{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"size fractionation\", experiment.library_source = \"TRANSCRIPTOMIC\" and tissue_curation = \"Whole Organism\"", "rows": [[25283, "SRR25764121", "SRX21486801", "SRS18719093", "SRP457111", "PRJNA1009808", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq]", "GSE241754", "Transcriptome Analysis", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. 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Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. 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Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. 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Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. 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Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT 256 cell 2.5 hpf tRNA seq rep1", "GSM7734773", null, "source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:256 cell 2.5 hpf|genotype:WT|geo loc name:missing|collection date:missing", "WT 256 cell 2.5 hpf tRNA seq rep1", "Read demultiplexing and adapter trimming performed with cutadapt v3.5  where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained  and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5\u2019 RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters   species Drer   cluster id 0.93   min cov 0.001   max mismatches 0.075   control condition Egg   deconv cov ratio 0.4   remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters  and on read counts summed by isotype. 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The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV04009.R1.fastq.gz", "fastq", 609590940.0, 4354221.0, "EV04009.R1.fastq.gz", "0:140", "A:155062144;C:147628702;G:168099121;T:138772205;N:28768", 140, null, null, null, 155062144, 147628702, 168099121, 138772205, 28768, "SRX23139234", "SRS20090275", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29740, "SRR27467673", "SRX23139233", "SRS20090278", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "1K cell BS 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|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 3 hpf  BS  rep2", "EV04008", "EV04008", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV04008.R1.fastq.gz", "fastq", 675505180.0, 4825037.0, "EV04008.R1.fastq.gz", "0:140", "A:178823976;C:121648962;G:198428643;T:176572292;N:31307", 140, null, null, null, 178823976, 121648962, 198428643, 176572292, 31307, "SRX23139233", "SRS20090278", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29741, "SRR27467674", "SRX23139232", "SRS20090272", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "1K cell DM 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|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 3 hpf  DM  rep2", "EV04007", "EV04007", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV04007.R1.fastq.gz", "fastq", 702064440.0, 5014746.0, "EV04007.R1.fastq.gz", "0:140", "A:176719694;C:166467163;G:207893965;T:150951950;N:31668", 140, null, null, null, 176719694, 166467163, 207893965, 150951950, 31668, "SRX23139232", "SRS20090272", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 2e-05, null, 0.0, null, 0.99997, null, 1.0, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29742, "SRR27467675", "SRX23139231", "SRS20090271", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "1K cell mock 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|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 3 hpf  mock  rep2", "EV04006", "EV04006", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV04006.R1.fastq.gz", "fastq", 664790700.0, 4748505.0, "EV04006.R1.fastq.gz", "0:140", "A:172014219;C:146545691;G:200358431;T:145840649;N:31710", 140, null, null, null, 172014219, 146545691, 200358431, 145840649, 31710, "SRX23139231", "SRS20090271", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 3e-05, null, 0.0, null, 0.99993, null, 1.0, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29743, "SRR27467676", "SRX23139230", "SRS20090273", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "4 cell DM 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|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 1 hpf  DM  rep2", "EV04004", "EV04004", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV04004.R1.fastq.gz", "fastq", 895671560.0, 6397654.0, "EV04004.R1.fastq.gz", "0:140", "A:206443066;C:147067097;G:365386937;T:176734600;N:39860", 140, null, null, null, 206443066, 147067097, 365386937, 176734600, 39860, "SRX23139230", "SRS20090273", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29744, "SRR27467677", "SRX23139229", "SRS20090274", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "4 cell mock 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|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 1 hpf  mock  rep2", "EV04003", "EV04003", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV04003.R1.fastq.gz", "fastq", 664112120.0, 4743658.0, "EV04003.R1.fastq.gz", "0:140", "A:163711695;C:142612940;G:211194350;T:146562626;N:30509", 140, null, null, null, 163711695, 142612940, 211194350, 146562626, 30509, "SRX23139229", "SRS20090274", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 2e-05, null, 0.0, null, 0.99997, null, 1.0, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29747, "SRR27467680", "SRX23139226", "SRS20090267", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "24h BS 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|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 24 hpf  BS  rep2", "EV03009", "EV03009", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV03009.R1.fastq.gz", "fastq", 168931280.0, 2222780.0, "EV03009.R1.fastq.gz", "0:76", "A:49803604;C:36479774;G:37758990;T:44874154;N:14758", 76, null, null, null, 49803604, 36479774, 37758990, 44874154, 14758, "SRX23139226", "SRS20090267", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.00034, null, 0.0002, null, 0.99965, null, 0.5, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [29748, "SRR27467681", "SRX23139225", "SRS20090266", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "24h DM 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|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 24 hpf  DM  rep2", "EV03008", "EV03008", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV03008.R1.fastq.gz", "fastq", 200878792.0, 2643142.0, "EV03008.R1.fastq.gz", "0:76", "A:46955288;C:54746275;G:55887832;T:43270561;N:18836", 76, null, null, null, 46955288, 54746275, 55887832, 43270561, 18836, "SRX23139225", "SRS20090266", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.29408, null, 0.00737, null, 0.91823, null, 0.54549, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [29749, "SRR27467682", "SRX23139224", "SRS20090269", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "24h mock 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|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 24 hpf  mock  rep2", "EV03007", "EV03007", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV03007.R1.fastq.gz", "fastq", 175642840.0, 2311090.0, "EV03007.R1.fastq.gz", "0:76", "A:44745275;C:48908904;G:44862157;T:37111895;N:14609", 76, null, null, null, 44745275, 48908904, 44862157, 37111895, 14609, "SRX23139224", "SRS20090269", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.06887, null, 0.00273, null, 0.96623, null, 0.48721, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [29750, "SRR27467683", "SRX23139223", "SRS20090265", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Bud BS 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|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 10 hpf  BS  rep2", "EV04014", "EV04014", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV04014.R1.fastq.gz", "fastq", 774901260.0, 5535009.0, "EV04014.R1.fastq.gz", "0:140", "A:193865579;C:138861953;G:251102013;T:191036071;N:35644", 140, null, null, null, 193865579, 138861953, 251102013, 191036071, 35644, "SRX23139223", "SRS20090265", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29751, "SRR27467684", "SRX23139222", "SRS20090264", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Bud DM 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|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 10 hpf  DM  rep2", "EV04013", "EV04013", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV04013.R1.fastq.gz", "fastq", 666372840.0, 4759806.0, "EV04013.R1.fastq.gz", "0:140", "A:172923134;C:142243998;G:211584978;T:139591020;N:29710", 140, null, null, null, 172923134, 142243998, 211584978, 139591020, 29710, "SRX23139222", "SRS20090264", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 3e-05, null, 0.0, null, 0.99991, null, 1.0, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29752, "SRR27467685", "SRX23139221", "SRS20090262", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Bud mock 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|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 10 hpf  mock  rep2", "EV04012", "EV04012", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV04012.R1.fastq.gz", "fastq", 628769540.0, 4491211.0, "EV04012.R1.fastq.gz", "0:140", "A:160925901;C:143204697;G:183224867;T:141385307;N:28768", 140, null, null, null, 160925901, 143204697, 183224867, 141385307, 28768, "SRX23139221", "SRS20090262", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 1e-05, null, 0.0, null, 0.99997, null, 1.0, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29753, "SRR27467686", "SRX23139220", "SRS20090263", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Dome BS 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|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 5 hpf  BS  rep2", "EV04011", "EV04011", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV04011.R1.fastq.gz", "fastq", 720913200.0, 5149380.0, "EV04011.R1.fastq.gz", "0:140", "A:185414155;C:126110104;G:238649631;T:170706590;N:32720", 140, null, null, null, 185414155, 126110104, 238649631, 170706590, 32720, "SRX23139220", "SRS20090263", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29754, "SRR27467687", "SRX23139219", "SRS20090259", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Dome DM 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|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 5 hpf  DM  rep2", "EV04010", "EV04010", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV04010.R1.fastq.gz", "fastq", 443650200.0, 3168930.0, "EV04010.R1.fastq.gz", "0:140", "A:114663509;C:102512276;G:135709753;T:90744641;N:20021", 140, null, null, null, 114663509, 102512276, 135709753, 90744641, 20021, "SRX23139219", "SRS20090259", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 1e-05, null, 0.0, null, 0.99997, null, 1.0, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29757, "SRR27437477", "SRX23109820", "SRS20064574", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "1K cell mock R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 3 hpf  mock  rep3", "EV07007", "EV07007", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07007.R1.fastq.gz", "fastq", 479994620.0, 3428533.0, "EV07007.R1.fastq.gz", "0:140", "A:124628886;C:116843590;G:123136721;T:115372734;N:12689", 140, null, null, null, 124628886, 116843590, 123136721, 115372734, 12689, "SRX23109820", "SRS20064574", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 6e-05, null, 1e-05, null, 0.99989, null, 1.0, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29758, "SRR27437478", "SRX23109819", "SRS20064573", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "4 cell BS R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 1 hpf  BS  rep3", "EV07006", "EV07006", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07006.R1.fastq.gz", "fastq", 2584527680.0, 18460912.0, "EV07006.R1.fastq.gz", "0:140", "A:685107500;C:367766834;G:717359848;T:814224206;N:69292", 140, null, null, null, 685107500, 367766834, 717359848, 814224206, 69292, "SRX23109819", "SRS20064573", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 2e-05, null, 1e-05, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29759, "SRR27437479", "SRX23109818", "SRS20064571", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "4 cell DM R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 1 hpf  DM  rep3", "EV07005", "EV07005", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07005.R1.fastq.gz", "fastq", 713829480.0, 5098782.0, "EV07005.R1.fastq.gz", "0:140", "A:183575304;C:168886779;G:213156258;T:148191838;N:19301", 140, null, null, null, 183575304, 168886779, 213156258, 148191838, 19301, "SRX23109818", "SRS20064571", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 5e-05, null, 0.0, null, 0.99989, null, 1.0, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29760, "SRR27437480", "SRX23109817", "SRS20064572", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "4 cell mock R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 1 hpf  mock  rep3", "EV07004", "EV07004", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07004.R1.fastq.gz", "fastq", 517336680.0, 3695262.0, "EV07004.R1.fastq.gz", "0:140", "A:136783049;C:131207858;G:139873280;T:109458276;N:14217", 140, null, null, null, 136783049, 131207858, 139873280, 109458276, 14217, "SRX23109817", "SRS20064572", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 7e-05, null, 0.0, null, 0.99981, null, 0.7, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29764, "SRR27437484", "SRX23109813", "SRS20064567", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "24h BS R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 24 hpf  BS  rep3", "EV07018", "EV07018", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07018.R1.fastq.gz", "fastq", 887731180.0, 6340937.0, "EV07018.R1.fastq.gz", "0:140", "A:204102176;C:148262233;G:350287017;T:185056779;N:22975", 140, null, null, null, 204102176, 148262233, 350287017, 185056779, 22975, "SRX23109813", "SRS20064567", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [29766, "SRR27437486", "SRX23109811", "SRS20064565", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "24h DM R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 24 hpf  DM  rep3", "EV07017", "EV07017", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07017.R1.fastq.gz", "fastq", 466089960.0, 3329214.0, "EV07017.R1.fastq.gz", "0:140", "A:117818387;C:108651920;G:144753443;T:94853810;N:12400", 140, null, null, null, 117818387, 108651920, 144753443, 94853810, 12400, "SRX23109811", "SRS20064565", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [29767, "SRR27437487", "SRX23109810", "SRS20064563", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "24h mock R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:24 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 24 hpf  mock  rep3", "EV07016", "EV07016", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07016.R1.fastq.gz", "fastq", 638674120.0, 4561958.0, "EV07016.R1.fastq.gz", "0:140", "A:159572532;C:147135537;G:186885553;T:145063254;N:17244", 140, null, null, null, 159572532, 147135537, 186885553, 145063254, 17244, "SRX23109810", "SRS20064563", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 4e-05, null, 0.0, null, 0.99993, null, 0.0, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [29768, "SRR27437488", "SRX23109809", "SRS20064564", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Bud BS R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 10 hpf  BS  rep3", "EV07015", "EV07015", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07015.R1.fastq.gz", "fastq", 598389400.0, 4274210.0, "EV07015.R1.fastq.gz", "0:140", "A:150315140;C:106310211;G:186765596;T:154982225;N:16228", 140, null, null, null, 150315140, 106310211, 186765596, 154982225, 16228, "SRX23109809", "SRS20064564", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29769, "SRR27437489", "SRX23109808", "SRS20064562", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Bud DM R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 10 hpf  DM  rep3", "EV07014", "EV07014", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07014.R1.fastq.gz", "fastq", 739056780.0, 5278977.0, "EV07014.R1.fastq.gz", "0:140", "A:197948890;C:178761090;G:200265458;T:162060992;N:20350", 140, null, null, null, 197948890, 178761090, 200265458, 162060992, 20350, "SRX23109808", "SRS20064562", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 3e-05, null, 0.0, null, 0.99995, null, 0.5, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29770, "SRR27437490", "SRX23109807", "SRS20064561", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Bud mock R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:10 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 10 hpf  mock  rep3", "EV07013", "EV07013", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07013.R1.fastq.gz", "fastq", 844338040.0, 6030986.0, "EV07013.R1.fastq.gz", "0:140", "A:217780710;C:182517044;G:251974206;T:192043675;N:22405", 140, null, null, null, 217780710, 182517044, 251974206, 192043675, 22405, "SRX23109807", "SRS20064561", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 4e-05, null, 0.0, null, 0.99993, null, 1.0, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29771, "SRR27437491", "SRX23109806", "SRS20064560", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Dome BS R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 5 hpf  BS  rep3", "EV07011", "EV07011", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07011.R1.fastq.gz", "fastq", 893528580.0, 6382347.0, "EV07011.R1.fastq.gz", "0:140", "A:240101890;C:155985797;G:262065322;T:235351334;N:24237", 140, null, null, null, 240101890, 155985797, 262065322, 235351334, 24237, "SRX23109806", "SRS20064560", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29772, "SRR27437492", "SRX23109805", "SRS20064559", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Dome DM R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 5 hpf  DM  rep3", "EV07012", "EV07012", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07012.R1.fastq.gz", "fastq", 797662600.0, 5697590.0, "EV07012.R1.fastq.gz", "0:140", "A:201908589;C:182656132;G:249672167;T:163404182;N:21530", 140, null, null, null, 201908589, 182656132, 249672167, 163404182, 21530, "SRX23109805", "SRS20064559", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 3e-05, null, 0.0, null, 0.99991, null, 0.75, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29773, "SRR27437493", "SRX23109804", "SRS20064558", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Dome mock R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 5 hpf  mock  rep3", "EV07010", "EV07010", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07010.R1.fastq.gz", "fastq", 467593280.0, 3339952.0, "EV07010.R1.fastq.gz", "0:140", "A:122604957;C:118747514;G:124074466;T:102153374;N:12969", 140, null, null, null, 122604957, 118747514, 124074466, 102153374, 12969, "SRX23109804", "SRS20064558", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 4e-05, null, 0.0, null, 0.99993, null, 1.0, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29774, "SRR27437494", "SRX23109803", "SRS20064557", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "1K cell BS R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 3 hpf  BS  rep3", "EV07008", "EV07008", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07008.R1.fastq.gz", "fastq", 705682040.0, 5040586.0, "EV07008.R1.fastq.gz", "0:140", "A:194506527;C:127442743;G:192893716;T:190818958;N:20096", 140, null, null, null, 194506527, 127442743, 192893716, 190818958, 20096, "SRX23109803", "SRS20064557", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29775, "SRR27437495", "SRX23109802", "SRS20064556", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "1K cell DM R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 3 hpf  DM  rep3", "EV07009", "EV07009", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07009.R1.fastq.gz", "fastq", 380716280.0, 2719402.0, "EV07009.R1.fastq.gz", "0:140", "A:95351632;C:89558330;G:115625953;T:80169603;N:10762", 140, null, null, null, 95351632, 89558330, 115625953, 80169603, 10762, "SRX23109802", "SRS20064556", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 6e-05, null, 1e-05, null, 0.99991, null, 0.75, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29778, "SRR27435863", "SRX23108233", "SRS20063070", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "1K cell mock 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:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 3 hpf  mock  rep4", "EV08010", "EV08010", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08010.R1.fastq.gz", "fastq", 678729520.0, 4848068.0, "EV08010.R1.fastq.gz", "0:140", "A:170672553;C:182320916;G:171865707;T:153824163;N:46181", 140, null, null, null, 170672553, 182320916, 171865707, 153824163, 46181, "SRX23108233", "SRS20063070", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0006, null, 4e-05, null, 0.99878, null, 0.79069, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29779, "SRR27435864", "SRX23108232", "SRS20063068", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "4 cell BS 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|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 1 hpf  BS  rep4", "EV08009", "EV08009", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08009.R1.fastq.gz", "fastq", 756964460.0, 5406889.0, "EV08009.R1.fastq.gz", "0:140", "A:191381054;C:111783194;G:185694475;T:268052883;N:52854", 140, null, null, null, 191381054, 111783194, 185694475, 268052883, 52854, "SRX23108232", "SRS20063068", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 1e-05, null, 0.0, null, 0.99997, null, 1.0, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29780, "SRR27435865", "SRX23108231", "SRS20063069", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "4 cell DM 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|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 1 hpf  DM  rep4", "EV08008", "EV08008", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08008.R1.fastq.gz", "fastq", 751794680.0, 5369962.0, "EV08008.R1.fastq.gz", "0:140", "A:194845808;C:197389162;G:194749636;T:164756481;N:53593", 140, null, null, null, 194845808, 197389162, 194749636, 164756481, 53593, "SRX23108231", "SRS20063069", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.00124, null, 0.00029, null, 0.99853, null, 0.77083, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29781, "SRR27435866", "SRX23108230", "SRS20063066", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "4 cell mock 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|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 1 hpf  mock  rep4", "EV08007", "EV08007", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08007.R1.fastq.gz", "fastq", 761961760.0, 5442584.0, "EV08007.R1.fastq.gz", "0:140", "A:194053323;C:191169414;G:194452160;T:182234253;N:52610", 140, null, null, null, 194053323, 191169414, 194452160, 182234253, 52610, "SRX23108230", "SRS20063066", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.00242, null, 0.00062, null, 0.99803, null, 0.81818, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29785, "SRR27435870", "SRX23108226", "SRS20063064", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "24h BS 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|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 24 hpf  BS  rep4", "EV08021", "EV08021", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08021.R1.fastq.gz", "fastq", 747571860.0, 5339799.0, "EV08021.R1.fastq.gz", "0:140", "A:185666613;C:121868156;G:181153824;T:258830310;N:52957", 140, null, null, null, 185666613, 121868156, 181153824, 258830310, 52957, "SRX23108226", "SRS20063064", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [29787, "SRR27435872", "SRX23108224", "SRS20063061", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "24h DM 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|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 24 hpf  DM  rep4", "EV08020", "EV08020", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08020.R1.fastq.gz", "fastq", 775090400.0, 5536360.0, "EV08020.R1.fastq.gz", "0:140", "A:198131068;C:205114604;G:198783890;T:173006366;N:54472", 140, null, null, null, 198131068, 205114604, 198783890, 173006366, 54472, "SRX23108224", "SRS20063061", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.00056, null, 4e-05, null, 0.9989, null, 0.71052, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [29788, "SRR27435873", "SRX23108223", "SRS20063060", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "24h mock 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|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 24 hpf  mock  rep4", "EV08019", "EV08019", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08019.R1.fastq.gz", "fastq", 763233240.0, 5451666.0, "EV08019.R1.fastq.gz", "0:140", "A:189362337;C:199268270;G:198509945;T:176040551;N:52137", 140, null, null, null, 189362337, 199268270, 198509945, 176040551, 52137, "SRX23108223", "SRS20063060", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.00036, null, 6e-05, null, 0.99939, null, 0.85365, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [29789, "SRR27435874", "SRX23108222", "SRS20063057", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Bud BS 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|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 10 hpf  BS  rep4", "EV08018", "EV08018", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08018.R1.fastq.gz", "fastq", 809203080.0, 5780022.0, "EV08018.R1.fastq.gz", "0:140", "A:209714496;C:130623600;G:197912909;T:270895413;N:56662", 140, null, null, null, 209714496, 130623600, 197912909, 270895413, 56662, "SRX23108222", "SRS20063057", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29790, "SRR27435875", "SRX23108221", "SRS20063059", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Bud DM 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|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 10 hpf  DM  rep4", "EV08017", "EV08017", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08017.R1.fastq.gz", "fastq", 722137500.0, 5158125.0, "EV08017.R1.fastq.gz", "0:140", "A:176408094;C:195907583;G:188487109;T:161283055;N:51659", 140, null, null, null, 176408094, 195907583, 188487109, 161283055, 51659, "SRX23108221", "SRS20063059", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.00053, null, 3e-05, null, 0.999, null, 0.70422, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29791, "SRR27435876", "SRX23108220", "SRS20063058", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Bud mock 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|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 10 hpf  mock  rep4", "EV08016", "EV08016", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08016.R1.fastq.gz", "fastq", 827605660.0, 5911469.0, "EV08016.R1.fastq.gz", "0:140", "A:204173663;C:224596562;G:206999037;T:191779555;N:56843", 140, null, null, null, 204173663, 224596562, 206999037, 191779555, 56843, "SRX23108220", "SRS20063058", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.00037, null, 2e-05, null, 0.99908, null, 0.7037, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29792, "SRR27435877", "SRX23108219", "SRS20063056", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Dome BS 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|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 5 hpf  BS  rep4", "EV08015", "EV08015", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08015.R1.fastq.gz", "fastq", 804598200.0, 5747130.0, "EV08015.R1.fastq.gz", "0:140", "A:215467427;C:134937180;G:189531758;T:264604493;N:57342", 140, null, null, null, 215467427, 134937180, 189531758, 264604493, 57342, "SRX23108219", "SRS20063056", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 2e-05, null, 0.0, null, 0.99995, null, 1.0, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29793, "SRR27435878", "SRX23108218", "SRS20063055", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Dome DM 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|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 5 hpf  DM  rep4", "EV08014", "EV08014", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08014.R1.fastq.gz", "fastq", 662443740.0, 4731741.0, "EV08014.R1.fastq.gz", "0:140", "A:164941700;C:167025964;G:177255084;T:153175163;N:45829", 140, null, null, null, 164941700, 167025964, 177255084, 153175163, 45829, "SRX23108218", "SRS20063055", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.00069, null, 0.0001, null, 0.9992, null, 0.83076, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29794, "SRR27435879", "SRX23108217", "SRS20063052", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Dome mock 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|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 5 hpf  mock  rep4", "EV08013", "EV08013", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08013.R1.fastq.gz", "fastq", 794760540.0, 5676861.0, "EV08013.R1.fastq.gz", "0:140", "A:197361776;C:210230329;G:205734036;T:181380205;N:54194", 140, null, null, null, 197361776, 210230329, 205734036, 181380205, 54194, "SRX23108217", "SRS20063052", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.00066, null, 9e-05, null, 0.99894, null, 0.78378, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29795, "SRR27435880", "SRX23108216", "SRS20063054", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "1K cell BS 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:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 3 hpf  BS  rep4", "EV08012", "EV08012", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08012.R1.fastq.gz", "fastq", 722593200.0, 5161380.0, "EV08012.R1.fastq.gz", "0:140", "A:188475497;C:119550806;G:173208825;T:241306038;N:52034", 140, null, null, null, 188475497, 119550806, 173208825, 241306038, 52034, "SRX23108216", "SRS20063054", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29796, "SRR27435881", "SRX23108215", "SRS20063053", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "1K cell DM 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:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: embryo 3 hpf  DM  rep4", "EV08011", "EV08011", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08011.R1.fastq.gz", "fastq", 753783380.0, 5384167.0, "EV08011.R1.fastq.gz", "0:140", "A:190029713;C:193734250;G:194752855;T:175212145;N:54417", 140, null, null, null, 190029713, 193734250, 194752855, 175212145, 54417, "SRX23108215", "SRS20063053", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.00076, null, 5e-05, null, 0.99859, null, 0.70873, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [36266, "SRR953577", "SRX336218", "SRS471213", "SRP028895", "PRJNA138095", "Transcriptome wide analysis of small RNA expression in early zebrafish development", "GSE27722", "Transcriptome Analysis", "During early vertebrate development  a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription.  The exact identity  expression levels  and function during early vertebrate development for most of these noncoding RNAs remains largely unknown.  miRNAs microRNAs and piRNAs piwi interacting RNAs are two classes of small non coding RNAs that play important roles in gene regulation during early embryonic development.  Here  we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system.  For miRNAs  the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined.  Significant sequence variation was observed at the five prime' and three prime' ends of miRNAs with a large number of extra nucleotides added in a non template directed manner.  We also identified a large and diverse set of piRNAs expressed during early development  far beyond that expected if piRNA expression is restricted to germ cells.  Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Overall design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through put sequencing", null, "pubmed:22408181", null, "embryo 1dpf rep1", "GSM686385", null, "source name:the whole embryo|strain:AB*WT|developmental stage:1dpf|tissue:the whole embryos", "embryo 1dpf rep1", "fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a \" x\" and the reads counts. e.g. unique ID x counts. alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences.  Small RNAs with perfect matches to the zebrafish genome Zv8 from Ensembl http://www.ensembl.org were retrieved using megaBLAST http://www.ncbi.nlm.nih.gov/blast/megablast.shtml and Bowtie http://bowtie bio.sourceforge.net/tutorial.shtml. To identify piRNAs  consensus sequences from zebrafish repetitive elements were retrieved from Repbase http://www.girinst.org/repbase/index.html and Repeat Maskers using the UCSC genome browser http://genome.ucsc.edu.  Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence. fasta files description: small RNA 15 30 nt alignment file description: piRNA map to repetitive elements", "the whole embryo", null, "Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.", "Embryos were raised at 28\u00c2\u00b0C in egg water 0.03% Instant Ocean marine salt mix for the initial several hours of development", "strain:AB*WT|developmental stage:1dpf|tissue:the whole embryos", "GSM686385", "GSM686385: embryo 1dpf rep1; Danio rerio; ncRNA Seq", "GSM686385", null, "1", "Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.", "GEO Accession:GSM686385", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP028895", null, null, "GSM686385_1dpf_Raw.txt", "fastq", 293700240.0, 8158340.0, "GSM686385 r1", "0:36", "A:74642033;C:62153879;G:83836688;T:69542606;N:3525034", 36, null, null, null, 74642033, 62153879, 83836688, 69542606, 3525034, "SRX336218", "SRS471213", "SRA098146", "GEO", "Lee Lab, Molecular Biology, Mass General Hospital", 1, 0.00386, null, 0.00274, null, 0.99758, null, 0.53623, null, 36, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-03-07", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [36267, "SRR953576", "SRX336217", "SRS471211", "SRP028895", "PRJNA138095", "Transcriptome wide analysis of small RNA expression in early zebrafish development", "GSE27722", "Transcriptome Analysis", "During early vertebrate development  a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription.  The exact identity  expression levels  and function during early vertebrate development for most of these noncoding RNAs remains largely unknown.  miRNAs microRNAs and piRNAs piwi interacting RNAs are two classes of small non coding RNAs that play important roles in gene regulation during early embryonic development.  Here  we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system.  For miRNAs  the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined.  Significant sequence variation was observed at the five prime' and three prime' ends of miRNAs with a large number of extra nucleotides added in a non template directed manner.  We also identified a large and diverse set of piRNAs expressed during early development  far beyond that expected if piRNA expression is restricted to germ cells.  Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Overall design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through put sequencing", null, "pubmed:22408181", null, "embryo Shield rep1", "GSM686384", null, "source name:the whole embryo|strain:AB*WT|developmental stage:Shield|tissue:the whole embryos", "embryo Shield rep1", "fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a \" x\" and the reads counts. e.g. unique ID x counts. alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences.  Small RNAs with perfect matches to the zebrafish genome Zv8 from Ensembl http://www.ensembl.org were retrieved using megaBLAST http://www.ncbi.nlm.nih.gov/blast/megablast.shtml and Bowtie http://bowtie bio.sourceforge.net/tutorial.shtml. To identify piRNAs  consensus sequences from zebrafish repetitive elements were retrieved from Repbase http://www.girinst.org/repbase/index.html and Repeat Maskers using the UCSC genome browser http://genome.ucsc.edu.  Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence. fasta files description: small RNA 15 30 nt alignment file description: piRNA map to repetitive elements", "the whole embryo", null, "Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.", "Embryos were raised at 28\u00c2\u00b0C in egg water 0.03% Instant Ocean marine salt mix for the initial several hours of development", "strain:AB*WT|developmental stage:Shield|tissue:the whole embryos", "GSM686384", "GSM686384: embryo Shield rep1; Danio rerio; ncRNA Seq", "GSM686384", null, "1", "Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.", "GEO Accession:GSM686384", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP028895", null, null, "GSM686384_Shield_Raw.txt", "fastq", 115067916.0, 3196331.0, "GSM686384 r1", "0:36", "A:28435718;C:21893278;G:31779352;T:26635839;N:6323729", 36, null, null, null, 28435718, 21893278, 31779352, 26635839, 6323729, "SRX336217", "SRS471211", "SRA098146", "GEO", "Lee Lab, Molecular Biology, Mass General Hospital", 1, 0.00278, null, 0.00217, null, 0.99933, null, 0.60606, null, 36, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-03-07", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [36268, "SRR953575", "SRX336216", "SRS471212", "SRP028895", "PRJNA138095", "Transcriptome wide analysis of small RNA expression in early zebrafish development", "GSE27722", "Transcriptome Analysis", "During early vertebrate development  a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription.  The exact identity  expression levels  and function during early vertebrate development for most of these noncoding RNAs remains largely unknown.  miRNAs microRNAs and piRNAs piwi interacting RNAs are two classes of small non coding RNAs that play important roles in gene regulation during early embryonic development.  Here  we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system.  For miRNAs  the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined.  Significant sequence variation was observed at the five prime' and three prime' ends of miRNAs with a large number of extra nucleotides added in a non template directed manner.  We also identified a large and diverse set of piRNAs expressed during early development  far beyond that expected if piRNA expression is restricted to germ cells.  Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Overall design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through put sequencing", null, "pubmed:22408181", null, "embryo sphere rep2", "GSM686383", null, "source name:the whole embryo|strain:AB*WT|developmental stage:sphere|tissue:the whole embryos", "embryo sphere rep2", "fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a \" x\" and the reads counts. e.g. unique ID x counts. alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences.  Small RNAs with perfect matches to the zebrafish genome Zv8 from Ensembl http://www.ensembl.org were retrieved using megaBLAST http://www.ncbi.nlm.nih.gov/blast/megablast.shtml and Bowtie http://bowtie bio.sourceforge.net/tutorial.shtml. To identify piRNAs  consensus sequences from zebrafish repetitive elements were retrieved from Repbase http://www.girinst.org/repbase/index.html and Repeat Maskers using the UCSC genome browser http://genome.ucsc.edu.  Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence. fasta files description: small RNA 15 30 nt alignment file description: piRNA map to repetitive elements", "the whole embryo", null, "Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.", "Embryos were raised at 28\u00c2\u00b0C in egg water 0.03% Instant Ocean marine salt mix for the initial several hours of development", "strain:AB*WT|developmental stage:sphere|tissue:the whole embryos", "GSM686383", "GSM686383: embryo sphere rep2; Danio rerio; ncRNA Seq", "GSM686383", null, "1", "Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.", "GEO Accession:GSM686383", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP028895", null, null, "GSM686383_Sphere_2_Raw.txt", "fastq", 369741456.0, 10270596.0, "GSM686383 r1", "0:36", "A:89854472;C:70044086;G:109552597;T:100266590;N:23711", 36, null, null, null, 89854472, 70044086, 109552597, 100266590, 23711, "SRX336216", "SRS471212", "SRA098146", "GEO", "Lee Lab, Molecular Biology, Mass General Hospital", 1, 0.00421, null, 0.00367, null, 0.99924, null, 0.51111, null, 36, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-03-07", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [36269, "SRR953574", "SRX336215", "SRS471209", "SRP028895", "PRJNA138095", "Transcriptome wide analysis of small RNA expression in early zebrafish development", "GSE27722", "Transcriptome Analysis", "During early vertebrate development  a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription.  The exact identity  expression levels  and function during early vertebrate development for most of these noncoding RNAs remains largely unknown.  miRNAs microRNAs and piRNAs piwi interacting RNAs are two classes of small non coding RNAs that play important roles in gene regulation during early embryonic development.  Here  we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system.  For miRNAs  the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined.  Significant sequence variation was observed at the five prime' and three prime' ends of miRNAs with a large number of extra nucleotides added in a non template directed manner.  We also identified a large and diverse set of piRNAs expressed during early development  far beyond that expected if piRNA expression is restricted to germ cells.  Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Overall design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through put sequencing", null, "pubmed:22408181", null, "embryo sphere rep1", "GSM686382", null, "source name:the whole embryo|strain:AB*WT|developmental stage:sphere|tissue:the whole embryos", "embryo sphere rep1", "fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a \" x\" and the reads counts. e.g. unique ID x counts. alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences.  Small RNAs with perfect matches to the zebrafish genome Zv8 from Ensembl http://www.ensembl.org were retrieved using megaBLAST http://www.ncbi.nlm.nih.gov/blast/megablast.shtml and Bowtie http://bowtie bio.sourceforge.net/tutorial.shtml. To identify piRNAs  consensus sequences from zebrafish repetitive elements were retrieved from Repbase http://www.girinst.org/repbase/index.html and Repeat Maskers using the UCSC genome browser http://genome.ucsc.edu.  Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence. fasta files description: small RNA 15 30 nt alignment file description: piRNA map to repetitive elements", "the whole embryo", null, "Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.", "Embryos were raised at 28\u00c2\u00b0C in egg water 0.03% Instant Ocean marine salt mix for the initial several hours of development", "strain:AB*WT|developmental stage:sphere|tissue:the whole embryos", "GSM686382", "GSM686382: embryo sphere rep1; Danio rerio; ncRNA Seq", "GSM686382", null, "1", "Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.", "GEO Accession:GSM686382", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP028895", null, null, "GSM686382_Sphere_1_Raw.txt", "fastq", 492502284.0, 13680619.0, "GSM686382 r1", "0:36", "A:114418890;C:99502519;G:142841794;T:135061742;N:677339", 36, null, null, null, 114418890, 99502519, 142841794, 135061742, 677339, "SRX336215", "SRS471209", "SRA098146", "GEO", "Lee Lab, Molecular Biology, Mass General Hospital", 1, 0.00828, null, 0.00636, null, 0.9964, null, 0.54822, null, 36, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-03-07", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [36270, "SRR953573", "SRX336214", "SRS471210", "SRP028895", "PRJNA138095", "Transcriptome wide analysis of small RNA expression in early zebrafish development", "GSE27722", "Transcriptome Analysis", "During early vertebrate development  a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription.  The exact identity  expression levels  and function during early vertebrate development for most of these noncoding RNAs remains largely unknown.  miRNAs microRNAs and piRNAs piwi interacting RNAs are two classes of small non coding RNAs that play important roles in gene regulation during early embryonic development.  Here  we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system.  For miRNAs  the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined.  Significant sequence variation was observed at the five prime' and three prime' ends of miRNAs with a large number of extra nucleotides added in a non template directed manner.  We also identified a large and diverse set of piRNAs expressed during early development  far beyond that expected if piRNA expression is restricted to germ cells.  Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Overall design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through put sequencing", null, "pubmed:22408181", null, "embryo 256 cell rep1", "GSM686381", null, "source name:the whole embryo|strain:AB* WT|developmental stage:256 cell|tissue:the whole embryos", "embryo 256 cell rep1", "fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a \" x\" and the reads counts. e.g. unique ID x counts. alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences.  Small RNAs with perfect matches to the zebrafish genome Zv8 from Ensembl http://www.ensembl.org were retrieved using megaBLAST http://www.ncbi.nlm.nih.gov/blast/megablast.shtml and Bowtie http://bowtie bio.sourceforge.net/tutorial.shtml. To identify piRNAs  consensus sequences from zebrafish repetitive elements were retrieved from Repbase http://www.girinst.org/repbase/index.html and Repeat Maskers using the UCSC genome browser http://genome.ucsc.edu.  Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence. fasta files description: small RNA 15 30 nt alignment file description: piRNA map to repetitive elements", "the whole embryo", null, "Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.", "Embryos were raised at 28\u00c2\u00b0C in egg water 0.03% Instant Ocean marine salt mix for the initial several hours of development", "strain:AB* WT|developmental stage:256 cell|tissue:the whole embryos", "GSM686381", "GSM686381: embryo 256 cell rep1; Danio rerio; ncRNA Seq", "GSM686381", null, "1", "Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.", "GEO Accession:GSM686381", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP028895", null, null, "GSM686381_256-cell_Raw.txt", "fastq", 177430716.0, 4928631.0, "GSM686381 r1", "0:36", "A:46047586;C:39494059;G:46591098;T:42305117;N:2992856", 36, null, null, null, 46047586, 39494059, 46591098, 42305117, 2992856, "SRX336214", "SRS471210", "SRA098146", "GEO", "Lee Lab, Molecular Biology, Mass General Hospital", 1, 0.01914, null, 0.01515, null, 0.99164, null, 0.52579, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-03-07", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [36278, "SRR352486", "SRX100938", "SRS266977", "SRP008845", "PRJNA146609", "Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution", "GSE32880", "Other", "Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome", null, "pubmed:22196729", null, "3P Seq Adult", "GSM813764", null, "source name:mixed gender adults|tissue:whole adult|developmental stage:mixed gender adults|genotype:wt", "3P Seq Adult", "Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. GSE24924", "mixed gender adults", "For adult fish  anesthetized fish were homogenized in the TissueRuptor Qiagen. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at \u201380C.", "3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html", "Zebrafish embryos or adults grown under standard condition", "tissue:whole adult|developmental stage:mixed gender adults|genotype:wt", "GSM813764", "GSM813764: 3P Seq Adult", "GSM813764: 3P Seq Adult", "GSM813764: 3P Seq Adult", "1", null, "GEO Accession:GSM813764", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP008845", null, "read name barcode proc directive:ignore", "3P_Seq_Adult.fastq", "fastq", 824962572.0, 22915627.0, "GSM813764 1", "0:36", "A:230176177;C:144743199;G:130818857;T:314618483;N:4605856", 36, null, null, null, 230176177, 144743199, 130818857, 314618483, 4605856, "SRX100938", "SRS266977", "SRA047033", "GEO", "Whitehead Institute for Biomedical Research", 1, 0.64306, null, 0.03985, null, 0.78102, null, 0.46237, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "3prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-10-11", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [36279, "SRR352485", "SRX100937", "SRS266976", "SRP008845", "PRJNA146609", "Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution", "GSE32880", "Other", "Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome", null, "pubmed:22196729", null, "3P Seq 72 hpf", "GSM813763", null, "tissue:whole embryo at 72 hpf embryo|developmental stage:72 hpf", "3P Seq 72 hpf", "Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. GSE24924", "whole embryo at 72 hpf", "Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at \u201380C.", "3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html", "Zebrafish embryos or adults grown under standard condition", "tissue:whole embryo|developmental stage:72 hpf", "GSM813763", "GSM813763: 3P Seq 72 hpf", "GSM813763: 3P Seq 72 hpf", "GSM813763: 3P Seq 72 hpf", "1", null, "GEO Accession:GSM813763", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP008845", null, "read name barcode proc directive:ignore", "3P_Seq_72hpf.fastq", "fastq", 875542968.0, 24320638.0, "GSM813763 1", "0:36", "A:246098313;C:139311840;G:129654215;T:353566279;N:6912321", 36, null, null, null, 246098313, 139311840, 129654215, 353566279, 6912321, "SRX100937", "SRS266976", "SRA047033", "GEO", "Whitehead Institute for Biomedical Research", 1, 0.72092, null, 0.09355, null, 0.7601, null, 0.4422, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "3prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [36280, "SRR352484", "SRX100936", "SRS266975", "SRP008845", "PRJNA146609", "Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution", "GSE32880", "Other", "Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome", null, "pubmed:22196729", null, "3P Seq 24 hpf", "GSM813762", null, "tissue:whole embryo at 24 hpf embryo|developmental stage:24 hpf", "3P Seq 24 hpf", "Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924", "whole embryo at 24 hpf", "Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at \u201380C.", "3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html", "Zebrafish embryos or adults grown under standard condition", "tissue:whole embryo|developmental stage:24 hpf", "GSM813762", "GSM813762: 3P Seq 24 hpf", "GSM813762: 3P Seq 24 hpf", "GSM813762: 3P Seq 24 hpf", "1", null, "GEO Accession:GSM813762", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP008845", null, "read name barcode proc directive:ignore", "3P_Seq_24hpf.fastq", "fastq", 951095592.0, 26419322.0, "GSM813762 1", "0:36", "A:261158914;C:169001356;G:163312440;T:350565754;N:7057128", 36, null, null, null, 261158914, 169001356, 163312440, 350565754, 7057128, "SRX100936", "SRS266975", "SRA047033", "GEO", "Whitehead Institute for Biomedical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "3prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-10-11", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [36281, "SRR352482", "SRX100935", "SRS266974", "SRP008845", "PRJNA146609", "Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution", "GSE32880", "Other", "Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome", null, "pubmed:22196729", null, "Strand specific RNA Seq 72 hpf", "GSM813761", null, "tissue:whole embryo at 72 hpf embryo|developmental stage:72 hpf", "Strand specific RNA Seq 72 hpf", "Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.", "whole embryo at 72 hpf", "Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at \u201380C.", "polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992", "Zebrafish embryos or adults grown under standard condition", "tissue:whole embryo|developmental stage:72 hpf", "GSM813761", "GSM813761: Strand specific RNA Seq 72 hpf", "GSM813761: Strand specific RNA Seq 72 hpf", "GSM813761: Strand specific RNA Seq 72 hpf", "1", null, "GEO Accession:GSM813761", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP008845", null, "read name barcode proc directive:ignore", "RNA_Seq_72hpf.1.fastq", "fastq", 734147136.0, 20392976.0, "GSM813761 1", "0:36", "A:175662892;C:172216317;G:208650086;T:171852136;N:5765705", 36, null, null, null, 175662892, 172216317, 208650086, 171852136, 5765705, "SRX100935", "SRS266974", "SRA047033", "GEO", "Whitehead Institute for Biomedical Research", 1, 0.4603, null, 0.10593, null, 0.88274, null, 0.59195, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [36282, "SRR352483", "SRX100935", "SRS266974", "SRP008845", "PRJNA146609", "Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution", "GSE32880", "Other", "Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome", null, "pubmed:22196729", null, "Strand specific RNA Seq 72 hpf", "GSM813761", null, "tissue:whole embryo at 72 hpf embryo|developmental stage:72 hpf", "Strand specific RNA Seq 72 hpf", "Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.", "whole embryo at 72 hpf", "Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at \u201380C.", "polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992", "Zebrafish embryos or adults grown under standard condition", "tissue:whole embryo|developmental stage:72 hpf", "GSM813761", "GSM813761: Strand specific RNA Seq 72 hpf", "GSM813761: Strand specific RNA Seq 72 hpf", "GSM813761: Strand specific RNA Seq 72 hpf", "1", null, "GEO Accession:GSM813761", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP008845", null, "read name barcode proc directive:ignore", "RNA_Seq_72hpf.2.fastq", "fastq", 924879168.0, 25691088.0, "GSM813761 2", "0:36", "A:218871678;C:217000200;G:266487098;T:214411336;N:8108856", 36, null, null, null, 218871678, 217000200, 266487098, 214411336, 8108856, "SRX100935", "SRS266974", "SRA047033", "GEO", "Whitehead Institute for Biomedical Research", 1, 0.47296, null, 0.10988, null, 0.86397, null, 0.59423, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [36283, "SRR352480", "SRX100934", "SRS266973", "SRP008845", "PRJNA146609", "Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution", "GSE32880", "Other", "Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome", null, "pubmed:22196729", null, "Strand specific RNA Seq 24 hpf", "GSM813760", null, "tissue:whole embryo at 24 hpf embryo|developmental stage:24 hpf", "Strand specific RNA Seq 24 hpf", "Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.", "whole embryo at 24 hpf", "Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at \u201380C.", "polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992", "Zebrafish embryos or adults grown under standard condition", "tissue:whole embryo|developmental stage:24 hpf", "GSM813760", "GSM813760: Strand specific RNA Seq 24 hpf", "GSM813760: Strand specific RNA Seq 24 hpf", "GSM813760: Strand specific RNA Seq 24 hpf", "1", null, "GEO Accession:GSM813760", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP008845", null, "read name barcode proc directive:ignore", "RNA_Seq_24hpf.1.fastq", "fastq", 759129588.0, 21086933.0, "GSM813760 1", "0:36", "A:169759696;C:187766678;G:221392768;T:174382883;N:5827563", 36, null, null, null, 169759696, 187766678, 221392768, 174382883, 5827563, "SRX100934", "SRS266973", "SRA047033", "GEO", "Whitehead Institute for Biomedical Research", 1, 0.52959, null, 0.10037, null, 0.87014, null, 0.61896, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-10-11", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [36284, "SRR352481", "SRX100934", "SRS266973", "SRP008845", "PRJNA146609", "Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution", "GSE32880", "Other", "Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome", null, "pubmed:22196729", null, "Strand specific RNA Seq 24 hpf", "GSM813760", null, "tissue:whole embryo at 24 hpf embryo|developmental stage:24 hpf", "Strand specific RNA Seq 24 hpf", "Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.", "whole embryo at 24 hpf", "Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at \u201380C.", "polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992", "Zebrafish embryos or adults grown under standard condition", "tissue:whole embryo|developmental stage:24 hpf", "GSM813760", "GSM813760: Strand specific RNA Seq 24 hpf", "GSM813760: Strand specific RNA Seq 24 hpf", "GSM813760: Strand specific RNA Seq 24 hpf", "1", null, "GEO Accession:GSM813760", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP008845", null, "read name barcode proc directive:ignore", "RNA_Seq_24hpf.2.fastq", "fastq", 916505136.0, 25458476.0, "GSM813760 2", "0:36", "A:203678661;C:227621613;G:269472018;T:207401580;N:8331264", 36, null, null, null, 203678661, 227621613, 269472018, 207401580, 8331264, "SRX100934", "SRS266973", "SRA047033", "GEO", "Whitehead Institute for Biomedical Research", 1, 0.54008, null, 0.10064, null, 0.85425, null, 0.61991, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-10-11", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [36731, "SRR836199", "SRX272888", "SRS417394", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq 5dpf", "GSM1131537", null, "tissue:Whole embryos|developmental stage:5 dpf molecule:ribosome footprinted RNA", "20120724 RPF Seq 5dpf", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:5 dpf molecule:ribosome footprinted RNA", "GSM1131537", "GSM1131537: 20120724 RPF Seq 5dpf; Danio rerio; RNA Seq", "GSM1131537 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131537", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_5dpf.fastq.gz", "fastq", 5339394852.0, 121349883.0, "GSM1131537 r1", "0:44", "A:993131212;C:1552513636;G:1792926993;T:1000757523;N:65488", 44, null, null, null, 993131212, 1552513636, 1792926993, 1000757523, 65488, "SRX272888", "SRS417394", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.04708, null, 0.00988, null, 0.99774, null, 0.7502, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [36732, "SRR836198", "SRX272887", "SRS417393", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq 28hpf", "GSM1131536", null, "tissue:Whole embryos|developmental stage:28 hpf molecule:ribosome footprinted RNA", "20120724 RPF Seq 28hpf", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:28 hpf molecule:ribosome footprinted RNA", "GSM1131536", "GSM1131536: 20120724 RPF Seq 28hpf; Danio rerio; RNA Seq", "GSM1131536 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131536", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_28hpf.fastq.gz", "fastq", 5844769480.0, 132835670.0, "GSM1131536 r1", "0:44", "A:967687923;C:1803414766;G:2048220630;T:1024594100;N:852061", 44, null, null, null, 967687923, 1803414766, 2048220630, 1024594100, 852061, "SRX272887", "SRS417393", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.054, null, 0.00377, null, 0.99762, null, 0.77752, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [36733, "SRR836197", "SRX272886", "SRS417392", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq Bud", "GSM1131535", null, "tissue:Whole embryos|developmental stage:Bud|strain:TL/AB|target molecule:ribosome footprinted RNA", "20120724 RPF Seq Bud", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:Bud|strain:TL/AB|target molecule:ribosome footprinted RNA", "GSM1131535", "GSM1131535: 20120724 RPF Seq Bud; Danio rerio; RNA Seq", "GSM1131535 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131535", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_Bud.fastq.gz", "fastq", 5245678988.0, 119219977.0, "GSM1131535 r1", "0:44", "A:785136766;C:1705642298;G:1892015387;T:862815185;N:69352", 44, null, null, null, 785136766, 1705642298, 1892015387, 862815185, 69352, "SRX272886", "SRS417392", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.0214, null, 0.00105, null, 0.99823, null, 0.906, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [36734, "SRR836196", "SRX272885", "SRS417391", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq Shield", "GSM1131534", null, "tissue:Whole embryos|developmental stage:Shield|strain:TL/AB|target molecule:ribosome footprinted RNA", "20120724 RPF Seq Shield", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:Shield|strain:TL/AB|target molecule:ribosome footprinted RNA", "GSM1131534", "GSM1131534: 20120724 RPF Seq Shield; Danio rerio; RNA Seq", "GSM1131534 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131534", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_Shield.fastq.gz", "fastq", 5407148516.0, 122889739.0, "GSM1131534 r1", "0:44", "A:1112688703;C:1598204601;G:1639649897;T:1055648833;N:956482", 44, null, null, null, 1112688703, 1598204601, 1639649897, 1055648833, 956482, "SRX272885", "SRS417391", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.01533, null, 0.0016, null, 0.99864, null, 0.73416, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [36735, "SRR836195", "SRX272884", "SRS417390", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq Dome", "GSM1131533", null, "tissue:Whole embryos|developmental stage:Dome|strain:TL/AB|target molecule:ribosome footprinted RNA", "20120724 RPF Seq Dome", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:Dome|strain:TL/AB|target molecule:ribosome footprinted RNA", "GSM1131533", "GSM1131533: 20120724 RPF Seq Dome; Danio rerio; RNA Seq", "GSM1131533 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131533", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_Dome.fastq.gz", "fastq", 5455941832.0, 123998678.0, "GSM1131533 r1", "0:44", "A:1174530251;C:1596486361;G:1605087499;T:1077423125;N:2414596", 44, null, null, null, 1174530251, 1596486361, 1605087499, 1077423125, 2414596, "SRX272884", "SRS417390", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.00739, null, 0.0007, null, 0.99898, null, 0.86907, null, 44, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [36736, "SRR836194", "SRX272883", "SRS417389", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq 1KCell", "GSM1131532", null, "tissue:Whole embryos|developmental stage:1k cells|strain:TL/AB|target molecule:ribosome footprinted RNA", "20120724 RPF Seq 1KCell", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:1k cells|strain:TL/AB|target molecule:ribosome footprinted RNA", "GSM1131532", "GSM1131532: 20120724 RPF Seq 1KCell; Danio rerio; RNA Seq", "GSM1131532 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131532", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_1KCell.fastq.gz", "fastq", 6177670620.0, 140401605.0, "GSM1131532 r1", "0:44", "A:1115906097;C:1874096579;G:1974799887;T:1211772717;N:1095340", 44, null, null, null, 1115906097, 1874096579, 1974799887, 1211772717, 1095340, "SRX272883", "SRS417389", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.02237, null, 0.00392, null, 0.99847, null, 0.87194, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [36737, "SRR836193", "SRX272882", "SRS417388", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq 256Cell", "GSM1131531", null, "tissue:Whole embryos|developmental stage:256 cells|strain:TL/AB|target molecule:ribosome footprinted RNA", "20120724 RPF Seq 256Cell", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:256 cells|strain:TL/AB|target molecule:ribosome footprinted RNA", "GSM1131531", "GSM1131531: 20120724 RPF Seq 256Cell; Danio rerio; RNA Seq", "GSM1131531 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131531", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_256Cell.fastq.gz", "fastq", 5883566700.0, 133717425.0, "GSM1131531 r1", "0:44", "A:1010263447;C:1822722383;G:1960819573;T:1088614485;N:1146812", 44, null, null, null, 1010263447, 1822722383, 1960819573, 1088614485, 1146812, "SRX272882", "SRS417388", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.02862, null, 0.0036, null, 0.99837, null, 0.90559, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [36738, "SRR836192", "SRX272881", "SRS417387", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq 2 4Cell", "GSM1131530", null, "tissue:Whole embryos|developmental stage:2 4 cells|strain:TL/AB|target molecule:ribosome footprinted RNA", "20120724 RPF Seq 2 4Cell", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:2 4 cells|strain:TL/AB|target molecule:ribosome footprinted RNA", "GSM1131530", "GSM1131530: 20120724 RPF Seq 2 4Cell; Danio rerio; RNA Seq", "GSM1131530 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131530", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_2-4Cell.fastq.gz", "fastq", 1568173420.0, 35640305.0, "GSM1131530 r1", "0:44", "A:256220962;C:489258424;G:538563811;T:283859833;N:270390", 44, null, null, null, 256220962, 489258424, 538563811, 283859833, 270390, "SRX272881", "SRS417387", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.0297, null, 0.00558, null, 0.99821, null, 0.89066, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [40707, "SRR3502888", "SRX1760541", "SRS1436386", "SRP072296", "PRJNA316313", "Codon optimality and mRNA decay in zebrafish and Xenopus", "PRJNA316313", "Other", "Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved \u201ccodon optimality code\u201d that shapes mRNA stability and translation efficiency across vertebrates.", null, null, null, "Zebrafish tRNA at 6hpf", "tRNA AB 6h", null, "strain:TUAB|age:6hpf|dev stage:Shield|sex:pooled male and female|tissue:Whole animal|collected by:Ariel Bazzini|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish tRNAs at 6hpf", "tRNA 6hpf zebrafish", "TGIRT tRNA Library", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP072296", null, null, "AB-tRNA_S9_R1_001.fastq.gz AB-tRNA_S9_R2_001.fastq.gz", "fastq fastq", 7860522000.0, 26201740.0, "tRNA zebrafish 6hpf", "0:150 1:150", "A:1945184302;C:2012637521;G:2171934357;T:1730625218;N:140602", 150, 150, null, null, 1945184302, 2012637521, 2171934357, 1730625218, 140602, "SRX1760541", "SRS1436386", "SRA395141", "Yale University|Giraldez Lab", "Yale University", 2, 0.04186, 0.04313, 0.00633, 0.00639, 0.96834, 0.96913, 0.53967, 0.5329, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-17", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [41244, "SRR3953261", "SRX1977497", "SRS1585138", "SRP079896", "PRJNA335352", "Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment", "GSE84845", "Transcriptome Analysis", "Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control  a dozen of validated zebrafish miRNAs  including dre miR 142a 3p  dre miR 142b 5p  dre miR 144 3p  dre miR 146a  dre miR 190a  dre miR 219 5p  dre miR 301b 3p  dre miR 459 5p  rno miR 33 5p  dre miR 735 3p  and dre miR 735 5p  significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank  vehicle and 2 different concentrations of BDE47 treatments.", null, "pubmed:28072866", null, "500 \u03bcg/l BDE47 treatment miRNA", "GSM2252184", null, "source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf", "500 \u03bcg/l BDE47 treatment miRNA", "Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data  clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.", "6 dpf larvae", null, "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", null, "strain:Tuebingen|tissue:whole larvae|age:6 dpf", "GSM2252184", "GSM2252184: 500 \u03bcg/l BDE47 treatment miRNA; Danio rerio; miRNA Seq", "GSM2252184", null, "1", "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2252184", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP079896", null, null, "Sample_500_1_filtered.fastq.gz", "fastq", 427211416.0, 18037304.0, "GSM2252184 r1", "0:23.68 1:0", "A:104654735;C:95575450;G:107353019;T:119612667;N:15545", 23, 0, null, null, 104654735, 95575450, 107353019, 119612667, 15545, "SRX1977497", "SRS1585138", "SRA444471", "GEO", "Tongji University", 1, 0.85356, null, 0.06282, null, 0.88609, null, 0.63407, null, 21, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-26", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [41245, "SRR3953260", "SRX1977496", "SRS1585141", "SRP079896", "PRJNA335352", "Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment", "GSE84845", "Transcriptome Analysis", "Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control  a dozen of validated zebrafish miRNAs  including dre miR 142a 3p  dre miR 142b 5p  dre miR 144 3p  dre miR 146a  dre miR 190a  dre miR 219 5p  dre miR 301b 3p  dre miR 459 5p  rno miR 33 5p  dre miR 735 3p  and dre miR 735 5p  significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank  vehicle and 2 different concentrations of BDE47 treatments.", null, "pubmed:28072866", null, "5 \u03bcg/l BDE47 treatment miRNA", "GSM2252183", null, "source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf", "5 \u03bcg/l BDE47 treatment miRNA", "Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data  clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.", "6 dpf larvae", null, "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", null, "strain:Tuebingen|tissue:whole larvae|age:6 dpf", "GSM2252183", "GSM2252183: 5 \u03bcg/l BDE47 treatment miRNA; Danio rerio; miRNA Seq", "GSM2252183", null, "1", "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2252183", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP079896", null, null, "Sample_5_1_filtered.fastq.gz", "fastq", 450698842.0, 19202408.0, "GSM2252183 r1", "0:23.47 1:0", "A:112159775;C:101086362;G:111723361;T:125713845;N:15499", 23, 0, null, null, 112159775, 101086362, 111723361, 125713845, 15499, "SRX1977496", "SRS1585141", "SRA444471", "GEO", "Tongji University", 1, 0.84838, null, 0.06014, null, 0.88637, null, 0.6441, null, 23, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-26", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [41246, "SRR3953259", "SRX1977495", "SRS1585136", "SRP079896", "PRJNA335352", "Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment", "GSE84845", "Transcriptome Analysis", "Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control  a dozen of validated zebrafish miRNAs  including dre miR 142a 3p  dre miR 142b 5p  dre miR 144 3p  dre miR 146a  dre miR 190a  dre miR 219 5p  dre miR 301b 3p  dre miR 459 5p  rno miR 33 5p  dre miR 735 3p  and dre miR 735 5p  significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank  vehicle and 2 different concentrations of BDE47 treatments.", null, "pubmed:28072866", null, "s DMSO vehicle miRNA", "GSM2252182", null, "source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf", "s DMSO vehicle miRNA", "Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data  clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.", "6 dpf larvae", null, "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", null, "strain:Tuebingen|tissue:whole larvae|age:6 dpf", "GSM2252182", "GSM2252182: s DMSO vehicle miRNA; Danio rerio; miRNA Seq", "GSM2252182", null, "1", "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2252182", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP079896", null, null, "Sample_s_1_filtered.fq.gz", "fastq", 383701320.0, 16988819.0, "GSM2252182 r1", "0:22.59 1:0", "A:97700155;C:85144858;G:93319367;T:107531046;N:5894", 22, 0, null, null, 97700155, 85144858, 93319367, 107531046, 5894, "SRX1977495", "SRS1585136", "SRA444471", "GEO", "Tongji University", 1, 0.86023, null, 0.05501, null, 0.89534, null, 0.59715, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-26", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [41247, "SRR3953258", "SRX1977494", "SRS1585137", "SRP079896", "PRJNA335352", "Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment", "GSE84845", "Transcriptome Analysis", "Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control  a dozen of validated zebrafish miRNAs  including dre miR 142a 3p  dre miR 142b 5p  dre miR 144 3p  dre miR 146a  dre miR 190a  dre miR 219 5p  dre miR 301b 3p  dre miR 459 5p  rno miR 33 5p  dre miR 735 3p  and dre miR 735 5p  significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank  vehicle and 2 different concentrations of BDE47 treatments.", null, "pubmed:28072866", null, "c Wildtype miRNA", "GSM2252181", null, "source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf", "c Wildtype miRNA", "Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data  clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.", "6 dpf larvae", null, "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", null, "strain:Tuebingen|tissue:whole larvae|age:6 dpf", "GSM2252181", "GSM2252181: c Wildtype miRNA; Danio rerio; miRNA Seq", "GSM2252181", null, "1", "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2252181", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP079896", null, null, "Sample_c_1_filtered.fastq.gz", "fastq", 413922462.0, 17365113.0, "GSM2252181 r1", "0:23.84 1:0", "A:102173642;C:93233248;G:103684592;T:114815345;N:15635", 23, 0, null, null, 102173642, 93233248, 103684592, 114815345, 15635, "SRX1977494", "SRS1585137", "SRA444471", "GEO", "Tongji University", 1, 0.85083, null, 0.06831, null, 0.88152, null, 0.63274, null, 27, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-26", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53033, "SRR9674344", "SRX6434730", "SRS5089289", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "rnpc3 WT 1 [miRNA seq]", "GSM3938561", null, "source name:Wildtype siblings of rnpc3 mutants  repeat 1|strain background:TAB 5|genotype/variation:Wildtype siblings of rnpc3 mutants|Stage:7 dpf|tissue:whole fish embryos", "rnpc3 WT 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Wildtype siblings of rnpc3 mutants  repeat 1", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Wildtype siblings of rnpc3 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938561", "GSM3938561: rnpc3 WT 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938561", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938561", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Rpc3_1Ctrl.fastq.gz", "fastq", 1129597674.0, 22148974.0, "GSM3938561 r1", "0:51", "A:255811479;C:280511308;G:313965625;T:279284342;N:24920", 51, null, null, null, 255811479, 280511308, 313965625, 279284342, 24920, "SRX6434730", "SRS5089289", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00979, null, 0.00166, null, 0.99588, null, 0.63728, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53034, "SRR9674343", "SRX6434729", "SRS5089288", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "smn1 WT 1 [miRNA seq]", "GSM3938560", null, "source name:Wildtype siblings of smn1 mutants  repeat 1|strain background:TAB 5|genotype/variation:Wildtype siblings of smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "smn1 WT 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Wildtype siblings of smn1 mutants  repeat 1", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Wildtype siblings of smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938560", "GSM3938560: smn1 WT 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938560", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938560", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Smn1_1Ctrl.fastq.gz", "fastq", 1381751976.0, 27093176.0, "GSM3938560 r1", "0:51", "A:323091185;C:348663819;G:380517013;T:329446099;N:33860", 51, null, null, null, 323091185, 348663819, 380517013, 329446099, 33860, "SRX6434729", "SRS5089288", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00712, null, 0.00142, null, 0.99642, null, 0.66315, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53035, "SRR9674342", "SRX6434728", "SRS5089287", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin5 WT 1 [miRNA seq]", "GSM3938559", null, "source name:Wildtype siblings of germin5 mutants  repeat 1|strain background:TAB 5|genotype/variation:Wildtype siblings of germin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin5 WT 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Wildtype siblings of germin5 mutants  repeat 1", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Wildtype siblings of germin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938559", "GSM3938559: gemin5 WT 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938559", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938559", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Gmn5_1Ctrl.fastq.gz", "fastq", 1347630171.0, 26424121.0, "GSM3938559 r1", "0:51", "A:307019777;C:335315873;G:378259746;T:327002846;N:31929", 51, null, null, null, 307019777, 335315873, 378259746, 327002846, 31929, "SRX6434728", "SRS5089287", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00723, null, 0.00127, null, 0.99582, null, 0.63934, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53036, "SRR9674341", "SRX6434727", "SRS5089286", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "smn1 hom 3 [miRNA seq]", "GSM3938558", null, "source name:Homozygous smn1 mutants  repeat 3|strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "smn1 hom 3 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous smn1 mutants  repeat 3", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938558", "GSM3938558: smn1 hom 3 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938558", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938558", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Smn1_3hom.fastq.gz", "fastq", 1269172638.0, 24885738.0, "GSM3938558 r1", "0:51", "A:290351922;C:320656517;G:354834895;T:303300306;N:28998", 51, null, null, null, 290351922, 320656517, 354834895, 303300306, 28998, "SRX6434727", "SRS5089286", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.0061, null, 0.00111, null, 0.9962, null, 0.5917, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53037, "SRR9674340", "SRX6434726", "SRS5089285", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "smn1 hom 2 [miRNA seq]", "GSM3938557", null, "source name:Homozygous smn1 mutants  repeat 2|strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "smn1 hom 2 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous smn1 mutants  repeat 2", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938557", "GSM3938557: smn1 hom 2 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938557", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938557", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Smn1_2hom.fastq.gz", "fastq", 1625802786.0, 31878486.0, "GSM3938557 r1", "0:51", "A:376836190;C:399950981;G:453572869;T:395403783;N:38963", 51, null, null, null, 376836190, 399950981, 453572869, 395403783, 38963, "SRX6434726", "SRS5089285", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00609, null, 0.00111, null, 0.99638, null, 0.63347, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53038, "SRR9674339", "SRX6434725", "SRS5089284", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "smn1 hom 1 [miRNA seq]", "GSM3938556", null, "source name:Homozygous smn1 mutants  repeat 1|strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "smn1 hom 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous smn1 mutants  repeat 1", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938556", "GSM3938556: smn1 hom 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938556", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938556", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Smn1_1hom.fastq.gz", "fastq", 1553527320.0, 30461320.0, "GSM3938556 r1", "0:51", "A:360279409;C:388795394;G:432335873;T:372080058;N:36586", 51, null, null, null, 360279409, 388795394, 432335873, 372080058, 36586, "SRX6434725", "SRS5089284", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00691, null, 0.00137, null, 0.99638, null, 0.61909, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53039, "SRR9674338", "SRX6434724", "SRS5089283", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin5 hom 3 [miRNA seq]", "GSM3938555", null, "source name:Homozygous gemin5 mutants  repeat 3|strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin5 hom 3 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin5 mutants  repeat 3", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938555", "GSM3938555: gemin5 hom 3 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938555", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938555", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Gmn5_3hom.fastq.gz", "fastq", 1162857936.0, 22801136.0, "GSM3938555 r1", "0:51", "A:267576310;C:282684680;G:327841913;T:284728561;N:26472", 51, null, null, null, 267576310, 282684680, 327841913, 284728561, 26472, "SRX6434724", "SRS5089283", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00597, null, 0.00114, null, 0.99618, null, 0.62386, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53040, "SRR9674337", "SRX6434723", "SRS5089282", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin5 hom 2 [miRNA seq]", "GSM3938554", null, "source name:Homozygous gemin5 mutants  repeat 2|strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin5 hom 2 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin5 mutants  repeat 2", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938554", "GSM3938554: gemin5 hom 2 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938554", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938554", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Gmn5_2hom.fastq.gz", "fastq", 1612392846.0, 31615546.0, "GSM3938554 r1", "0:51", "A:360634123;C:389619637;G:457463377;T:404638471;N:37238", 51, null, null, null, 360634123, 389619637, 457463377, 404638471, 37238, "SRX6434723", "SRS5089282", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00538, null, 0.00085, null, 0.99677, null, 0.62726, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53041, "SRR9674336", "SRX6434722", "SRS5089281", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin5 hom 1 [miRNA seq]", "GSM3938553", null, "source name:Homozygous gemin5 mutants  repeat 1|strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin5 hom 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin5 mutants  repeat 1", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938553", "GSM3938553: gemin5 hom 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938553", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938553", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Gmn5_1hom.fastq.gz", "fastq", 1734523362.0, 34010262.0, "GSM3938553 r1", "0:51", "A:400823854;C:428868747;G:484830308;T:419961177;N:39276", 51, null, null, null, 400823854, 428868747, 484830308, 419961177, 39276, "SRX6434722", "SRS5089281", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00485, null, 0.00098, null, 0.99636, null, 0.65384, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53042, "SRR9674335", "SRX6434721", "SRS5089280", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin6 hom 3 [miRNA seq]", "GSM3938552", null, "source name:Homozygous gemin6 mutants  repeat 3|strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin6 hom 3 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin6 mutants  repeat 3", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938552", "GSM3938552: gemin6 hom 3 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938552", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938552", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G6_3.fastq.gz", "fastq", 3450343851.0, 67653801.0, "GSM3938552 r1", "0:51", "A:777873635;C:888116741;G:969513398;T:814785464;N:54613", 51, null, null, null, 777873635, 888116741, 969513398, 814785464, 54613, "SRX6434721", "SRS5089280", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01435, null, 0.00222, null, 0.99486, null, 0.71333, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53043, "SRR9674334", "SRX6434720", "SRS5089279", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin6 hom 2 [miRNA seq]", "GSM3938551", null, "source name:Homozygous gemin6 mutants  repeat 2|strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin6 hom 2 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin6 mutants  repeat 2", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938551", "GSM3938551: gemin6 hom 2 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938551", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938551", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G6_2.fastq.gz", "fastq", 1586876781.0, 31115231.0, "GSM3938551 r1", "0:51", "A:373921059;C:393906222;G:435371208;T:383652895;N:25397", 51, null, null, null, 373921059, 393906222, 435371208, 383652895, 25397, "SRX6434720", "SRS5089279", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01456, null, 0.00199, null, 0.99488, null, 0.65884, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53044, "SRR9674333", "SRX6434719", "SRS5089278", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin6 hom 1 [miRNA seq]", "GSM3938550", null, "source name:Homozygous gemin6 mutants  repeat 1|strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin6 hom 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin6 mutants  repeat 1", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938550", "GSM3938550: gemin6 hom 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938550", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938550", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G6_1.fastq.gz", "fastq", 1632291159.0, 32005709.0, "GSM3938550 r1", "0:51", "A:387703621;C:405051941;G:452019824;T:387489473;N:26300", 51, null, null, null, 387703621, 405051941, 452019824, 387489473, 26300, "SRX6434719", "SRS5089278", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01378, null, 0.00168, null, 0.99482, null, 0.66266, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53045, "SRR9674332", "SRX6434718", "SRS5089277", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin4 hom 3 [miRNA seq]", "GSM3938549", null, "source name:Homozygous gemin4 mutants  repeat 3|strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin4 hom 3 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin4 mutants  repeat 3", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938549", "GSM3938549: gemin4 hom 3 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938549", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938549", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G4_3.fastq.gz", "fastq", 1079490837.0, 21166487.0, "GSM3938549 r1", "0:51", "A:247548301;C:266526237;G:295997407;T:269401582;N:17310", 51, null, null, null, 247548301, 266526237, 295997407, 269401582, 17310, "SRX6434718", "SRS5089277", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01616, null, 0.00211, null, 0.99486, null, 0.65494, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53046, "SRR9674331", "SRX6434717", "SRS5089276", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin4 hom 2 [miRNA seq]", "GSM3938548", null, "source name:Homozygous gemin4 mutants  repeat 2|strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin4 hom 2 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin4 mutants  repeat 2", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938548", "GSM3938548: gemin4 hom 2 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938548", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938548", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G4_2.fastq.gz", "fastq", 6427925862.0, 126037762.0, "GSM3938548 r1", "0:51", "A:1491339645;C:1560095279;G:1804953332;T:1571434430;N:103176", 51, null, null, null, 1491339645, 1560095279, 1804953332, 1571434430, 103176, "SRX6434717", "SRS5089276", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01032, null, 0.00157, null, 0.99504, null, 0.70577, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53047, "SRR9674330", "SRX6434716", "SRS5089275", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin4 hom 1 [miRNA seq]", "GSM3938547", null, "source name:Homozygous gemin4 mutants  repeat 1|strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin4 hom 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin4 mutants  repeat 1", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938547", "GSM3938547: gemin4 hom 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938547", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938547", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G4_1.fastq.gz", "fastq", 3063591624.0, 60070424.0, "GSM3938547 r1", "0:51", "A:710248035;C:750319193;G:848095316;T:754879685;N:49395", 51, null, null, null, 710248035, 750319193, 848095316, 754879685, 49395, "SRX6434716", "SRS5089275", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01137, null, 0.00151, null, 0.99527, null, 0.69096, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 232, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_selection\" = :p0 and \"experiment.library_source\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "size fractionation", "p1": "TRANSCRIPTOMIC", "p2": "Whole Organism"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism", "results": [{"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 109, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&experiment.library_strategy=miRNA-Seq", "selected": false}, {"value": "ncRNA-Seq", "label": "ncRNA-Seq", "count": 49, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&experiment.library_strategy=ncRNA-Seq", "selected": false}, {"value": "OTHER", "label": "OTHER", "count": 45, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&experiment.library_strategy=OTHER", "selected": false}, {"value": "RNA-Seq", "label": "RNA-Seq", "count": 29, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 232, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&tissue_curation=Whole+Organism", "selected": true}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism", "results": [{"value": "size fractionation", "label": "size fractionation", "count": 232, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 217, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&experiment.library_layout=SINGLE", "selected": false}, {"value": "PAIRED", "label": "PAIRED", "count": 15, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 232, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism", "results": [{"value": "Embryo", "label": "Embryo", "count": 129, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&devstage_curation_coarse=Embryo", "selected": false}, {"value": "Larval", "label": "Larval", "count": 62, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&devstage_curation_coarse=Larval", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 40, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&devstage_curation_coarse=Multi-stage", "selected": false}, {"value": "Adult", "label": "Adult", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&devstage_curation_coarse=Adult", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism", "results": [{"value": "Larval", "label": "Larval", "count": 62, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&devstage_curation=Larval", "selected": false}, {"value": "Hatching", "label": "Hatching", "count": 47, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&devstage_curation=Hatching", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 40, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&devstage_curation=Multi-stage", "selected": false}, {"value": "Blastula", "label": "Blastula", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&devstage_curation=Blastula", "selected": false}, {"value": "Gastrula", "label": "Gastrula", "count": 22, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&devstage_curation=Gastrula", "selected": false}, {"value": "Pharyngula", "label": "Pharyngula", "count": 17, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&devstage_curation=Pharyngula", "selected": false}, {"value": "Cleavage", "label": "Cleavage", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&devstage_curation=Cleavage", "selected": false}, {"value": "Zygote", "label": "Zygote", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&devstage_curation=Zygote", "selected": false}, {"value": "Adult", "label": "Adult", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&devstage_curation=Adult", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&devstage_curation=Undetermined", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 232, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&tissue_curation_coarse=All+anatomical+structures", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism", "results": [{"value": "Whole Organism", "label": "Whole Organism", "count": 232, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism", "results": [{"value": "unknown", "label": "unknown", "count": 157, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&technology=unknown", "selected": false}, {"value": "bulk", "label": "bulk", "count": 75, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&technology=bulk", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": "53047", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism&_next=53047", "private": false, "allow_execute_sql": true, "query_ms": 81.97746900259517}