{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_strategy = \"OTHER\" and tissue_curation = \"Whole Organism\"", "rows": [[9803, "ERR3909553", "ERX3918377", "ERS4309135", "ERP120006", "PRJEB36776", "CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "E-MTAB-8795", "Transcriptome Analysis", "The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. 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Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. 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Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. 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Methods Mol Biol 1543 57 109.", "Red1", "SAMEA6544755", "UNIVERSITY OF BIRMINGHAM", "ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544755|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Red1|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:G1 slow cycling|organism part:whole organism|sample name:E MTAB 8795:Red1|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "E MTAB 8795:Red1 s", "Red1 s", "CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.", "Experimental Factor: fraction:G1 slow cycling", "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP120006", "Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25", "14SomiteRed1_ACAGAT_L003_R1_001.fastq.gz", "fastq", 755180370.0, 16781786.0, "E MTAB 8795:Red1", "0:45 1:0", "A:179369537;C:157573419;G:260889303;T:157277751;N:70360", 45, 0, null, null, 179369537, 157573419, 260889303, 157277751, 70360, "ERX3918372", "ERS4309130", "ERA2381432", "UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive", "UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive", 1, 0.00451, null, 0.00099, null, 0.99314, null, 0.66248, null, 45, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-02-13", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [9809, "ERR3909547", "ERX3918371", "ERS4309129", "ERP120006", "PRJEB36776", "CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "E-MTAB-8795", "Transcriptome Analysis", "The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13", null, "Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.", "Green3", "SAMEA6544754", "UNIVERSITY OF BIRMINGHAM", "ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544754|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Green3|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:S/G2/M rapid cycling|organism part:whole organism|sample name:E MTAB 8795:Green3|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "E MTAB 8795:Green3 s", "Green3 s", "CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.", "Experimental Factor: fraction:S/G2/M rapid cycling", "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP120006", "Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25", "14SomiteGreen3_GAGTGA_L003_R1_001.fastq.gz", "fastq", 819288855.0, 18206419.0, "E MTAB 8795:Green3", "0:45 1:0", "A:189173618;C:170597494;G:286250625;T:173188944;N:78174", 45, 0, null, null, 189173618, 170597494, 286250625, 173188944, 78174, "ERX3918371", "ERS4309129", "ERA2381432", "UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive", "UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive", 1, 0.00439, null, 0.001, null, 0.99377, null, 0.68367, null, 45, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-02-13", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [9810, "ERR3909546", "ERX3918370", "ERS4309128", "ERP120006", "PRJEB36776", "CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "E-MTAB-8795", "Transcriptome Analysis", "The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13", null, "Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.", "Green2", "SAMEA6544753", "UNIVERSITY OF BIRMINGHAM", "ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544753|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Green2|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:S/G2/M rapid cycling|organism part:whole organism|sample name:E MTAB 8795:Green2|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "E MTAB 8795:Green2 s", "Green2 s", "CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.", "Experimental Factor: fraction:S/G2/M rapid cycling", "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP120006", "Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25", "14SomiteGreen2_CTGACG_L003_R1_001.fastq.gz", "fastq", 697971375.0, 15510475.0, "E MTAB 8795:Green2", "0:45 1:0", "A:160028926;C:147075253;G:245773112;T:145025474;N:68610", 45, 0, null, null, 160028926, 147075253, 245773112, 145025474, 68610, "ERX3918370", "ERS4309128", "ERA2381432", "UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive", "UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive", 1, 0.00489, null, 0.00085, null, 0.99586, null, 0.80163, null, 45, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-02-13", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [9811, "ERR3909545", "ERX3918369", "ERS4309127", "ERP120006", "PRJEB36776", "CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "E-MTAB-8795", "Transcriptome Analysis", "The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics.", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13", null, "Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.", "Green1", "SAMEA6544752", "UNIVERSITY OF BIRMINGHAM", "ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544752|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Green1|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:S/G2/M rapid cycling|organism part:whole organism|sample name:E MTAB 8795:Green1|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "E MTAB 8795:Green1 s", "Green1 s", "CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109.", "Experimental Factor: fraction:S/G2/M rapid cycling", "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "ERP120006", "Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red", "ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25", "14SomiteGreen1_CACTGA_L003_R1_001.fastq.gz", "fastq", 826595640.0, 18368792.0, "E MTAB 8795:Green1", "0:45 1:0", "A:193728088;C:171605661;G:287824557;T:173352680;N:84654", 45, 0, null, null, 193728088, 171605661, 287824557, 173352680, 84654, "ERX3918369", "ERS4309127", "ERA2381432", "UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive", "UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive", 1, 0.00505, null, 0.00101, null, 0.99287, null, 0.58198, null, 45, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-02-13", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [25295, "SRR25764045", "SRX21486723", "SRS18719024", "SRP457105", "PRJNA1009809", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [Ribo Seq]", "GSE241753", "Other", "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. 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 bud 10 hpf Ribo seq rep1", "GSM7734770", null, "source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|treatment:100 \u00b5g/ml CHX 100 \u00b5g/ml TIG|geo loc name:missing|collection date:missing", "WT bud 10 hpf Ribo seq rep1", "We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018] which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters b 100 single l 180 s 20 t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms all RNAfold dependencies in Scikit ribo were omitted and the index was built separately for each chromosome. To make the hg38 GTF compatible with Scikit ribo transcript/UTR annotations were removed. For each transcript the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates taking into account the gene strand. To estimate codon dwell times short 20 23 nt and long 28 33 nt ribosome footprints were analyzed separately. rRNA filtered reads were aligned to GRCz11.108 using STAR v2.6.1c [Dobin et al. 2013] the following options: outFilterMultimapNmax 1 seedSearchStartLmax 15 outSAMtype BAM SortedByCoordinate outFilterMismatchNmax 2 alignEndsType EndToEnd quantMode TranscriptomeSAM outSAMattributes NH HI AS nM NM MD We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018] which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters b 100 single l 180 s 20 t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms all RNAfold dependencies in Scikit ribo were omitted and the index was built separately for each chromosome. To make the GRCz11 GTF compatible with Scikit ribo transcript/UTR annotations were removed. For each transcript the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates taking into account the gene strand. To estimate codon dwell times we utilised ribosome footprints with length 30 34 nt. Assembly: GRCz11 Supplementary files format and content: csv; codon dwell times from scikit ribo for all samples Supplementary files format and content: csv; transcript per million TPM counts per transcript in MANE annotation Library strategy: Ribo Seq", "Gastrula", "unperturbed growth conditions in E3 medium for zebrafish embryos.", "200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 \u00b5g/ml CHX and 100 \u00b5g/ml TIG 0.1% NP 40 10 \u00b5g/ml aprotinin 20 \u00b5M leupeptin 2.5 \u00b5M pepstatin A 0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously triturated through a 26G gauge needle and spun down for 7 minutes at 16 000xg/ 4\u00b0C. Supernatant was transferred to a new tube. 20 \u00b5g RNA in 200 \u00b5l polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22\u00b0C. post incubation on ice for 5 minutes extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4\u00b0C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose 20 mM Tris pH=8.0 140 mM KCl 5 mM MgCl2 1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4\u00b0C. Ribosome pellets were rinsed once dissolved in 200 \u00b5l drug free polysome lysis buffer and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22\u00b0C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia 2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 \u00b5l LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their 5\u2019 ends McGlinzy 2017 with T4 RNA Ligase 2 truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single end sequencing was performed on a NextSeq 500 platform Illumina.", "Embryos were grown in standard housing conditions namely28\u00b0C at a 14/10 hour light/dark cycle.", "strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|treatment:100 \u00b5g/ml CHX 100 \u00b5g/ml TIG", "GSM7734770", "GSM7734770: WT bud 10 hpf Ribo seq rep1; Danio rerio; OTHER", "GSM7734770 r1", "GSM7734770", "1", "200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 \u00b5g/ml CHX and 100 \u00b5g/ml TIG 0.1% NP 40 10 \u00b5g/ml aprotinin 20 \u00b5M leupeptin 2.5 \u00b5M pepstatin A 0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously triturated through a 26G gauge needle and spun down for 7 minutes at 16 000xg/ 4\u00b0C. Supernatant was transferred to a new tube. 20 \u00b5g RNA in 200 \u00b5l polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22\u00b0C. post incubation on ice for 5 minutes extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4\u00b0C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose 20 mM Tris pH=8.0 140 mM KCl 5 mM MgCl2 1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4\u00b0C. Ribosome pellets were rinsed once dissolved in 200 \u00b5l drug free polysome lysis buffer and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22\u00b0C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia 2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 \u00b5l LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their five prime ends McGlinzy 2017 with T4 RNA Ligase 2 truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single end sequencing was performed on a NextSeq 500 platform Illumina.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP457105", null, null, "WT_ribo_bud_1.fastq.gz", "fastq", 1476985703.0, 55745002.0, "GSM7734770 r1", "0:26.50", "A:266369385;C:466461341;G:473469631;T:270671671;N:13675", 26, null, null, null, 266369385, 466461341, 473469631, 270671671, 13675, "SRX21486723", "SRS18719024", "SRA1700409", "Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.773, null, 0.14121, null, 0.82242, null, 0.78464, null, 30, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Germany", "2023-08-28", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [25296, "SRR25764046", "SRX21486722", "SRS18719023", "SRP457105", "PRJNA1009809", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [Ribo Seq]", "GSE241753", "Other", "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. 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 sphere 4 hpf Ribo seq rep1", "GSM7734769", null, "source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|treatment:100 \u00b5g/ml CHX 100 \u00b5g/ml TIG|geo loc name:missing|collection date:missing", "WT sphere 4 hpf Ribo seq rep1", "We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018] which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters b 100 single l 180 s 20 t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms all RNAfold dependencies in Scikit ribo were omitted and the index was built separately for each chromosome. To make the hg38 GTF compatible with Scikit ribo transcript/UTR annotations were removed. For each transcript the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates taking into account the gene strand. To estimate codon dwell times short 20 23 nt and long 28 33 nt ribosome footprints were analyzed separately. rRNA filtered reads were aligned to GRCz11.108 using STAR v2.6.1c [Dobin et al. 2013] the following options: outFilterMultimapNmax 1 seedSearchStartLmax 15 outSAMtype BAM SortedByCoordinate outFilterMismatchNmax 2 alignEndsType EndToEnd quantMode TranscriptomeSAM outSAMattributes NH HI AS nM NM MD We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018] which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters b 100 single l 180 s 20 t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms all RNAfold dependencies in Scikit ribo were omitted and the index was built separately for each chromosome. To make the GRCz11 GTF compatible with Scikit ribo transcript/UTR annotations were removed. For each transcript the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates taking into account the gene strand. To estimate codon dwell times we utilised ribosome footprints with length 30 34 nt. Assembly: GRCz11 Supplementary files format and content: csv; codon dwell times from scikit ribo for all samples Supplementary files format and content: csv; transcript per million TPM counts per transcript in MANE annotation Library strategy: Ribo Seq", "Blastula", "unperturbed growth conditions in E3 medium for zebrafish embryos.", "200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 \u00b5g/ml CHX and 100 \u00b5g/ml TIG 0.1% NP 40 10 \u00b5g/ml aprotinin 20 \u00b5M leupeptin 2.5 \u00b5M pepstatin A 0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously triturated through a 26G gauge needle and spun down for 7 minutes at 16 000xg/ 4\u00b0C. Supernatant was transferred to a new tube. 20 \u00b5g RNA in 200 \u00b5l polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22\u00b0C. post incubation on ice for 5 minutes extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4\u00b0C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose 20 mM Tris pH=8.0 140 mM KCl 5 mM MgCl2 1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4\u00b0C. Ribosome pellets were rinsed once dissolved in 200 \u00b5l drug free polysome lysis buffer and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22\u00b0C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia 2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 \u00b5l LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their 5\u2019 ends McGlinzy 2017 with T4 RNA Ligase 2 truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single end sequencing was performed on a NextSeq 500 platform Illumina.", "Embryos were grown in standard housing conditions namely28\u00b0C at a 14/10 hour light/dark cycle.", "strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|treatment:100 \u00b5g/ml CHX 100 \u00b5g/ml TIG", "GSM7734769", "GSM7734769: WT sphere 4 hpf Ribo seq rep1; Danio rerio; OTHER", "GSM7734769 r1", "GSM7734769", "1", "200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 \u00b5g/ml CHX and 100 \u00b5g/ml TIG 0.1% NP 40 10 \u00b5g/ml aprotinin 20 \u00b5M leupeptin 2.5 \u00b5M pepstatin A 0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously triturated through a 26G gauge needle and spun down for 7 minutes at 16 000xg/ 4\u00b0C. Supernatant was transferred to a new tube. 20 \u00b5g RNA in 200 \u00b5l polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22\u00b0C. post incubation on ice for 5 minutes extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4\u00b0C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose 20 mM Tris pH=8.0 140 mM KCl 5 mM MgCl2 1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4\u00b0C. Ribosome pellets were rinsed once dissolved in 200 \u00b5l drug free polysome lysis buffer and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22\u00b0C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia 2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 \u00b5l LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their five prime ends McGlinzy 2017 with T4 RNA Ligase 2 truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single end sequencing was performed on a NextSeq 500 platform Illumina.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP457105", null, null, "WT_ribo_sphere_1.fastq.gz", "fastq", 1336027898.0, 47907512.0, "GSM7734769 r1", "0:27.89", "A:229038284;C:439455963;G:429428292;T:238088512;N:16847", 27, null, null, null, 229038284, 439455963, 429428292, 238088512, 16847, "SRX21486722", "SRS18719023", "SRA1700409", "Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.85867, null, 0.20418, null, 0.8776, null, 0.79481, null, 24, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Germany", "2023-08-28", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [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. 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"], [35567, "SRR32928199", "SRX28203119", "SRS24552825", "SRP575522", "PRJNA1244443", "An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing", "PRJNA1244443", "Other", "Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.", null, "expt2.broad.48.enzymatic.P01.F01.fq.gz", null, "seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt2 broad sequencing of many cells at low depth 48hpf enzymatic dissociation replicate 6", "100", "100", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "expt2.broad.48.enzymatic.P01.F01.fq.gz", "fastq", 800436.0, 9529.0, "expt2.broad.48.enzymatic.P01.F01.fq.gz", "0:84", "A:247920;C:168170;G:180799;T:203153;N:394", 84, null, null, null, 247920, 168170, 180799, 203153, 394, "SRX28203119", "SRS24552825", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [35568, "SRR32928200", "SRX28203118", "SRS24552823", "SRP575522", "PRJNA1244443", "An improved high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing", "PRJNA1244443", "Other", "Zebrafish are an ideal system to study the effects of chemical genetic and environmental perturbations on development due to their high fecundity and fast growth. Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. 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Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt1.12.bead.P1.H3.fq.gz", null, "seq depth:NA|Experiment id:1|dissociation method:bead|replicate:22|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt1 12hpf bead dissociation replicate 22", "22", "22", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.E12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 5", "210", "210", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.D12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 4", "209", "209", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.C12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 3", "208", "208", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.B12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 2", "207", "207", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.A12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf enzymatic dissociation replicate 1", "206", "206", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.H11.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:bead|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 8", "205", "205", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.G11.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:bead|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3 96hpf bead dissociation replicate 7", "204", "204", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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