, null, "Wildtype", null, "strain:AB|age:3 dpf|sex:pooled male and female|tissue:whole embryo|genotype:Wildtype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Zebrafish Embryos: 3 dpf wildtype", "8525X2", "8525X2", "Sequencing libraries 18 pM were chemically denatured and applied to an Illumina TruSeq v3 single read flowcell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina TruSeq SR Cluster Kit v3 cBot HS GD 401 3001.   Following transfer of the flowcell to an Illumina HiSeq 2500 instrument HCS v2.0.12 and RTA v1.17.21.3  a 50 cycle single read sequence run was performed using TruSeq SBS v3 sequencing reagents FC 401 3002.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP351480", null, null, "8525X2_111104_SN141_0409_BD0DR0ABXX_1.txt", "fastq", 2333527350.0, 46670547.0, "8525X2 111104 SN141 0409 BD0DR0ABXX 1.txt", "0:50", "A:618004841;C:556758932;G:533915120;T:624433832;N:414625", 50, null, null, null, 618004841, 556758932, 533915120, 624433832, 414625, "SRX13446016", "SRS11345215", "SRA1345457", "Brigham Young University|Physiology and Developmental Biology", "University of Utah", 1, 0.93172, null, 0.07657, null, 0.66216, null, 0.45209, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2021-12-18", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [70056, "SRR19392694", "SRX15447454", "SRS13169844", "SRP376956", "PRJNA842165", "Danio rerio Raw sequence reads", "PRJNA842165", "Whole Genome Sequencing", "the RNA seq of 45dpf whole fish", null, null, null, null, "whole zebrafish", null, "breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "mut 3 45dpf", "mut 3 45dpf", "RNAseq of whole fish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP376956", null, null, "6Hmut_3_R1.fastq.gz 6Hmut_3_R2.fastq.gz", "fastq fastq", 6560549850.0, 21723675.0, "6Hmut 3 R1.fastq.gz", "0:151 1:151", "A:1737437159;C:1534810355;G:1561501860;T:1726789854;N:10622", 151, 151, null, null, 1737437159, 1534810355, 1561501860, 1726789854, 10622, "SRX15447454", "SRS13169844", "SRA1426081", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.93435, 0.93393, 0.06267, 0.06345, 0.65776, 0.65871, 0.49762, 0.49344, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-25", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [70057, "SRR19392695", "SRX15447453", "SRS13169844", "SRP376956", "PRJNA842165", "Danio rerio Raw sequence reads", "PRJNA842165", "Whole Genome Sequencing", "the RNA seq of 45dpf whole fish", null, null, null, null, "whole zebrafish", null, "breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "mut 2 45dpf", "mut 2 45dpf", "RNAseq of whole fish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP376956", null, null, "6Hmut_2_R1.fastq.gz 6Hmut_2_R2.fastq.gz", "fastq fastq", 6478614532.0, 21452366.0, "6Hmut 2 R1.fastq.gz", "0:151 1:151", "A:1722746415;C:1511301958;G:1537581513;T:1706974238;N:10408", 151, 151, null, null, 1722746415, 1511301958, 1537581513, 1706974238, 10408, "SRX15447453", "SRS13169844", "SRA1426081", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.94033, 0.93884, 0.0793, 0.07897, 0.66979, 0.67063, 0.51091, 0.50721, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-25", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [70058, "SRR19392696", "SRX15447452", "SRS13169844", "SRP376956", "PRJNA842165", "Danio rerio Raw sequence reads", "PRJNA842165", "Whole Genome Sequencing", "the RNA seq of 45dpf whole fish", null, null, null, null, "whole zebrafish", null, "breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "mut 1 45dpf", "mut 1 45dpf", "RNAseq of whole fish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP376956", null, null, "6Hmut_1_R1.fastq.gz 6Hmut_1_R2.fastq.gz", "fastq fastq", 7131696780.0, 23614890.0, "6Hmut 1 R1.fastq.gz", "0:151 1:151", "A:1896556650;C:1662708805;G:1692110221;T:1880309012;N:12092", 151, 151, null, null, 1896556650, 1662708805, 1692110221, 1880309012, 12092, "SRX15447452", "SRS13169844", "SRA1426081", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.93784, 0.93841, 0.07685, 0.07715, 0.65969, 0.65999, 0.50615, 0.51174, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-25", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [70059, "SRR19392697", "SRX15447451", "SRS13169844", "SRP376956", "PRJNA842165", "Danio rerio Raw sequence reads", "PRJNA842165", "Whole Genome Sequencing", "the RNA seq of 45dpf whole fish", null, null, null, null, "whole zebrafish", null, "breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "wt 3 45dpf", "wt 3 45dpf", "RNAseq of whole fish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP376956", null, null, "wt_3_R1.fastq.gz wt_3_R2.fastq.gz", "fastq fastq", 6772530000.0, 22575100.0, "wt 3 R1.fastq.gz", "0:150 1:150", "A:1761127291;C:1612285256;G:1643602723;T:1755489964;N:24766", 150, 150, null, null, 1761127291, 1612285256, 1643602723, 1755489964, 24766, "SRX15447451", "SRS13169844", "SRA1426081", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.94155, 0.94016, 0.04781, 0.04747, 0.67054, 0.67227, 0.49488, 0.49322, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-25", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [70060, "SRR19392698", "SRX15447450", "SRS13169844", "SRP376956", "PRJNA842165", "Danio rerio Raw sequence reads", "PRJNA842165", "Whole Genome Sequencing", "the RNA seq of 45dpf whole fish", null, null, null, null, "whole zebrafish", null, "breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "wt 2 45dpf", "wt 2 45dpf", "RNAseq of whole fish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP376956", null, null, "wt_2_R1.fastq.gz wt_2_R2.fastq.gz", "fastq fastq", 7643857500.0, 25479525.0, "wt 2 R1.fastq.gz", "0:150 1:150", "A:1983773833;C:1824285264;G:1856615811;T:1979155020;N:27572", 150, 150, null, null, 1983773833, 1824285264, 1856615811, 1979155020, 27572, "SRX15447450", "SRS13169844", "SRA1426081", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.93966, 0.93936, 0.04464, 0.04509, 0.66947, 0.67006, 0.47294, 0.48847, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-25", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [70061, "SRR19392699", "SRX15447449", "SRS13169844", "SRP376956", "PRJNA842165", "Danio rerio Raw sequence reads", "PRJNA842165", "Whole Genome Sequencing", "the RNA seq of 45dpf whole fish", null, null, null, null, "whole zebrafish", null, "breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of zebrafish", "wt 1 45dpf", "wt 1 45dpf", "RNAseq of whole fish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP376956", null, null, "wt_1_R1.fastq.gz wt_1_R2.fastq.gz", "fastq fastq", 7810923300.0, 26036411.0, "wt 1 R1.fastq.gz", "0:150 1:150", "A:2023252187;C:1867703140;G:1901935578;T:2018003438;N:28957", 150, 150, null, null, 2023252187, 1867703140, 1901935578, 2018003438, 28957, "SRX15447449", "SRS13169844", "SRA1426081", "Huazhong Agricultural university|Huazhong Agricultural university", "Huazhong Agricultural university", 2, 0.94254, 0.94222, 0.04298, 0.04298, 0.66884, 0.67073, 0.47763, 0.48746, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-05-25", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [72671, "SRR23060055", "SRX19013379", "SRS16433016", "SRP417129", "PRJNA922890", "Danio rerio Raw sequence reads", "PRJNA922890", "Whole Genome Sequencing", "normal reference transcriptome of zebrafish", null, null, null, null, "BPA225 3", null, "strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "Z908", "Z908", "normal RNA seq of zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417129", null, null, "BPA225_3_Clean_Data1.fq.gz BPA225_3_Clean_Data2.fq.gz", "fastq fastq", 5922430705.0, 21094865.0, "BPA225 3 Clean Data1.fq.gz", null, 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Zebrafish larvae were either infected with CyHV 3 or mock infected with PBS at three dpf. Larvae were sampled at 1  2 and 4 days post infection dpi. Samples were taken in triplicate at each time point each replicate consisted of five pooled larvae. For each sample  immediately post euthanasia  five whole larvae were lysed together in 700 \u03bcL QIAZol Qiagen and lysate was stored at  80C. post phase separation  RNA was extracted from the aqueous layer as per RNeasy kit with on column DNase digestion. Samples were analysed by Agilent 2100 Bioanalyzer to confirm that all samples exhibited RIN values >9.5. RNA sequencing libraries were prepared using TruSeq Stranded mRNA kit Illumina  as per manufacturers instructions. Sequencing was conducted using the Illumina NextSeq 500 System. Data consists of original raw output from RNAseq with no adapter or quality trimming .fastq fromat. 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Zebrafish larvae were either infected with CyHV 3 or mock infected with PBS at three dpf. Larvae were sampled at 1  2 and 4 days post infection dpi. Samples were taken in triplicate at each time point each replicate consisted of five pooled larvae. For each sample  immediately post euthanasia  five whole larvae were lysed together in 700 \u03bcL QIAZol Qiagen and lysate was stored at  80C. post phase separation  RNA was extracted from the aqueous layer as per RNeasy kit with on column DNase digestion. Samples were analysed by Agilent 2100 Bioanalyzer to confirm that all samples exhibited RIN values >9.5. RNA sequencing libraries were prepared using TruSeq Stranded mRNA kit Illumina  as per manufacturers instructions. Sequencing was conducted using the Illumina NextSeq 500 System. Data consists of original raw output from RNAseq with no adapter or quality trimming .fastq fromat. Please refer to publication for further details.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP420252", null, null, "Zeb_D1_C_3.fastq.gz", "fastq", 1268486018.0, 16804712.0, "Zeb D1 C 3.fastq.gz", "0:75.48 1:0", "A:310132973;C:308973329;G:294595195;T:354552044;N:232477", 75, 0, null, null, 310132973, 308973329, 294595195, 354552044, 232477, "SRX19229354", "SRS16634369", "SRA1582637", "University of Liege|Faculty of Veterinary Medicine", "University of Liege", 1, 0.95439, null, 0.09536, null, 0.65293, null, 0.44831, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2023-01-31", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [73922, "SRR23286018", "SRX19229353", "SRS16634369", "SRP420252", "PRJNA929940", "Transcriptomic Analysis of Zebrafish Larvae infected with Cyprinid Herpesvirus 3", "PRJNA929940", "Other", "The goal of this experiment was to characterise the response to Cyprinid Herpesvirus 3 CyHV 3 infection in WT AB zebrafish larvae in terms of the interferon stimulated gene ISG upregulation and the potential involvement of programmed cell death.", null, null, null, null, "CyHV 3 Infected and Mock Infected WT AB Zebrafish Larvae 3 dpf sampled at 1  2 and 3 dpi", null, "strain:WT AB|age:3 dpf stage:larvae|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Mock Infected WT AB Zebrafish Larvae 1 dpi  Replicate 2", "D1 M 2", "D1 M 2", "The goal of this experiment was to characterise the response to Cyprinid Herpesvirus 3 CyHV 3 infection in WT AB zebrafish larvae in terms of the interferon stimulated gene ISG upregulation and the potential involvement of programmed cell death. Zebrafish larvae were either infected with CyHV 3 or mock infected with PBS at three dpf. Larvae were sampled at 1  2 and 4 days post infection dpi. Samples were taken in triplicate at each time point each replicate consisted of five pooled larvae. For each sample  immediately post euthanasia  five whole larvae were lysed together in 700 \u03bcL QIAZol Qiagen and lysate was stored at  80C. post phase separation  RNA was extracted from the aqueous layer as per RNeasy kit with on column DNase digestion. Samples were analysed by Agilent 2100 Bioanalyzer to confirm that all samples exhibited RIN values >9.5. RNA sequencing libraries were prepared using TruSeq Stranded mRNA kit Illumina  as per manufacturers instructions. Sequencing was conducted using the Illumina NextSeq 500 System. Data consists of original raw output from RNAseq with no adapter or quality trimming .fastq fromat. Please refer to publication for further details.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP420252", null, null, "Zeb_D1_C_2.fastq.gz", "fastq", 1233401032.0, 16329742.0, "Zeb D1 C 2.fastq.gz", "0:75.53 1:0", "A:298532651;C:302322311;G:288824793;T:343650292;N:70985", 75, 0, null, null, 298532651, 302322311, 288824793, 343650292, 70985, "SRX19229353", "SRS16634369", "SRA1582637", "University of Liege|Faculty of Veterinary Medicine", "University of Liege", 1, 0.95745, null, 0.09061, null, 0.65062, null, 0.44324, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2023-01-31", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [73923, "SRR23286019", "SRX19229352", "SRS16634369", "SRP420252", "PRJNA929940", "Transcriptomic Analysis of Zebrafish Larvae infected with Cyprinid Herpesvirus 3", "PRJNA929940", "Other", "The goal of this experiment was to characterise the response to Cyprinid Herpesvirus 3 CyHV 3 infection in WT AB zebrafish larvae in terms of the interferon stimulated gene ISG upregulation and the potential involvement of programmed cell death.", null, null, null, null, "CyHV 3 Infected and Mock Infected WT AB Zebrafish Larvae 3 dpf sampled at 1  2 and 3 dpi", null, "strain:WT AB|age:3 dpf stage:larvae|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Mock Infected WT AB Zebrafish Larvae 1 dpi  Replicate 1", "D1 M 1", "D1 M 1", "The goal of this experiment was to characterise the response to Cyprinid Herpesvirus 3 CyHV 3 infection in WT AB zebrafish larvae in terms of the interferon stimulated gene ISG upregulation and the potential involvement of programmed cell death. Zebrafish larvae were either infected with CyHV 3 or mock infected with PBS at three dpf. Larvae were sampled at 1  2 and 4 days post infection dpi. Samples were taken in triplicate at each time point each replicate consisted of five pooled larvae. For each sample  immediately post euthanasia  five whole larvae were lysed together in 700 \u03bcL QIAZol Qiagen and lysate was stored at  80C. post phase separation  RNA was extracted from the aqueous layer as per RNeasy kit with on column DNase digestion. Samples were analysed by Agilent 2100 Bioanalyzer to confirm that all samples exhibited RIN values >9.5. RNA sequencing libraries were prepared using TruSeq Stranded mRNA kit Illumina  as per manufacturers instructions. Sequencing was conducted using the Illumina NextSeq 500 System. Data consists of original raw output from RNAseq with no adapter or quality trimming .fastq fromat. Please refer to publication for further details.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP420252", null, null, "Zeb_D1_C_1.fastq.gz", "fastq", 1288846672.0, 17064063.0, "Zeb D1 C 1.fastq.gz", "0:75.53 1:0", "A:317538424;C:311698120;G:298072422;T:361458272;N:79434", 75, 0, null, null, 317538424, 311698120, 298072422, 361458272, 79434, "SRX19229352", "SRS16634369", "SRA1582637", "University of Liege|Faculty of Veterinary Medicine", "University of Liege", 1, 0.95462, null, 0.09956, null, 0.64977, null, 0.45345, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2023-01-31", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [73924, "SRR23286020", "SRX19229351", "SRS16634369", "SRP420252", "PRJNA929940", "Transcriptomic Analysis of Zebrafish Larvae infected with Cyprinid Herpesvirus 3", "PRJNA929940", "Other", "The goal of this experiment was to characterise the response to Cyprinid Herpesvirus 3 CyHV 3 infection in WT AB zebrafish larvae in terms of the interferon stimulated gene ISG upregulation and the potential involvement of programmed cell death.", null, null, null, null, "CyHV 3 Infected and Mock Infected WT AB Zebrafish Larvae 3 dpf sampled at 1  2 and 3 dpi", null, "strain:WT AB|age:3 dpf stage:larvae|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "CyHV 3 Infected WT AB Zebrafish Larvae 1 dpi Replicate 3", "D1 I 3", "D1 I 3", "The goal of this experiment was to characterise the response to Cyprinid Herpesvirus 3 CyHV 3 infection in WT AB zebrafish larvae in terms of the interferon stimulated gene ISG upregulation and the potential involvement of programmed cell death. Zebrafish larvae were either infected with CyHV 3 or mock infected with PBS at three dpf. Larvae were sampled at 1  2 and 4 days post infection dpi. Samples were taken in triplicate at each time point each replicate consisted of five pooled larvae. For each sample  immediately post euthanasia  five whole larvae were lysed together in 700 \u03bcL QIAZol Qiagen and lysate was stored at  80C. post phase separation  RNA was extracted from the aqueous layer as per RNeasy kit with on column DNase digestion. Samples were analysed by Agilent 2100 Bioanalyzer to confirm that all samples exhibited RIN values >9.5. RNA sequencing libraries were prepared using TruSeq Stranded mRNA kit Illumina  as per manufacturers instructions. Sequencing was conducted using the Illumina NextSeq 500 System. Data consists of original raw output from RNAseq with no adapter or quality trimming .fastq fromat. Please refer to publication for further details.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP420252", null, null, "Zeb_D1_I_3.fastq.gz", "fastq", 1201925958.0, 15913939.0, "Zeb D1 I 3.fastq.gz", "0:75.53 1:0", "A:300443973;C:288585078;G:274455100;T:338365565;N:76242", 75, 0, null, null, 300443973, 288585078, 274455100, 338365565, 76242, "SRX19229351", "SRS16634369", "SRA1582637", "University of Liege|Faculty of Veterinary Medicine", "University of Liege", 1, 0.9509, null, 0.10141, null, 0.64912, null, 0.45155, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2023-01-31", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [73925, "SRR23286021", "SRX19229350", "SRS16634369", "SRP420252", "PRJNA929940", "Transcriptomic Analysis of Zebrafish Larvae infected with Cyprinid Herpesvirus 3", "PRJNA929940", "Other", "The goal of this experiment was to characterise the response to Cyprinid Herpesvirus 3 CyHV 3 infection in WT AB zebrafish larvae in terms of the interferon stimulated gene ISG upregulation and the potential involvement of programmed cell death.", null, null, null, null, "CyHV 3 Infected and Mock Infected WT AB Zebrafish Larvae 3 dpf sampled at 1  2 and 3 dpi", null, "strain:WT AB|age:3 dpf stage:larvae|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Mock Infected WT AB Zebrafish Larvae 4 dpi Replicate 3", "D4 M 3", "D4 M 3", "The goal of this experiment was to characterise the response to Cyprinid Herpesvirus 3 CyHV 3 infection in WT AB zebrafish larvae in terms of the interferon stimulated gene ISG upregulation and the potential involvement of programmed cell death. Zebrafish larvae were either infected with CyHV 3 or mock infected with PBS at three dpf. Larvae were sampled at 1  2 and 4 days post infection dpi. Samples were taken in triplicate at each time point each replicate consisted of five pooled larvae. For each sample  immediately post euthanasia  five whole larvae were lysed together in 700 \u03bcL QIAZol Qiagen and lysate was stored at  80C. post phase separation  RNA was extracted from the aqueous layer as per RNeasy kit with on column DNase digestion. Samples were analysed by Agilent 2100 Bioanalyzer to confirm that all samples exhibited RIN values >9.5. RNA sequencing libraries were prepared using TruSeq Stranded mRNA kit Illumina  as per manufacturers instructions. Sequencing was conducted using the Illumina NextSeq 500 System. Data consists of original raw output from RNAseq with no adapter or quality trimming .fastq fromat. Please refer to publication for further details.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP420252", null, null, "Zeb_D4_C_3.fastq.gz", "fastq", 1524002689.0, 20175910.0, "Zeb D4 C 3.fastq.gz", "0:75.54 1:0", "A:367807831;C:374119516;G:357128331;T:424899738;N:47273", 75, 0, null, null, 367807831, 374119516, 357128331, 424899738, 47273, "SRX19229350", "SRS16634369", "SRA1582637", "University of Liege|Faculty of Veterinary Medicine", "University of Liege", 1, 0.95682, null, 0.09558, null, 0.66107, null, 0.45582, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2023-01-31", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [73926, "SRR23286022", "SRX19229349", "SRS16634369", "SRP420252", "PRJNA929940", "Transcriptomic Analysis of Zebrafish Larvae infected with Cyprinid Herpesvirus 3", "PRJNA929940", "Other", "The goal of this experiment was to characterise the response to Cyprinid Herpesvirus 3 CyHV 3 infection in WT AB zebrafish larvae in terms of the interferon stimulated gene ISG upregulation and the potential involvement of programmed cell death.", null, null, null, null, "CyHV 3 Infected and Mock Infected WT AB Zebrafish Larvae 3 dpf sampled at 1  2 and 3 dpi", null, "strain:WT AB|age:3 dpf stage:larvae|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Mock Infected WT AB Zebrafish Larvae 4 dpi Replicate 2", "D4 M 2", "D4 M 2", "The goal of this experiment was to characterise the response to Cyprinid Herpesvirus 3 CyHV 3 infection in WT AB zebrafish larvae in terms of the interferon stimulated gene ISG upregulation and the potential involvement of programmed cell death. Zebrafish larvae were either infected with CyHV 3 or mock infected with PBS at three dpf. Larvae were sampled at 1  2 and 4 days post infection dpi. Samples were taken in triplicate at each time point each replicate consisted of five pooled larvae. For each sample  immediately post euthanasia  five whole larvae were lysed together in 700 \u03bcL QIAZol Qiagen and lysate was stored at  80C. post phase separation  RNA was extracted from the aqueous layer as per RNeasy kit with on column DNase digestion. Samples were analysed by Agilent 2100 Bioanalyzer to confirm that all samples exhibited RIN values >9.5. RNA sequencing libraries were prepared using TruSeq Stranded mRNA kit Illumina  as per manufacturers instructions. Sequencing was conducted using the Illumina NextSeq 500 System. Data consists of original raw output from RNAseq with no adapter or quality trimming .fastq fromat. Please refer to publication for further details.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP420252", null, null, "Zeb_D4_C_2.fastq.gz", "fastq", 1346483243.0, 17826732.0, "Zeb D4 C 2.fastq.gz", "0:75.53 1:0", "A:326980169;C:328517917;G:315896052;T:375007649;N:81456", 75, 0, null, null, 326980169, 328517917, 315896052, 375007649, 81456, "SRX19229349", "SRS16634369", "SRA1582637", "University of Liege|Faculty of Veterinary Medicine", "University of Liege", 1, 0.95433, null, 0.09983, null, 0.65928, null, 0.45769, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2023-01-31", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [73927, "SRR23286023", "SRX19229348", "SRS16634369", "SRP420252", "PRJNA929940", "Transcriptomic Analysis of Zebrafish Larvae infected with Cyprinid Herpesvirus 3", "PRJNA929940", "Other", "The goal of this experiment was to characterise the response to Cyprinid Herpesvirus 3 CyHV 3 infection in WT AB zebrafish larvae in terms of the interferon stimulated gene ISG upregulation and the potential involvement of programmed cell death.", null, null, null, null, "CyHV 3 Infected and Mock Infected WT AB Zebrafish Larvae 3 dpf sampled at 1  2 and 3 dpi", null, "strain:WT AB|age:3 dpf stage:larvae|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Mock Infected WT AB Zebrafish Larvae 4 dpi Replicate 1", "D4 M 1", "D4 M 1", "The goal of this experiment was to characterise the response to Cyprinid Herpesvirus 3 CyHV 3 infection in WT AB zebrafish larvae in terms of the interferon stimulated gene ISG upregulation and the potential involvement of programmed cell death. Zebrafish larvae were either infected with CyHV 3 or mock infected with PBS at three dpf. Larvae were sampled at 1  2 and 4 days post infection dpi. Samples were taken in triplicate at each time point each replicate consisted of five pooled larvae. For each sample  immediately post euthanasia  five whole larvae were lysed together in 700 \u03bcL QIAZol Qiagen and lysate was stored at  80C. post phase separation  RNA was extracted from the aqueous layer as per RNeasy kit with on column DNase digestion. Samples were analysed by Agilent 2100 Bioanalyzer to confirm that all samples exhibited RIN values >9.5. RNA sequencing libraries were prepared using TruSeq Stranded mRNA kit Illumina  as per manufacturers instructions. Sequencing was conducted using the Illumina NextSeq 500 System. Data consists of original raw output from RNAseq with no adapter or quality trimming .fastq fromat. Please refer to publication for further details.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP420252", null, null, "Zeb_D4_C_1.fastq.gz", "fastq", 1321138333.0, 17491239.0, "Zeb D4 C 1.fastq.gz", "0:75.53 1:0", "A:321477796;C:321935265;G:308343149;T:369304479;N:77644", 75, 0, null, null, 321477796, 321935265, 308343149, 369304479, 77644, "SRX19229348", "SRS16634369", "SRA1582637", "University of Liege|Faculty of Veterinary Medicine", "University of Liege", 1, 0.95491, null, 0.0995, null, 0.65518, null, 0.46152, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2023-01-31", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [73928, "SRR23286024", "SRX19229347", "SRS16634369", "SRP420252", "PRJNA929940", "Transcriptomic Analysis of Zebrafish Larvae infected with Cyprinid Herpesvirus 3", "PRJNA929940", "Other", "The goal of this experiment was to characterise the response to Cyprinid Herpesvirus 3 CyHV 3 infection in WT AB zebrafish larvae in terms of the interferon stimulated gene ISG upregulation and the potential involvement of programmed cell death.", null, null, null, null, "CyHV 3 Infected and Mock Infected WT AB Zebrafish Larvae 3 dpf sampled at 1  2 and 3 dpi", null, "strain:WT AB|age:3 dpf stage:larvae|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "CyHV 3 Infected WT AB Zebrafish Larvae 4 dpi Replicate 3", "D4 I 3", "D4 I 3", "The goal of this experiment was to characterise the response to Cyprinid Herpesvirus 3 CyHV 3 infection in WT AB zebrafish larvae in terms of the interferon stimulated gene ISG upregulation and the potential involvement of programmed cell death. Zebrafish larvae were either infected with CyHV 3 or mock infected with PBS at three dpf. Larvae were sampled at 1  2 and 4 days post infection dpi. Samples were taken in triplicate at each time point each replicate consisted of five pooled larvae. For each sample  immediately post euthanasia  five whole larvae were lysed together in 700 \u03bcL QIAZol Qiagen and lysate was stored at  80C. post phase separation  RNA was extracted from the aqueous layer as per RNeasy kit with on column DNase digestion. Samples were analysed by Agilent 2100 Bioanalyzer to confirm that all samples exhibited RIN values >9.5. RNA sequencing libraries were prepared using TruSeq Stranded mRNA kit Illumina  as per manufacturers instructions. Sequencing was conducted using the Illumina NextSeq 500 System. Data consists of original raw output from RNAseq with no adapter or quality trimming .fastq fromat. 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Zebrafish larvae were either infected with CyHV 3 or mock infected with PBS at three dpf. Larvae were sampled at 1  2 and 4 days post infection dpi. Samples were taken in triplicate at each time point each replicate consisted of five pooled larvae. For each sample  immediately post euthanasia  five whole larvae were lysed together in 700 \u03bcL QIAZol Qiagen and lysate was stored at  80C. post phase separation  RNA was extracted from the aqueous layer as per RNeasy kit with on column DNase digestion. Samples were analysed by Agilent 2100 Bioanalyzer to confirm that all samples exhibited RIN values >9.5. RNA sequencing libraries were prepared using TruSeq Stranded mRNA kit Illumina  as per manufacturers instructions. Sequencing was conducted using the Illumina NextSeq 500 System. Data consists of original raw output from RNAseq with no adapter or quality trimming .fastq fromat. 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