{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"size fractionation\", experiment.library_strategy = \"OTHER\" and tissue_curation_coarse = \"All anatomical structures\"", "rows": [[29739, "SRR27467672", "SRX23139234", "SRS20090275", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "Dome 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: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 rep2", "EV04009", "EV04009", "RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. 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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, "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"], [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", "1520Application ReadForward11Application ReadReverse77", "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"]], "truncated": false, "filtered_table_rows_count": 45, "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_strategy\" = :p1 and \"tissue_curation_coarse\" = :p2 order by rowid limit 101", "params": {"p0": "size 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45, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=size+fractionation&experiment.library_strategy=OTHER&tissue_curation_coarse=All+anatomical+structures&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "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_strategy=OTHER&tissue_curation_coarse=All+anatomical+structures", "results": [{"value": "size fractionation", "label": "size fractionation", "count": 45, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_strategy=OTHER&tissue_curation_coarse=All+anatomical+structures", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": 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