rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
29746,SRR27467679,SRX23139227,SRS20090270,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary BS R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  BS  rep2,EV02003,EV02003,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.,,,OTHER,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,SRP482074,,,EV02003.R1.fastq.gz EV02003.R2.fastq.gz,fastq fastq,1031891720.0,3416860.0,EV02003.R1.fastq.gz,0:151 1:151,A:264464363;C:153440613;G:408557241;T:205367487;N:62016,151,151,,,264464363,153440613,408557241,205367487,62016,SRX23139227,SRS20090270,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,2,0.0,0.00019,0.0,0.00015,1.0,0.99993,,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Adult,Adult,Gonad,Reproductive System
29755,SRR27467688,SRX23139218,SRS20090261,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary DM R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  DM  rep2,EV02002,EV02002,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.,,,OTHER,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,SRP482074,,,EV02002.R1.fastq.gz EV02002.R2.fastq.gz,fastq fastq,861320308.0,2852054.0,EV02002.R1.fastq.gz,0:151 1:151,A:205625519;C:162178974;G:334206312;T:159256900;N:52603,151,151,,,205625519,162178974,334206312,159256900,52603,SRX23139218,SRS20090261,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,2,2e-05,0.00049,0.0,0.00027,1.0,0.99947,,0.44444,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Adult,Adult,Gonad,Reproductive System
29756,SRR27467689,SRX23139217,SRS20090260,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary mock R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  mock  rep2,EV02001,EV02001,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.,,,OTHER,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,SRP482074,,,EV02001.R1.fastq.gz EV02001.R2.fastq.gz,fastq fastq,520371066.0,1723083.0,EV02001.R1.fastq.gz,0:151 1:151,A:116107273;C:90896560;G:218652568;T:94682244;N:32421,151,151,,,116107273,90896560,218652568,94682244,32421,SRX23139217,SRS20090260,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,2,2e-05,0.00086,0.0,0.00078,0.99995,0.99981,0.0,0.61538,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Adult,Adult,Gonad,Reproductive System
40707,SRR3502888,SRX1760541,SRS1436386,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,Zebrafish tRNA at 6hpf,tRNA AB 6h,,strain:TUAB|age:6hpf|dev stage:Shield|sex:pooled male and female|tissue:Whole animal|collected by:Ariel Bazzini|genotype:WT|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish tRNAs at 6hpf,tRNA 6hpf zebrafish,TGIRT tRNA Library,1,,,OTHER,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP072296,,,AB-tRNA_S9_R1_001.fastq.gz AB-tRNA_S9_R2_001.fastq.gz,fastq fastq,7860522000.0,26201740.0,tRNA zebrafish 6hpf,0:150 1:150,A:1945184302;C:2012637521;G:2171934357;T:1730625218;N:140602,150,150,,,1945184302,2012637521,2171934357,1730625218,140602,SRX1760541,SRS1436386,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.04186,0.04313,0.00633,0.00639,0.96834,0.96913,0.53967,0.5329,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures