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
9170,ERR216332,ERX190997,ERS094086,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689285,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689285|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:29Z 1355130|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:29Z 1355130|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#6,4927108,Illumina sequencing of library 4927108  constructed from sample accession ERS094086 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence GCCAATGT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#6.bam,bam,3849223200.0,25661488.0,SC RUN 7896 6#6,0:75 1:75,A:1052343872;C:867977827;G:867966925;T:1060514703;N:419873,75,75,,,1052343872,867977827,867966925,1060514703,419873,ERX190997,ERS094086,ERA182034,SC,Wellcome Sanger Institute,2,0.94843,0.9504,0.09374,0.09366,0.71421,0.71916,0.5306,0.52809,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
9171,ERR216331,ERX190996,ERS094085,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689286,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:15Z|External Id:SAMEA1689286|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:15Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355129|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355129|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#5,4927107,Illumina sequencing of library 4927107  constructed from sample accession ERS094085 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence ACAGTGGT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#5.bam,bam,5957027700.0,39713518.0,SC RUN 7896 6#5,0:75 1:75,A:1634176455;C:1344899134;G:1345048404;T:1632256963;N:646744,75,75,,,1634176455,1344899134,1345048404,1632256963,646744,ERX190996,ERS094085,ERA182034,SC,Wellcome Sanger Institute,2,0.94169,0.94387,0.09489,0.09587,0.69406,0.69869,0.51459,0.51918,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
9172,ERR216330,ERX190995,ERS094084,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689283,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689283|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355128|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:28Z 1355128|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#4,4927106,Illumina sequencing of library 4927106  constructed from sample accession ERS094084 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence TGACCACT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#4.bam,bam,4130918700.0,27539458.0,SC RUN 7896 6#4,0:75 1:75,A:1129107864;C:933544249;G:934913323;T:1132901907;N:451357,75,75,,,1129107864,933544249,934913323,1132901907,451357,ERX190995,ERS094084,ERA182034,SC,Wellcome Sanger Institute,2,0.94225,0.94433,0.09272,0.09299,0.70043,0.70534,0.51333,0.52182,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
9173,ERR216329,ERX190994,ERS094083,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689282,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689282|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:27Z 1355127|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:27Z 1355127|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#3,4927105,Illumina sequencing of library 4927105  constructed from sample accession ERS094083 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence TTAGGCAT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#3.bam,bam,5102725800.0,34018172.0,SC RUN 7896 6#3,0:75 1:75,A:1400946711;C:1145033579;G:1143298888;T:1412890130;N:556492,75,75,,,1400946711,1145033579,1143298888,1412890130,556492,ERX190994,ERS094083,ERA182034,SC,Wellcome Sanger Institute,2,0.93688,0.93952,0.07363,0.07321,0.69645,0.70161,0.48708,0.48926,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
9174,ERR216328,ERX190993,ERS094082,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689281,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:female|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T10:04:12Z|ENA LAST UPDATE:2018 03 08T15:36:11Z|External Id:SAMEA1689281|INSDC center name:SC|INSDC first public:2013 01 07T10:04:12Z|INSDC last update:2018 03 08T15:36:11Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:26Z 1355126|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:26Z 1355126|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#2,4927104,Illumina sequencing of library 4927104  constructed from sample accession ERS094082 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence CGATGTTT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#2.bam,bam,4350577950.0,29003853.0,SC RUN 7896 6#2,0:75 1:75,A:1214100125;C:955724962;G:954429461;T:1225838270;N:485132,75,75,,,1214100125,955724962,954429461,1225838270,485132,ERX190993,ERS094082,ERA182034,SC,Wellcome Sanger Institute,2,0.92911,0.93026,0.0749,0.07514,0.69418,0.69775,0.48934,0.49,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
9175,ERR216327,ERX190992,ERS094081,ERP001234,PRJEB2894,ZF adult transcriptome,ZF_adult_transcriptome-sc-2012-02-20T14:37:57Z-2125,Transcriptome Analysis,Paired end sequence data from the Illumina HiSeq was prepared from male and female adult zebrafish for transcript ome analysis.,,,,,SAMEA1689284,SC,ArrayExpress DevelopmentalStage:Adult|ArrayExpress OrganismPart:Whole body|ArrayExpress Sex:male|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2013 01 07T17:02:18Z|ENA LAST UPDATE:2018 03 08T15:36:37Z|External Id:SAMEA1689284|INSDC center name:SC|INSDC first public:2013 01 07T17:02:18Z|INSDC last update:2018 03 08T15:36:37Z|INSDC status:public|Submitter Id:Adult zebrafish body sc 2012 02 09T16:35:23Z 1355125|common name:zebrafish|sample description:Total RNA from zebrafish body|sample name:Adult zebrafish body sc 2012 02 09T16:35:23Z 1355125|scientific name:Danio rerio|strain:SAT,,,,,,,,,1,SC EXP 7896 6#1,4927103,Illumina sequencing of library 4927103  constructed from sample accession ERS094081 for study accession ERP001234.  This is part of an Illumina multiplexed sequencing run 7896 6.  This submission includes reads tagged with the sequence ATCACGTT.,Illumina cDNA protocol,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP001234,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2013 01 07|ENA LAST UPDATE:2018 11 16,7896_6#1.bam,bam,5063629350.0,33757529.0,SC RUN 7896 6#1,0:75 1:75,A:1416301768;C:1110273098;G:1105481234;T:1431015934;N:557316,75,75,,,1416301768,1110273098,1105481234,1431015934,557316,ERX190992,ERS094081,ERA182034,SC,Wellcome Sanger Institute,2,0.93508,0.93634,0.11212,0.11206,0.70009,0.70538,0.50126,0.49177,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2013-01-07,Adult,Adult,Trunk,Surface Structure
39615,SRR1873565,SRX915245,SRS870229,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,adult,GSM1630509,,source name:entire adult|strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:adult|age:1 year,adult,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,entire adult,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:adult|age:1 year,GSM1630509,GSM1630509: adult; Danio rerio; miRNA Seq,GSM1630509,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630509,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,361024.0,6498.0,GSM1630509 r1,0:4 1:51.56,A:104704;C:84406;G:83224;T:87843;N:847,4,51,,,104704,84406,83224,87843,847,SRX915245,SRS870229,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,51,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Adult,Adult,Trunk,Surface Structure
41421,SRR4423115,SRX2245299,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult male whole body,94 3,94 3,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,maleRID0094BC03smallZF.fastq,fastq,697814234.0,14408051.0,maleRID0094BC03smallZF.fastq,0:48.43,A:165337411;C:177790468;G:184204311;T:170482044;N:0,48,,,,165337411,177790468,184204311,170482044,0,SRX2245299,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.70426,,0.16215,,0.91027,,0.5459,,120,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
41423,SRR4423113,SRX2245297,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: Adult male whole body,99 5,99 5,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,maleRID0099BC05LargeZF.fastq,fastq,3606425618.0,40350582.0,maleRID0099BC05LargeZF.fastq,0:89.38,A:900873268;C:899774590;G:1079098037;T:726679723;N:0,89,,,,900873268,899774590,1079098037,726679723,0,SRX2245297,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.90069,,0.21287,,0.95726,,0.72186,,53,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
41425,SRR4423111,SRX2245295,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult male whole body,88 3,88 3,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,maleRID0088BC03smallZF.fastq,fastq,523776538.0,11118832.0,maleRID0088BC03smallZF.fastq,0:47.11,A:123827431;C:133478804;G:138882662;T:127587641;N:0,47,,,,123827431,133478804,138882662,127587641,0,SRX2245295,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.69556,,0.16368,,0.9093,,0.54838,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
41427,SRR4423109,SRX2245293,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult male whole body,93 3,93 3,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,maleRID0093BC03smallZF.fastq,fastq,692750598.0,14286031.0,maleRID0093BC03smallZF.fastq,0:48.49,A:164412063;C:176380331;G:182539801;T:169418403;N:0,48,,,,164412063,176380331,182539801,169418403,0,SRX2245293,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.70738,,0.16645,,0.90948,,0.55306,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
47611,SRR6671794,SRX3648486,SRS2913085,SRP132190,PRJNA432942,Zebrafish genes regulated in response to Mucor circinelloides infection,PRJNA432942,Other,Determination of the genes that can be important for the defense of the host to infection for Mucorales fungi  using zebrafish and the fungus Mucor circinelloides as host and pathogen model  respectively. Total RNA was sequenced RNA seq from abdominal organs of infected fish.,,,,,PBS2,,strain:AB|dev stage:Adult|sex:not determined|tissue:Abdomen|treatment:Control innoculated with PBS|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Darnio rerio: uninffected,PBS2,PBS2,Total RNA isolated from uninfected abdominal tissue was used to generate the library using truseq kit,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP132190,,,PBS2_GCCAAT_L001_R1_001_BH8U70ADXX.filt.fastq.gz,fastq,792892359.0,15546909.0,PBS2 GCCAAT L001 R1 001 BH8U70ADXX.filt.fastq.gz,0:51,A:207417646;C:188867370;G:187996499;T:208448675;N:162169,51,,,,207417646,188867370,187996499,208448675,162169,SRX3648486,SRS2913085,SRA655550,University of Murcia|Genetics and Microbiology,University of Murcia,1,0.92826,,0.02642,,0.72815,,0.45776,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Spain,2018-09-28,Adult,Adult,Trunk,Surface Structure
47612,SRR6671795,SRX3648485,SRS2913084,SRP132190,PRJNA432942,Zebrafish genes regulated in response to Mucor circinelloides infection,PRJNA432942,Other,Determination of the genes that can be important for the defense of the host to infection for Mucorales fungi  using zebrafish and the fungus Mucor circinelloides as host and pathogen model  respectively. Total RNA was sequenced RNA seq from abdominal organs of infected fish.,,,,,RDRZ,,strain:AB|dev stage:Adult|sex:not determined|tissue:Abdomen|treatment:Infected with Mucor circinelloides spores|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Darnio rerio: infected with Mucor circinelloides,RDRZ,RDRZ,Total RNA isolated from abdominal tissue infected with Mucor circinelloides was used to generate the library using truseq kit,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP132190,,,RDRZ_TGACCA_L001_R1_001_BH8U70ADXX.filt.fastq.gz,fastq,741005418.0,14529518.0,RDRZ TGACCA L001 R1 001 BH8U70ADXX.filt.fastq.gz,0:51,A:192330774;C:178252917;G:175501754;T:194766886;N:153087,51,,,,192330774,178252917,175501754,194766886,153087,SRX3648485,SRS2913084,SRA655550,University of Murcia|Genetics and Microbiology,University of Murcia,1,0.91685,,0.03703,,0.70873,,0.49947,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Spain,2018-09-28,Adult,Adult,Trunk,Surface Structure
52281,SRR9077085,SRX5852372,SRS4776365,SRP198708,PRJNA543385,mRNA sequence of zebrafish head and body,PRJNA543385,Other,RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing,,,,body2 mock,s11,,breed:zebrafish|dev stage:adult|sex:NA|tissue:body6|BioSampleModel:Model organism or animal,,,,,,,,,body2 mock,WC TC 060,WC TC 060,TRUEseq standardised protocol,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP198708,,,WC_TC_060_S11.R2.fastq.gz WC_TC_060_S11.R1.fastq.gz,fastq fastq,6570204104.0,43225027.0,WC TC 060 S11.R1.fastq.gz,0:101 1:51,A:1688920476;C:1591936403;G:1547543861;T:1736945913;N:4857451,101,51,,,1688920476,1591936403,1547543861,1736945913,4857451,SRX5852372,SRS4776365,SRA887738,Southern University of Science and Technology|Department of Biology,Southern University of Science and Technology,2,0.96893,0.96531,0.06012,0.06428,0.74002,0.74308,0.44405,0.45056,101,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,China,2019-10-08,Adult,Adult,Trunk,Surface Structure
52282,SRR9077086,SRX5852371,SRS4776364,SRP198708,PRJNA543385,mRNA sequence of zebrafish head and body,PRJNA543385,Other,RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing,,,,body2 control,s12,,breed:zebrafish|dev stage:adult|sex:NA|tissue:body7|BioSampleModel:Model organism or animal,,,,,,,,,body2 control,WC TC 061,WC TC 061,TRUEseq standardised protocol,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP198708,,,WC_TC_061_S12.R1.fastq.gz WC_TC_061_S12.R2.fastq.gz,fastq fastq,5298115192.0,34856021.0,WC TC 061 S12.R1.fastq.gz,0:101 1:51,A:1365002199;C:1284749208;G:1236476294;T:1407970678;N:3916813,101,51,,,1365002199,1284749208,1236476294,1407970678,3916813,SRX5852371,SRS4776364,SRA887738,Southern University of Science and Technology|Department of Biology,Southern University of Science and Technology,2,0.96855,0.96437,0.06631,0.06978,0.72819,0.73158,0.43805,0.4516,101,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,China,2019-10-08,Adult,Adult,Trunk,Surface Structure
52283,SRR9077087,SRX5852370,SRS4776363,SRP198708,PRJNA543385,mRNA sequence of zebrafish head and body,PRJNA543385,Other,RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing,,,,body2 kd,s13,,breed:zebrafish|dev stage:adult|sex:NA|tissue:body8|BioSampleModel:Model organism or animal,,,,,,,,,body2 kd,WC TC 062,WC TC 062,TRUEseq standardised protocol,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP198708,,,WC_TC_062_S13.R1.fastq.gz WC_TC_062_S13.R2.fastq.gz,fastq fastq,6381036304.0,41980502.0,WC TC 062 S13.R1.fastq.gz,0:101 1:51,A:1647560028;C:1537878827;G:1499984084;T:1690940053;N:4673312,101,51,,,1647560028,1537878827,1499984084,1690940053,4673312,SRX5852370,SRS4776363,SRA887738,Southern University of Science and Technology|Department of Biology,Southern University of Science and Technology,2,0.96684,0.96194,0.06383,0.06747,0.73608,0.74052,0.45347,0.4621,101,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,China,2019-10-08,Adult,Adult,Trunk,Surface Structure
52284,SRR9077088,SRX5852369,SRS4776362,SRP198708,PRJNA543385,mRNA sequence of zebrafish head and body,PRJNA543385,Other,RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing,,,,body2 kd+wt,s14,,breed:zebrafish|dev stage:adult|sex:NA|tissue:body9|BioSampleModel:Model organism or animal,,,,,,,,,body2 kd+wt,WC TC 063,WC TC 063,TRUEseq standardised protocol,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP198708,,,WC_TC_063_S14.R1.fastq.gz WC_TC_063_S14.R2.fastq.gz,fastq fastq,5465511120.0,35957310.0,WC TC 063 S14.R1.fastq.gz,0:101 1:51,A:1414511882;C:1316966059;G:1276815442;T:1453177754;N:4039983,101,51,,,1414511882,1316966059,1276815442,1453177754,4039983,SRX5852369,SRS4776362,SRA887738,Southern University of Science and Technology|Department of Biology,Southern University of Science and Technology,2,0.96743,0.96269,0.06264,0.06717,0.73768,0.74002,0.43946,0.44951,101,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,China,2019-10-08,Adult,Adult,Trunk,Surface Structure
52289,SRR9077093,SRX5852364,SRS4776357,SRP198708,PRJNA543385,mRNA sequence of zebrafish head and body,PRJNA543385,Other,RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing,,,,body1 mock,s6,,breed:zebrafish|dev stage:adult|sex:NA|tissue:body1|BioSampleModel:Model organism or animal,,,,,,,,,body1 mock,WC TC 055,WC TC 055,TRUEseq standardised protocol,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP198708,,,WC_TC_055_S6.R1.fastq.gz WC_TC_055_S6.R2.fastq.gz,fastq fastq,5140707792.0,33820446.0,WC TC 055 S6.R1.fastq.gz,0:101 1:51,A:1316539385;C:1252228375;G:1214956681;T:1353162802;N:3820549,101,51,,,1316539385,1252228375,1214956681,1353162802,3820549,SRX5852364,SRS4776357,SRA887738,Southern University of Science and Technology|Department of Biology,Southern University of Science and Technology,2,0.97114,0.96587,0.05961,0.06293,0.73596,0.73979,0.43233,0.4586,101,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,China,2019-10-08,Adult,Adult,Trunk,Surface Structure
52290,SRR9077094,SRX5852363,SRS4776356,SRP198708,PRJNA543385,mRNA sequence of zebrafish head and body,PRJNA543385,Other,RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing,,,,body1 control,s7,,breed:zebrafish|dev stage:adult|sex:NA|tissue:body2|BioSampleModel:Model organism or animal,,,,,,,,,body1 control,WC TC 056,WC TC 056,TRUEseq standardised protocol,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP198708,,,WC_TC_056_S7.R1.fastq.gz WC_TC_056_S7.R2.fastq.gz,fastq fastq,5020859136.0,33031968.0,WC TC 056 S7.R1.fastq.gz,0:101 1:51,A:1291539287;C:1214422587;G:1184146239;T:1327013927;N:3737096,101,51,,,1291539287,1214422587,1184146239,1327013927,3737096,SRX5852363,SRS4776356,SRA887738,Southern University of Science and Technology|Department of Biology,Southern University of Science and Technology,2,0.96884,0.96505,0.0623,0.06643,0.73572,0.73904,0.44643,0.45988,101,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,China,2019-10-08,Adult,Adult,Trunk,Surface Structure
52291,SRR9077095,SRX5852362,SRS4776355,SRP198708,PRJNA543385,mRNA sequence of zebrafish head and body,PRJNA543385,Other,RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing,,,,body1 kd+wt,s9,,breed:zebrafish|dev stage:adult|sex:NA|tissue:body4|BioSampleModel:Model organism or animal,,,,,,,,,body1 kd+wt,WC TC 058,WC TC 058,TRUEseq standardised protocol,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP198708,,,WC_TC_058_S9.R1.fastq.gz WC_TC_058_S9.R2.fastq.gz,fastq fastq,6018676056.0,39596553.0,WC TC 058 S9.R1.fastq.gz,0:101 1:51,A:1548315021;C:1452922375;G:1413529417;T:1599423213;N:4486030,101,51,,,1548315021,1452922375,1413529417,1599423213,4486030,SRX5852362,SRS4776355,SRA887738,Southern University of Science and Technology|Department of Biology,Southern University of Science and Technology,2,0.96912,0.96439,0.06373,0.06781,0.73612,0.73988,0.44769,0.46236,101,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,China,2019-10-08,Adult,Adult,Trunk,Surface Structure
52293,SRR9077097,SRX5852360,SRS4776353,SRP198708,PRJNA543385,mRNA sequence of zebrafish head and body,PRJNA543385,Other,RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing,,,,body1 kd+mt,s10,,breed:zebrafish|dev stage:adult|sex:NA|tissue:body5|BioSampleModel:Model organism or animal,,,,,,,,,body1 kd+mt,WC TC 059,WC TC 059,TRUEseq standardised protocol,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP198708,,,WC_TC_059_S10.R2.fastq.gz WC_TC_059_S10.R1.fastq.gz,fastq fastq,6271465432.0,41259641.0,WC TC 059 S10.R1.fastq.gz,0:101 1:51,A:1629820249;C:1502782160;G:1459060597;T:1675172643;N:4629783,101,51,,,1629820249,1502782160,1459060597,1675172643,4629783,SRX5852360,SRS4776353,SRA887738,Southern University of Science and Technology|Department of Biology,Southern University of Science and Technology,2,0.96576,0.96033,0.06782,0.07173,0.73547,0.74014,0.45453,0.45359,101,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,China,2019-10-08,Adult,Adult,Trunk,Surface Structure
52294,SRR9077098,SRX5852359,SRS4776352,SRP198708,PRJNA543385,mRNA sequence of zebrafish head and body,PRJNA543385,Other,RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing,,,,body1 kd,s8,,breed:zebrafish|dev stage:adult|sex:NA|tissue:body3|BioSampleModel:Model organism or animal,,,,,,,,,body1 kd,WC TC 057,WC TC 057,TRUEseq standardised protocol,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP198708,,,WC_TC_057_S8.R1.fastq.gz WC_TC_057_S8.R2.fastq.gz,fastq fastq,4742849768.0,31202959.0,WC TC 057 S8.R1.fastq.gz,0:101 1:51,A:1229413754;C:1139873278;G:1110810068;T:1259324043;N:3428625,101,51,,,1229413754,1139873278,1110810068,1259324043,3428625,SRX5852359,SRS4776352,SRA887738,Southern University of Science and Technology|Department of Biology,Southern University of Science and Technology,2,0.96593,0.96237,0.06455,0.06966,0.73618,0.74126,0.45216,0.4641,101,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,China,2019-10-08,Adult,Adult,Trunk,Surface Structure
52295,SRR9077099,SRX5852358,SRS4776351,SRP198708,PRJNA543385,mRNA sequence of zebrafish head and body,PRJNA543385,Other,RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing,,,,body2 kd+mt,s15,,breed:zebrafish|dev stage:adult|sex:NA|tissue:body|BioSampleModel:Model organism or animal,,,,,,,,,body2 kd+mt,WC TC 064,WC TC 064,TRUEseq standardised protocol,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP198708,,,WC_TC_064_S15.R2.fastq.gz WC_TC_064_S15.R1.fastq.gz,fastq fastq,5256312456.0,34581003.0,WC TC 064 S15.R1.fastq.gz,0:101 1:51,A:1366908192;C:1258394092;G:1221379603;T:1405741204;N:3889365,101,51,,,1366908192,1258394092,1221379603,1405741204,3889365,SRX5852358,SRS4776351,SRA887738,Southern University of Science and Technology|Department of Biology,Southern University of Science and Technology,2,0.96533,0.96121,0.06858,0.07356,0.73547,0.7387,0.46254,0.46106,101,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,China,2019-10-08,Adult,Adult,Trunk,Surface Structure
53490,SRR9945454,SRX6694025,SRS5251307,SRP218026,PRJNA557895,The origin and evolution of RNA editing in Metazoan,PRJNA557895,Other,We shed light on the origin and evolution of RNA editing in Metazoan by selected representative 22 species  18 of which were sequenced by ourselves.,,,,,Replicate 2 for D.rerio,,isolate:Drer 2|age:not collected|dev stage:not collected|sex:not collected|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,Strand specific RNA seq of Danio rerio rep2: whole body,DrerWHANIddyEAAORAAPEI 218,DrerWHANIddyEAAORAAPEI 218,Both genomic DNA and total RNA were extracted from the whole body of an adult. The strand specific RNA seq library was prepared using the TruSeq Stranded mRNA LT Sample Prep RS 122 2101  Illumina and sequenced on the Illumina HiSeq 4000 platform according to the manufacturer's instructions. The DNA library was prepared using the MGIEasy DNA Library Prep Kit V1.1  MGI Tech and sequenced on the BGISEQ 500RS platform according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP218026,,,170403_I133_FCHGL72BBXX_L7_WHANIddyEAAORAAPEI-218_1.fq.gz 170403_I133_FCHGL72BBXX_L7_WHANIddyEAAORAAPEI-218_2.fq.gz 170403_I133_FCHGL72BBXX_L8_WHANIddyEAAORAAPEI-218_1.fq.gz 170403_I133_FCHGL72BBXX_L8_WHANIddyEAAORAAPEI-218_2.fq.gz,fastq fastq fastq fastq,36897471600.0,184487358.0,170403 I133 FCHGL72BBXX L7 WHANIddyEAAORAAPEI 218 1.fq.gz,0:100 1:100,A:9529576187;C:8838331599;G:9026934437;T:9496422810;N:6206567,100,100,,,9529576187,8838331599,9026934437,9496422810,6206567,SRX6694025,SRS5251307,SRA937931,"Kunming Institute of Zoology, Chinese Academy of Sciences|State Key Laboratory of Genetic Resources and Evol","Kunming Institute of Zoology, Chinese Academy of Sciences",2,0.95202,0.95483,0.0516,0.0503,0.70853,0.71224,0.50665,0.50669,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,China,2019-08-11,Adult,Adult,Trunk,Surface Structure
53491,SRR9945455,SRX6694024,SRS5251306,SRP218026,PRJNA557895,The origin and evolution of RNA editing in Metazoan,PRJNA557895,Other,We shed light on the origin and evolution of RNA editing in Metazoan by selected representative 22 species  18 of which were sequenced by ourselves.,,,,,Replicate 1 for D.rerio,,isolate:Drer 1|age:not collected|dev stage:not collected|sex:not collected|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,Strand specific RNA seq of Danio rerio rep1: whole body,DrerWHINSpmnpBABRAAPEI 219,DrerWHINSpmnpBABRAAPEI 219,Both genomic DNA and total RNA were extracted from the whole body of an adult. The strand specific RNA seq library was prepared using the TruSeq Stranded mRNA LT Sample Prep RS 122 2101  Illumina  and the DNA library was constructed according to the standard protocol provided by Illumina San Diego  CA  USA. Paired end sequencing was performed for the two libraries on the HiSeq 4000 platform according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP218026,,,160415_I136_FCH7MJKBBXX_L4_WHINSpmnpBABRAAPEI-219_1.fq.gz 160415_I136_FCH7MJKBBXX_L4_WHINSpmnpBABRAAPEI-219_2.fq.gz,fastq fastq,23885022200.0,119425111.0,160415 I136 FCH7MJKBBXX L4 WHINSpmnpBABRAAPEI 219 1.fq.gz,0:100 1:100,A:6260820125;C:5693318287;G:5662248033;T:6264079999;N:4555756,100,100,,,6260820125,5693318287,5662248033,6264079999,4555756,SRX6694024,SRS5251306,SRA937931,"Kunming Institute of Zoology, Chinese Academy of Sciences|State Key Laboratory of Genetic Resources and Evol","Kunming Institute of Zoology, Chinese Academy of Sciences",2,0.9539,0.95672,0.05875,0.05826,0.70782,0.70885,0.50825,0.51884,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,China,2019-08-11,Adult,Adult,Trunk,Surface Structure
53492,SRR9945460,SRX6694019,SRS5251305,SRP218026,PRJNA557895,The origin and evolution of RNA editing in Metazoan,PRJNA557895,Other,We shed light on the origin and evolution of RNA editing in Metazoan by selected representative 22 species  18 of which were sequenced by ourselves.,,,,,Replicate 3 for D.rerio,,isolate:Drer 3|age:not collected|dev stage:not collected|sex:not collected|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,Strand specific RNA seq of Danio rerio rep3: whole body,DrerWHANIddyEAAPRAAPEI 219,DrerWHANIddyEAAPRAAPEI 219,Both genomic DNA and total RNA were extracted from the whole body of an adult. The strand specific RNA seq library was prepared using the TruSeq Stranded mRNA LT Sample Prep RS 122 2101  Illumina and sequenced on the Illumina HiSeq 4000 platform according to the manufacturer's instructions. The DNA library was prepared using the MGIEasy DNA Library Prep Kit V1.1  MGI Tech and sequenced on the BGISEQ 500RS platform according to the manufacturer's instructions.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP218026,,,170403_I133_FCHGL72BBXX_L6_WHANIddyEAAPRAAPEI-219_1.fq.gz 170403_I133_FCHGL72BBXX_L6_WHANIddyEAAPRAAPEI-219_2.fq.gz,fastq fastq,28065364200.0,140326821.0,170403 I133 FCHGL72BBXX L6 WHANIddyEAAPRAAPEI 219 1.fq.gz,0:100 1:100,A:7411372143;C:6577171300;G:6693925569;T:7377537100;N:5358088,100,100,,,7411372143,6577171300,6693925569,7377537100,5358088,SRX6694019,SRS5251305,SRA937931,"Kunming Institute of Zoology, Chinese Academy of Sciences|State Key Laboratory of Genetic Resources and Evol","Kunming Institute of Zoology, Chinese Academy of Sciences",2,0.94764,0.95274,0.06893,0.06709,0.68966,0.69154,0.49095,0.52264,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,China,2019-08-11,Adult,Adult,Trunk,Surface Structure
61775,SRR13015641,SRX9466595,SRS7678751,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here  we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw  unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,body tissue of parents from cross 2,male cross 2 adult body transcriptome,,strain:AB wildtype|dev stage:adult|sex:male|tissue:body|embryos derived by cross:single cross 2|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq body  zebrafish male from single cross 2  lane2,PJ KH 036 2,PJ KH 036 2,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_036_S36_L004_R1_001.fastq.gz PJ_KH_036_S36_L004_R2_001.fastq.gz,fastq fastq,6478281728.0,21451264.0,PJ KH 036 S36 L004 R1 001.fastq.gz,0:151 1:151,A:1648862369;C:1591549903;G:1631652727;T:1605015568;N:1201161,151,151,,,1648862369,1591549903,1631652727,1605015568,1201161,SRX9466595,SRS7678751,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.9608,0.96246,0.02387,0.02325,0.78386,0.78608,0.5048,0.50714,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Adult,Adult,Trunk,Surface Structure
61776,SRR13015642,SRX9466594,SRS7678751,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here  we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw  unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,body tissue of parents from cross 2,male cross 2 adult body transcriptome,,strain:AB wildtype|dev stage:adult|sex:male|tissue:body|embryos derived by cross:single cross 2|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq body  zebrafish male from single cross 2  lane1,PJ KH 036 1,PJ KH 036 1,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_036_S36_L003_R1_001.fastq.gz PJ_KH_036_S36_L003_R2_001.fastq.gz,fastq fastq,6439955814.0,21324357.0,PJ KH 036 S36 L003 R1 001.fastq.gz,0:151 1:151,A:1639459063;C:1581604775;G:1623817049;T:1594197994;N:876933,151,151,,,1639459063,1581604775,1623817049,1594197994,876933,SRX9466594,SRS7678751,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.96081,0.96284,0.02389,0.02312,0.78393,0.78713,0.50411,0.50535,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Adult,Adult,Trunk,Surface Structure
61777,SRR13015643,SRX9466593,SRS7678749,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here  we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw  unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,body tissue of parents from cross 2,female cross 2 adult body transcriptome,,strain:AB wildtype|dev stage:adult|sex:female|tissue:body|embryos derived by cross:single cross 2|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq body  zebrafish female from single cross 2  lane2,PJ KH 035 2,PJ KH 035 2,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_035_S35_L004_R1_001.fastq.gz PJ_KH_035_S35_L004_R2_001.fastq.gz,fastq fastq,9422957190.0,31201845.0,PJ KH 035 S35 L004 R1 001.fastq.gz,0:151 1:151,A:2404649667;C:2302545232;G:2348124627;T:2365889998;N:1747666,151,151,,,2404649667,2302545232,2348124627,2365889998,1747666,SRX9466593,SRS7678749,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.94329,0.9456,0.02717,0.02634,0.71029,0.71451,0.46936,0.47075,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Adult,Adult,Trunk,Surface Structure
61779,SRR13015645,SRX9466591,SRS7678749,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here  we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw  unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,body tissue of parents from cross 2,female cross 2 adult body transcriptome,,strain:AB wildtype|dev stage:adult|sex:female|tissue:body|embryos derived by cross:single cross 2|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq body  zebrafish female from single cross 2  lane1,PJ KH 035 1,PJ KH 035 1,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_035_S35_L003_R1_001.fastq.gz PJ_KH_035_S35_L003_R2_001.fastq.gz,fastq fastq,9366027774.0,31013337.0,PJ KH 035 S35 L003 R1 001.fastq.gz,0:151 1:151,A:2391627126;C:2287177887;G:2335767866;T:2350185771;N:1269124,151,151,,,2391627126,2287177887,2335767866,2350185771,1269124,SRX9466591,SRS7678749,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.94406,0.94614,0.02757,0.02656,0.70968,0.71366,0.468,0.46571,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Adult,Adult,Trunk,Surface Structure
61780,SRR13015646,SRX9466590,SRS7678748,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here  we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw  unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,body tissue of parents from cross 1,male cross 1 adult body transcriptome,,strain:AB wildtype|dev stage:adult|sex:male|tissue:body|embryos derived by cross:single cross 1|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq body  zebrafish male from single cross 1  lane2,PJ KH 034 2,PJ KH 034 2,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_034_S34_L004_R1_001.fastq.gz PJ_KH_034_S34_L004_R2_001.fastq.gz,fastq fastq,7735112712.0,25612956.0,PJ KH 034 S34 L004 R1 001.fastq.gz,0:151 1:151,A:1974870696;C:1890581361;G:1943734005;T:1924490964;N:1435686,151,151,,,1974870696,1890581361,1943734005,1924490964,1435686,SRX9466590,SRS7678748,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.96448,0.966,0.03488,0.03342,0.72594,0.72985,0.49998,0.49893,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Adult,Adult,Trunk,Surface Structure
61781,SRR13015647,SRX9466589,SRS7678748,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here  we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw  unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,body tissue of parents from cross 1,male cross 1 adult body transcriptome,,strain:AB wildtype|dev stage:adult|sex:male|tissue:body|embryos derived by cross:single cross 1|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq body  zebrafish male from single cross 1  lane1,PJ KH 034 1,PJ KH 034 1,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_034_S34_L003_R1_001.fastq.gz PJ_KH_034_S34_L003_R2_001.fastq.gz,fastq fastq,7674468092.0,25412146.0,PJ KH 034 S34 L003 R1 001.fastq.gz,0:151 1:151,A:1959722716;C:1874876878;G:1930984650;T:1907843658;N:1040190,151,151,,,1959722716,1874876878,1930984650,1907843658,1040190,SRX9466589,SRS7678748,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.96342,0.9657,0.03463,0.03334,0.72638,0.73196,0.49758,0.50234,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Adult,Adult,Trunk,Surface Structure
61782,SRR13015648,SRX9466588,SRS7678747,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here  we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw  unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,body tissue of parents from cross 1,female cross 1 adult body transcriptome,,strain:AB wildtype|dev stage:adult|sex:female|tissue:body|embryos derived by cross:single cross 1|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq body  zebrafish female from single cross 1  lane2,PJ KH 033 2,PJ KH 033 2,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_033_S33_L004_R1_001.fastq.gz PJ_KH_033_S33_L004_R2_001.fastq.gz,fastq fastq,6190583240.0,20498620.0,PJ KH 033 S33 L004 R1 001.fastq.gz,0:151 1:151,A:1564701976;C:1533323455;G:1577799625;T:1513606117;N:1152067,151,151,,,1564701976,1533323455,1577799625,1513606117,1152067,SRX9466588,SRS7678747,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.95429,0.95588,0.02079,0.01982,0.75779,0.76065,0.44557,0.45493,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Adult,Adult,Trunk,Surface Structure
61783,SRR13015649,SRX9466587,SRS7678747,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here  we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw  unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,body tissue of parents from cross 1,female cross 1 adult body transcriptome,,strain:AB wildtype|dev stage:adult|sex:female|tissue:body|embryos derived by cross:single cross 1|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq body  zebrafish female from single cross 1  lane1,PJ KH 033 1,PJ KH 033 1,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_033_S33_L003_R1_001.fastq.gz PJ_KH_033_S33_L003_R2_001.fastq.gz,fastq fastq,6121465406.0,20269753.0,PJ KH 033 S33 L003 R1 001.fastq.gz,0:151 1:151,A:1547607194;C:1515704901;G:1561793302;T:1495528175;N:831834,151,151,,,1547607194,1515704901,1561793302,1495528175,831834,SRX9466587,SRS7678747,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.9549,0.95671,0.02143,0.02065,0.75844,0.76138,0.49503,0.50077,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Adult,Adult,Trunk,Surface Structure
70846,SRR20822767,SRX16842343,SRS14446856,SRP389580,PRJNA865512,TCR alpha and beta repseq,PRJNA865512,Other,TCR Repertoire sequencing raw reads TCR alpha and beta for several species,,pubmed:37344590,,,ZF 6,,strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 6|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,ZF 39,ZF 39,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP389580,,,ZF_Tu2_10_R1.fastq.gz ZF_Tu2_10_R2.fastq.gz ZF_Tu2_11_R1.fastq.gz ZF_Tu2_11_R2.fastq.gz ZF_Tu2_12_R1.fastq.gz ZF_Tu2_12_R2.fastq.gz ZF_Tu2_13_R1.fastq.gz ZF_Tu2_13_R2.fastq.gz ZF_Tu2_14_R1.fastq.gz ZF_Tu2_14_R2.fastq.gz ZF_Tu2_15_R1.fastq.gz ZF_Tu2_15_R2.fastq.gz ZF_Tu2_16_R1.fastq.gz ZF_Tu2_16_R2.fastq.gz ZF_Tu2_1_R1.fastq.gz ZF_Tu2_1_R2.fastq.gz ZF_Tu2_2_R1.fastq.gz ZF_Tu2_2_R2.fastq.gz ZF_Tu2_3_R1.fastq.gz ZF_Tu2_3_R2.fastq.gz ZF_Tu2_4_R1.fastq.gz ZF_Tu2_4_R2.fastq.gz ZF_Tu2_5_R1.fastq.gz ZF_Tu2_5_R2.fastq.gz ZF_Tu2_6_R1.fastq.gz ZF_Tu2_6_R2.fastq.gz ZF_Tu2_7_R1.fastq.gz ZF_Tu2_7_R2.fastq.gz ZF_Tu2_8_R1.fastq.gz ZF_Tu2_8_R2.fastq.gz ZF_Tu2_9_R1.fastq.gz ZF_Tu2_9_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,19600815900.0,39045450.0,ZF Tu2 10 R1.fastq.gz,0:251 1:251,A:5586816283;C:3957164453;G:4183919538;T:5872635753;N:279873,251,251,,,5586816283,3957164453,4183919538,5872635753,279873,SRX16842343,SRS14446856,SRA1468938,Max Planck Institut|Boehm,Max Planck Institut,2,0.23669,0.0002,0.00499,0.00015,0.98908,0.99993,0.27742,0.8,251,251,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70847,SRR20822058,SRX16841660,SRS14446856,SRP389580,PRJNA865512,TCR alpha and beta repseq,PRJNA865512,Other,TCR Repertoire sequencing raw reads TCR alpha and beta for several species,,pubmed:37344590,,,ZF 6,,strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 6|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,ZF 37,ZF 37,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP389580,,,ZF_Tu2_10_R1.fastq.gz ZF_Tu2_10_R2.fastq.gz ZF_Tu2_11_R1.fastq.gz ZF_Tu2_11_R2.fastq.gz ZF_Tu2_12_R1.fastq.gz ZF_Tu2_12_R2.fastq.gz ZF_Tu2_13_R1.fastq.gz ZF_Tu2_13_R2.fastq.gz ZF_Tu2_14_R1.fastq.gz ZF_Tu2_14_R2.fastq.gz ZF_Tu2_15_R1.fastq.gz ZF_Tu2_15_R2.fastq.gz ZF_Tu2_16_R1.fastq.gz ZF_Tu2_16_R2.fastq.gz ZF_Tu2_1_R1.fastq.gz ZF_Tu2_1_R2.fastq.gz ZF_Tu2_2_R1.fastq.gz ZF_Tu2_2_R2.fastq.gz ZF_Tu2_3_R1.fastq.gz ZF_Tu2_3_R2.fastq.gz ZF_Tu2_4_R1.fastq.gz ZF_Tu2_4_R2.fastq.gz ZF_Tu2_5_R1.fastq.gz ZF_Tu2_5_R2.fastq.gz ZF_Tu2_6_R1.fastq.gz ZF_Tu2_6_R2.fastq.gz ZF_Tu2_7_R1.fastq.gz ZF_Tu2_7_R2.fastq.gz ZF_Tu2_8_R1.fastq.gz ZF_Tu2_8_R2.fastq.gz ZF_Tu2_9_R1.fastq.gz ZF_Tu2_9_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,28345644856.0,56465428.0,ZF Tu2 10 R1.fastq.gz,0:251 1:251,A:8023828983;C:5867289387;G:5956780834;T:8497336426;N:409226,251,251,,,8023828983,5867289387,5956780834,8497336426,409226,SRX16841660,SRS14446856,SRA1468916,Max Planck Institut|Boehm,Max Planck Institut,2,0.24302,0.00391,0.0049,0.0036,0.98766,0.99965,0.25169,0.2619,251,251,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70848,SRR20821267,SRX16840871,SRS14445862,SRP389580,PRJNA865512,TCR alpha and beta repseq,PRJNA865512,Other,TCR Repertoire sequencing raw reads TCR alpha and beta for several species,,pubmed:37344590,,,ZF 5,,strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 5|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,ZF 15 5,ZF 15 5,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP389580,,,ZF_5_01_R1.fastq.gz ZF_5_01_R2.fastq.gz ZF_5_02_R1.fastq.gz ZF_5_02_R2.fastq.gz ZF_5_03_R1.fastq.gz ZF_5_03_R2.fastq.gz ZF_5_04_R1.fastq.gz ZF_5_04_R2.fastq.gz ZF_5_05_R1.fastq.gz ZF_5_05_R2.fastq.gz ZF_5_06_R1.fastq.gz ZF_5_06_R2.fastq.gz ZF_5_07_R1.fastq.gz ZF_5_07_R2.fastq.gz ZF_5_08_R1.fastq.gz ZF_5_08_R2.fastq.gz ZF_5_09_R1.fastq.gz ZF_5_09_R2.fastq.gz ZF_5_10_R1.fastq.gz ZF_5_10_R2.fastq.gz ZF_5_11_R1.fastq.gz ZF_5_11_R2.fastq.gz ZF_5_12_R1.fastq.gz ZF_5_12_R2.fastq.gz ZF_5_13_R1.fastq.gz ZF_5_13_R2.fastq.gz ZF_5_14_R1.fastq.gz ZF_5_14_R2.fastq.gz ZF_5_15_R1.fastq.gz ZF_5_15_R2.fastq.gz ZF_5_16_R1.fastq.gz ZF_5_16_R2.fastq.gz ZF_5_17_R1.fastq.gz ZF_5_17_R2.fastq.gz ZF_5_18_R1.fastq.gz ZF_5_18_R2.fastq.gz ZF_5_19_R1.fastq.gz ZF_5_19_R2.fastq.gz ZF_5_20_R1.fastq.gz ZF_5_20_R2.fastq.gz ZF_5_21_R1.fastq.gz ZF_5_21_R2.fastq.gz ZF_5_22_R1.fastq.gz ZF_5_22_R2.fastq.gz ZF_5_23_R1.fastq.gz ZF_5_23_R2.fastq.gz ZF_5_24_R1.fastq.gz ZF_5_24_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,20320004000.0,40640008.0,ZF 5 01 R1.fastq.gz,0:250 1:250,A:5513136568;C:4158821282;G:4255839821;T:6389137086;N:3069243,250,250,,,5513136568,4158821282,4255839821,6389137086,3069243,SRX16840871,SRS14445862,SRA1468898,Max Planck Institut|Boehm,Max Planck Institut,2,0.48427,3e-05,0.0017,1e-05,0.99663,0.99997,0.55487,1.0,250,250,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70849,SRR20821266,SRX16840870,SRS14445861,SRP389580,PRJNA865512,TCR alpha and beta repseq,PRJNA865512,Other,TCR Repertoire sequencing raw reads TCR alpha and beta for several species,,pubmed:37344590,,,ZF 4,,strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 4|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,ZF 15 4,ZF 15 4,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP389580,,,ZF_4_01_R1.fastq.gz ZF_4_01_R2.fastq.gz ZF_4_02_R1.fastq.gz ZF_4_02_R2.fastq.gz ZF_4_03_R1.fastq.gz ZF_4_03_R2.fastq.gz ZF_4_04_R1.fastq.gz ZF_4_04_R2.fastq.gz ZF_4_05_R1.fastq.gz ZF_4_05_R2.fastq.gz ZF_4_06_R1.fastq.gz ZF_4_06_R2.fastq.gz ZF_4_07_R1.fastq.gz ZF_4_07_R2.fastq.gz ZF_4_08_R1.fastq.gz ZF_4_08_R2.fastq.gz ZF_4_09_R1.fastq.gz ZF_4_09_R2.fastq.gz ZF_4_10_R1.fastq.gz ZF_4_10_R2.fastq.gz ZF_4_11_R1.fastq.gz ZF_4_11_R2.fastq.gz ZF_4_12_R1.fastq.gz ZF_4_12_R2.fastq.gz ZF_4_13_R1.fastq.gz ZF_4_13_R2.fastq.gz ZF_4_14_R1.fastq.gz ZF_4_14_R2.fastq.gz ZF_4_15_R1.fastq.gz ZF_4_15_R2.fastq.gz ZF_4_16_R1.fastq.gz ZF_4_16_R2.fastq.gz ZF_4_17_R1.fastq.gz ZF_4_17_R2.fastq.gz ZF_4_18_R1.fastq.gz ZF_4_18_R2.fastq.gz ZF_4_19_R1.fastq.gz ZF_4_19_R2.fastq.gz ZF_4_20_R1.fastq.gz ZF_4_20_R2.fastq.gz ZF_4_21_R1.fastq.gz ZF_4_21_R2.fastq.gz ZF_4_22_R1.fastq.gz ZF_4_22_R2.fastq.gz ZF_4_23_R1.fastq.gz ZF_4_23_R2.fastq.gz ZF_4_24_R1.fastq.gz ZF_4_24_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,26480052500.0,52960105.0,ZF 4 01 R1.fastq.gz,0:250 1:250,A:7438425276;C:5364918772;G:5496497801;T:8176167902;N:4042749,250,250,,,7438425276,5364918772,5496497801,8176167902,4042749,SRX16840870,SRS14445861,SRA1468898,Max Planck Institut|Boehm,Max Planck Institut,2,0.21859,0.00094,0.00058,0.00078,0.99734,0.99989,0.24747,0.38095,250,250,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70850,SRR20821265,SRX16840869,SRS14445860,SRP389580,PRJNA865512,TCR alpha and beta repseq,PRJNA865512,Other,TCR Repertoire sequencing raw reads TCR alpha and beta for several species,,pubmed:37344590,,,ZF 3,,strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 3|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,ZF 15 3,ZF 15 3,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP389580,,,ZF_3_01_R1.fastq.gz ZF_3_04_R1.fastq.gz ZF_3_04_R2.fastq.gz ZF_3_05_R1.fastq.gz ZF_3_05_R2.fastq.gz ZF_3_06_R1.fastq.gz ZF_3_06_R2.fastq.gz ZF_3_07_R1.fastq.gz ZF_3_07_R2.fastq.gz ZF_3_08_R1.fastq.gz ZF_3_08_R2.fastq.gz ZF_3_09_R1.fastq.gz ZF_3_09_R2.fastq.gz ZF_3_10_R1.fastq.gz ZF_3_10_R2.fastq.gz ZF_3_11_R1.fastq.gz ZF_3_11_R2.fastq.gz ZF_3_12_R1.fastq.gz ZF_3_12_R2.fastq.gz ZF_3_13_R1.fastq.gz ZF_3_13_R2.fastq.gz ZF_3_14_R1.fastq.gz ZF_3_14_R2.fastq.gz ZF_3_15_R1.fastq.gz ZF_3_15_R2.fastq.gz ZF_3_16_R1.fastq.gz ZF_3_16_R2.fastq.gz ZF_3_17_R1.fastq.gz ZF_3_17_R2.fastq.gz ZF_3_18_R1.fastq.gz ZF_3_18_R2.fastq.gz ZF_3_19_R1.fastq.gz ZF_3_19_R2.fastq.gz ZF_3_03_R2.fastq.gz ZF_3_03_R1.fastq.gz ZF_3_02_R2.fastq.gz ZF_3_02_R1.fastq.gz ZF_3_01_R2.fastq.gz ZF_3_20_R1.fastq.gz ZF_3_20_R2.fastq.gz ZF_3_21_R1.fastq.gz ZF_3_21_R2.fastq.gz ZF_3_22_R1.fastq.gz ZF_3_22_R2.fastq.gz ZF_3_23_R1.fastq.gz ZF_3_23_R2.fastq.gz ZF_3_24_R1.fastq.gz ZF_3_24_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,29081958500.0,58163917.0,ZF 3 01 R1.fastq.gz,0:250 1:250,A:7805451909;C:6022172769;G:6087748826;T:9162169304;N:4415692,250,250,,,7805451909,6022172769,6087748826,9162169304,4415692,SRX16840869,SRS14445860,SRA1468898,Max Planck Institut|Boehm,Max Planck Institut,2,0.62325,0.00106,0.0032,0.00082,0.98957,0.99979,0.66228,0.16,250,250,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70851,SRR20821268,SRX16840868,SRS14446084,SRP389580,PRJNA865512,TCR alpha and beta repseq,PRJNA865512,Other,TCR Repertoire sequencing raw reads TCR alpha and beta for several species,,pubmed:37344590,,,ZF 2,,strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 2|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,ZF 15 2,ZF 15 2,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP389580,,,ZF_2_01_R1.fastq.gz ZF_2_01_R2.fastq.gz ZF_2_02_R1.fastq.gz ZF_2_02_R2.fastq.gz ZF_2_03_R1.fastq.gz ZF_2_03_R2.fastq.gz ZF_2_04_R1.fastq.gz ZF_2_04_R2.fastq.gz ZF_2_05_R1.fastq.gz ZF_2_05_R2.fastq.gz ZF_2_06_R1.fastq.gz ZF_2_06_R2.fastq.gz ZF_2_07_R1.fastq.gz ZF_2_07_R2.fastq.gz ZF_2_08_R1.fastq.gz ZF_2_08_R2.fastq.gz ZF_2_09_R1.fastq.gz ZF_2_09_R2.fastq.gz ZF_2_10_R1.fastq.gz ZF_2_10_R2.fastq.gz ZF_2_11_R1.fastq.gz ZF_2_11_R2.fastq.gz ZF_2_12_R1.fastq.gz ZF_2_12_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,11339660500.0,22679321.0,ZF 2 01 R1.fastq.gz,0:250 1:250,A:3182635402;C:2291052382;G:2349897358;T:3514348167;N:1727191,250,250,,,3182635402,2291052382,2349897358,3514348167,1727191,SRX16840868,SRS14446084,SRA1468898,Max Planck Institut|Boehm,Max Planck Institut,2,0.27918,0.0001,0.00045,9e-05,0.99701,1.0,0.09245,,250,250,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70852,SRR20821269,SRX16840867,SRS14416088,SRP389580,PRJNA865512,TCR alpha and beta repseq,PRJNA865512,Other,TCR Repertoire sequencing raw reads TCR alpha and beta for several species,,pubmed:37344590,,,ZF 1,,strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 1|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,ZF 15 1,ZF 15 1,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP389580,,,ZF_1_01_R1.fastq.gz ZF_1_01_R2.fastq.gz ZF_1_02_R1.fastq.gz ZF_1_02_R2.fastq.gz ZF_1_03_R1.fastq.gz ZF_1_03_R2.fastq.gz ZF_1_04_R1.fastq.gz ZF_1_04_R2.fastq.gz ZF_1_05_R1.fastq.gz ZF_1_05_R2.fastq.gz ZF_1_06_R1.fastq.gz ZF_1_06_R2.fastq.gz ZF_1_07_R1.fastq.gz ZF_1_07_R2.fastq.gz ZF_1_08_R1.fastq.gz ZF_1_08_R2.fastq.gz ZF_1_09_R1.fastq.gz ZF_1_09_R2.fastq.gz ZF_1_10_R1.fastq.gz ZF_1_10_R2.fastq.gz ZF_1_11_R1.fastq.gz ZF_1_11_R2.fastq.gz ZF_1_12_R1.fastq.gz ZF_1_12_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,11128555000.0,22257110.0,ZF 1 01 R1.fastq.gz,0:250 1:250,A:3130611303;C:2262908040;G:2314518134;T:3418822646;N:1694877,250,250,,,3130611303,2262908040,2314518134,3418822646,1694877,SRX16840867,SRS14416088,SRA1468898,Max Planck Institut|Boehm,Max Planck Institut,2,0.26276,0.0002,0.00063,0.00019,0.99669,1.0,0.16038,,250,250,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70853,SRR20821016,SRX16840621,SRS14445862,SRP389580,PRJNA865512,TCR alpha and beta repseq,PRJNA865512,Other,TCR Repertoire sequencing raw reads TCR alpha and beta for several species,,pubmed:37344590,,,ZF 5,,strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 5|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,ZF 15 5,ZF 15 5,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP389580,,,Fish_5_s1_R1.fastq.gz Fish_5_s1_R2.fastq.gz Fish_5_s2_R1.fastq.gz Fish_5_s2_R2.fastq.gz Fish_5_s3_R1.fastq.gz Fish_5_s3_R2.fastq.gz Fish_5_s4_R1.fastq.gz Fish_5_s4_R2.fastq.gz Fish_5_s5_R1.fastq.gz Fish_5_s5_R2.fastq.gz Fish_5_s6_R1.fastq.gz Fish_5_s6_R2.fastq.gz Fish_5_s7_R1.fastq.gz Fish_5_s7_R2.fastq.gz Fish_5_s8_R1.fastq.gz Fish_5_s8_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,12404050000.0,24808100.0,Fish 5 s1 R1.fastq.gz,0:250 1:250,A:3320455167;C:2599567608;G:2616971343;T:3833147517;N:33908365,250,250,,,3320455167,2599567608,2616971343,3833147517,33908365,SRX16840621,SRS14445862,SRA1468889,Max Planck Institut|Boehm,Max Planck Institut,2,0.46656,1e-05,0.00102,0.0,0.99715,1.0,0.67642,,250,250,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70854,SRR20821017,SRX16840620,SRS14445861,SRP389580,PRJNA865512,TCR alpha and beta repseq,PRJNA865512,Other,TCR Repertoire sequencing raw reads TCR alpha and beta for several species,,pubmed:37344590,,,ZF 4,,strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 4|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,ZF 15 4,ZF 15 4,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP389580,,,Fish_4_s1_R1.fastq.gz Fish_4_s1_R2.fastq.gz Fish_4_s2_R1.fastq.gz Fish_4_s2_R2.fastq.gz Fish_4_s3_R1.fastq.gz Fish_4_s3_R2.fastq.gz Fish_4_s4_R1.fastq.gz Fish_4_s4_R2.fastq.gz Fish_4_s5_R1.fastq.gz Fish_4_s5_R2.fastq.gz Fish_4_s6_R1.fastq.gz Fish_4_s6_R2.fastq.gz Fish_4_s7_R1.fastq.gz Fish_4_s7_R2.fastq.gz Fish_4_s8_R1.fastq.gz Fish_4_s8_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,14690229000.0,29380458.0,Fish 4 s1 R1.fastq.gz,0:250 1:250,A:4100988732;C:3028728956;G:3105063955;T:4415320433;N:40126924,250,250,,,4100988732,3028728956,3105063955,4415320433,40126924,SRX16840620,SRS14445861,SRA1468889,Max Planck Institut|Boehm,Max Planck Institut,2,0.20173,4e-05,9e-05,3e-05,0.99886,0.99997,0.02749,0.0,250,250,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70855,SRR20821018,SRX16840619,SRS14445860,SRP389580,PRJNA865512,TCR alpha and beta repseq,PRJNA865512,Other,TCR Repertoire sequencing raw reads TCR alpha and beta for several species,,pubmed:37344590,,,ZF 3,,strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 3|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,ZF 15 3,ZF 15 3,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP389580,,,Fish_3_s1_R1.fastq.gz Fish_3_s1_R2.fastq.gz Fish_3_s2_R1.fastq.gz Fish_3_s2_R2.fastq.gz Fish_3_s3_R1.fastq.gz Fish_3_s3_R2.fastq.gz Fish_3_s4_R1.fastq.gz Fish_3_s4_R2.fastq.gz Fish_3_s5_R1.fastq.gz Fish_3_s5_R2.fastq.gz Fish_3_s6_R1.fastq.gz Fish_3_s6_R2.fastq.gz Fish_3_s7_R1.fastq.gz Fish_3_s7_R2.fastq.gz Fish_3_s8_R1.fastq.gz Fish_3_s8_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,11142784000.0,22285568.0,Fish 3 s1 R1.fastq.gz,0:250 1:250,A:2958284498;C:2329155931;G:2358380909;T:3466617016;N:30345646,250,250,,,2958284498,2329155931,2358380909,3466617016,30345646,SRX16840619,SRS14445860,SRA1468889,Max Planck Institut|Boehm,Max Planck Institut,2,0.56406,2e-05,0.00159,1e-05,0.99868,1.0,0.67877,,250,250,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70856,SRR20821019,SRX16840618,SRS14416088,SRP389580,PRJNA865512,TCR alpha and beta repseq,PRJNA865512,Other,TCR Repertoire sequencing raw reads TCR alpha and beta for several species,,pubmed:37344590,,,ZF 1,,strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 1|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,ZF 15 1,ZF 15 1,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP389580,,,Fish_1_s1_R1.fastq.gz Fish_1_s1_R2.fastq.gz Fish_1_s2_R1.fastq.gz Fish_1_s2_R2.fastq.gz Fish_1_s3_R1.fastq.gz Fish_1_s3_R2.fastq.gz Fish_1_s4_R1.fastq.gz Fish_1_s4_R2.fastq.gz Fish_1_s5_R1.fastq.gz Fish_1_s5_R2.fastq.gz Fish_1_s6_R1.fastq.gz Fish_1_s6_R2.fastq.gz Fish_1_s7_R1.fastq.gz Fish_1_s7_R2.fastq.gz Fish_1_s8_R1.fastq.gz Fish_1_s8_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,23425111500.0,46850223.0,Fish 1 s1 R1.fastq.gz,0:250 1:250,A:6539165809;C:4856848776;G:4965848496;T:6999397120;N:63851299,250,250,,,6539165809,4856848776,4965848496,6999397120,63851299,SRX16840618,SRS14416088,SRA1468889,Max Planck Institut|Boehm,Max Planck Institut,2,0.22816,3e-05,3e-05,2e-05,0.99931,1.0,0.01795,,250,250,B,T,mate2 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70857,SRR20774919,SRX16794795,SRS14416088,SRP389580,PRJNA865512,TCR alpha and beta repseq,PRJNA865512,Other,TCR Repertoire sequencing raw reads TCR alpha and beta for several species,,pubmed:37344590,,,ZF 1,,strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 1|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,ZF 14,ZF 14,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389580,,,ZF_1_R1.fastq.gz ZF_1_R2.fastq.gz ZF_2_R1.fastq.gz ZF_2_R2.fastq.gz ZF_3_R1.fastq.gz ZF_3_R2.fastq.gz ZF_4_R1.fastq.gz ZF_4_R2.fastq.gz ZF_5_R1.fastq.gz ZF_5_R2.fastq.gz ZF_6_R1.fastq.gz ZF_6_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,2060446800.0,3434078.0,ZF 1 R1.fastq.gz,0:300 1:300,A:583057434;C:430231786;G:436041334;T:600779904;N:10336342,300,300,,,583057434,430231786,436041334,600779904,10336342,SRX16794795,SRS14416088,SRA1467929,Max Planck Institut|Boehm,Max Planck Institut,2,0.22937,0.00332,0.00094,0.00296,0.99853,0.99977,0.07993,0.34426,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-03,Adult,Adult,Trunk,Surface Structure
70858,SRR20770403,SRX16790285,SRS14416088,SRP389580,PRJNA865512,TCR alpha and beta repseq,PRJNA865512,Other,TCR Repertoire sequencing raw reads TCR alpha and beta for several species,,pubmed:37344590,,,ZF 1,,strain:Tuebingen|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:16 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 1|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,ZF 13,ZF 13,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389580,,,ZF_1_R1.fastq.gz ZF_1_R2.fastq.gz ZF_2_R1.fastq.gz ZF_2_R2.fastq.gz ZF_3_R1.fastq.gz ZF_3_R2.fastq.gz ZF_4_R1.fastq.gz ZF_4_R2.fastq.gz ZF_5_R1.fastq.gz ZF_5_R2.fastq.gz ZF_6_R1.fastq.gz ZF_6_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,404958600.0,674931.0,ZF 1 R1.fastq.gz,0:300 1:300,A:115477181;C:85168234;G:86149957;T:118163222;N:6,300,300,,,115477181,85168234,86149957,118163222,6,SRX16790285,SRS14416088,SRA1467850,Max Planck Institut|Boehm,Max Planck Institut,2,0.22832,0.00294,0.00097,0.00267,0.9987,0.99981,0.06408,0.06382,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-03,Adult,Adult,Trunk,Surface Structure
70865,SRR21025648,SRX17041895,SRS14626477,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,Cb mutant ZF,ZF B1,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Cb mutant fish 1|BioSampleModel:Model organism or animal,,,,,,,,,TCR Cbeta mutant zebrafish repertoire,ZF B1 39,ZF B1 39,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,ZF_B_1_R1.fastq.gz ZF_B_1_R2.fastq.gz,fastq fastq,542089800.0,903483.0,ZF B 1 R1.fastq.gz,0:300 1:300,A:135658810;C:102336162;G:99078828;T:137378936;N:67637064,300,300,,,135658810,102336162,99078828,137378936,67637064,SRX17041895,SRS14626477,SRA1474283,Max Planck Institut|Boehm,Max Planck Institut,2,0.12189,0.0,0.00343,0.0,0.99504,1.0,0.39007,,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-12,Adult,Adult,Trunk,Surface Structure
70866,SRR21025649,SRX17041894,SRS14626476,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,Ca mutant ZF,ZF A3,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Ca mutant fish 3|BioSampleModel:Model organism or animal,,,,,,,,,TCR Calpha mutant zebrafish repertoire,ZF A3 39,ZF A3 39,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,ZF_A_3_R1.fastq.gz ZF_A_3_R2.fastq.gz,fastq fastq,308308200.0,513847.0,ZF A 3 R1.fastq.gz,0:300 1:300,A:78000370;C:58841499;G:57272527;T:75682806;N:38510998,300,300,,,78000370,58841499,57272527,75682806,38510998,SRX17041894,SRS14626476,SRA1474283,Max Planck Institut|Boehm,Max Planck Institut,2,0.12647,0.0,0.00605,0.0,0.99492,1.0,0.53455,,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-12,Adult,Adult,Trunk,Surface Structure
70867,SRR21025650,SRX17041893,SRS14626475,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,Ca mutant ZF,ZF A2,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Ca mutant fish 2|BioSampleModel:Model organism or animal,,,,,,,,,TCR Calpha mutant zebrafish repertoire,ZF A2 39,ZF A2 39,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,ZF_A_2_R1.fastq.gz ZF_A_2_R2.fastq.gz,fastq fastq,478462200.0,797437.0,ZF A 2 R1.fastq.gz,0:300 1:300,A:121169167;C:89660025;G:88748678;T:119119069;N:59765261,300,300,,,121169167,89660025,88748678,119119069,59765261,SRX17041893,SRS14626475,SRA1474283,Max Planck Institut|Boehm,Max Planck Institut,2,0.14904,0.0,0.00506,0.0,0.995,1.0,0.41067,,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-12,Adult,Adult,Trunk,Surface Structure
70868,SRR21025651,SRX17041892,SRS14626474,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,Ca mutant ZF,ZF A1,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Ca mutant fish 1|BioSampleModel:Model organism or animal,,,,,,,,,TCR Calpha mutant zebrafish repertoire,ZF A1 39,ZF A1 39,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,ZF_A_1_R1.fastq.gz ZF_A_1_R2.fastq.gz,fastq fastq,678536400.0,1130894.0,ZF A 1 R1.fastq.gz,0:300 1:300,A:171085705;C:127441930;G:123964513;T:171506152;N:84538100,300,300,,,171085705,127441930,123964513,171506152,84538100,SRX17041892,SRS14626474,SRA1474283,Max Planck Institut|Boehm,Max Planck Institut,2,0.15972,0.0,0.00626,0.0,0.99358,1.0,0.41112,,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-12,Adult,Adult,Trunk,Surface Structure
70869,SRR21025647,SRX17041891,SRS14626540,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,Ca mutant ZF,ZF e7,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 1|BioSampleModel:Model organism or animal,,,,,,,,,TCR Calpha mutant zebrafish repertoire,ZF e7 39,ZF e7 39,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP389887,,,ZF_E7_1_R1.fastq.gz ZF_E7_1_R2.fastq.gz ZF_E7_2_R1.fastq.gz ZF_E7_2_R2.fastq.gz ZF_E7_3_R1.fastq.gz ZF_E7_3_R2.fastq.gz ZF_E7_4_R1.fastq.gz ZF_E7_4_R2.fastq.gz ZF_E7_5_R1.fastq.gz ZF_E7_5_R2.fastq.gz ZF_E7_6_R1.fastq.gz ZF_E7_6_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,3743030974.0,7456237.0,ZF E7 1 R1.fastq.gz,0:251 1:251,A:1059538576;C:756862432;G:800743054;T:1125844134;N:42778,251,251,,,1059538576,756862432,800743054,1125844134,42778,SRX17041891,SRS14626540,SRA1474280,Max Planck Institut|Boehm,Max Planck Institut,2,0.17475,4e-05,0.00048,3e-05,0.99606,1.0,0.06216,,251,251,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-12,Adult,Adult,Trunk,Surface Structure
70870,SRR21025625,SRX17041869,SRS14626540,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,Ca mutant ZF,ZF e7,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 1|BioSampleModel:Model organism or animal,,,,,,,,,TCR Calpha mutant zebrafish repertoire,ZF e7 37,ZF e7 37,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP389887,,,ZF_E7_1_R1.fastq.gz ZF_E7_1_R2.fastq.gz ZF_E7_2_R1.fastq.gz ZF_E7_2_R2.fastq.gz ZF_E7_3_R1.fastq.gz ZF_E7_3_R2.fastq.gz ZF_E7_4_R1.fastq.gz ZF_E7_4_R2.fastq.gz ZF_E7_5_R1.fastq.gz ZF_E7_5_R2.fastq.gz ZF_E7_6_R1.fastq.gz ZF_E7_6_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,6358841530.0,12667015.0,ZF E7 1 R1.fastq.gz,0:251 1:251,A:1780832978;C:1325459337;G:1324964858;T:1927430147;N:154210,251,251,,,1780832978,1325459337,1324964858,1927430147,154210,SRX17041869,SRS14626540,SRA1474264,Max Planck Institut|Boehm,Max Planck Institut,2,0.17062,0.00202,0.00036,0.00201,0.9961,1.0,0.45331,,251,251,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-12,Adult,Adult,Trunk,Surface Structure
70871,SRR21025558,SRX17041805,SRS14626477,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,Cb mutant ZF,ZF B1,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Cb mutant fish 1|BioSampleModel:Model organism or animal,,,,,,,,,TCR Cbeta mutant zebrafish repertoire,ZF B1 37,ZF B1 37,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,ZF_B_1_R1.fastq.gz ZF_B_1_R2.fastq.gz,fastq fastq,690565200.0,1150942.0,ZF B 1 R1.fastq.gz,0:300 1:300,A:190561034;C:142350146;G:136690824;T:190637972;N:30325224,300,300,,,190561034,142350146,136690824,190637972,30325224,SRX17041805,SRS14626477,SRA1474258,Max Planck Institut|Boehm,Max Planck Institut,2,0.11811,9e-05,0.00424,4e-05,0.99472,0.99995,0.43275,0.5,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-12,Adult,Adult,Trunk,Surface Structure
70872,SRR21025559,SRX17041804,SRS14626476,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,Ca mutant ZF,ZF A3,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Ca mutant fish 3|BioSampleModel:Model organism or animal,,,,,,,,,TCR Calpha mutant zebrafish repertoire,ZF A3 37,ZF A3 37,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,ZF_A_3_R1.fastq.gz ZF_A_3_R2.fastq.gz,fastq fastq,460708800.0,767848.0,ZF A 3 R1.fastq.gz,0:300 1:300,A:128444122;C:96066218;G:93502400;T:122577077;N:20118983,300,300,,,128444122,96066218,93502400,122577077,20118983,SRX17041804,SRS14626476,SRA1474258,Max Planck Institut|Boehm,Max Planck Institut,2,0.12334,8e-05,0.00785,5e-05,0.99486,0.99997,0.57556,1.0,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-12,Adult,Adult,Trunk,Surface Structure
70873,SRR21025560,SRX17041803,SRS14626475,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,Ca mutant ZF,ZF A2,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Ca mutant fish 2|BioSampleModel:Model organism or animal,,,,,,,,,TCR Calpha mutant zebrafish repertoire,ZF A2 37,ZF A2 37,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,ZF_A_2_R1.fastq.gz ZF_A_2_R2.fastq.gz,fastq fastq,665948400.0,1109914.0,ZF A 2 R1.fastq.gz,0:300 1:300,A:185901193;C:135612243;G:135145305;T:180035490;N:29254169,300,300,,,185901193,135612243,135145305,180035490,29254169,SRX17041803,SRS14626475,SRA1474258,Max Planck Institut|Boehm,Max Planck Institut,2,0.14435,0.0,0.00709,0.0,0.99429,1.0,0.46577,,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-12,Adult,Adult,Trunk,Surface Structure
70874,SRR21025561,SRX17041802,SRS14626474,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,Ca mutant ZF,ZF A1,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Ca mutant fish 1|BioSampleModel:Model organism or animal,,,,,,,,,TCR Calpha mutant zebrafish repertoire,ZF A1 37,ZF A1 37,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,ZF_A_1_R1.fastq.gz ZF_A_1_R2.fastq.gz,fastq fastq,988403400.0,1647339.0,ZF A 1 R1.fastq.gz,0:300 1:300,A:274811390;C:202503190;G:195476681;T:272202966;N:43409173,300,300,,,274811390,202503190,195476681,272202966,43409173,SRX17041802,SRS14626474,SRA1474258,Max Planck Institut|Boehm,Max Planck Institut,2,0.15605,0.0001,0.0075,6e-05,0.99304,0.99997,0.44452,0.0,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-12,Adult,Adult,Trunk,Surface Structure
70875,SRR20823554,SRX16843129,SRS14446944,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,,CF 8,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 8|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,CF 25 8,CF 25 8,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,CF_8i_1_R1.fastq.gz CF_8i_1_R2.fastq.gz CF_8i_2_R1.fastq.gz CF_8i_2_R2.fastq.gz CF_8i_3_R1.fastq.gz CF_8i_3_R2.fastq.gz CF_8i_4_R1.fastq.gz CF_8i_4_R2.fastq.gz CF_8ii_1_R1.fastq.gz CF_8ii_1_R2.fastq.gz CF_8ii_2_R1.fastq.gz CF_8ii_2_R2.fastq.gz CF_8ii_3_R1.fastq.gz CF_8ii_3_R2.fastq.gz CF_8ii_4_R1.fastq.gz CF_8ii_4_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,353982600.0,589971.0,CF 8i 1 R1.fastq.gz,0:300 1:300,A:95337236;C:72187591;G:66351347;T:119978210;N:128216,300,300,,,95337236,72187591,66351347,119978210,128216,SRX16843129,SRS14446944,SRA1468943,Max Planck Institut|Boehm,Max Planck Institut,2,0.15841,0.00021,0.00079,0.00015,0.99961,0.99995,0.44832,0.0,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70876,SRR20823555,SRX16843128,SRS14446943,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,,CF 7,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 7|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,CF 25 7,CF 25 7,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,CF_7i_1_R1.fastq.gz CF_7i_1_R2.fastq.gz CF_7i_2_R1.fastq.gz CF_7i_2_R2.fastq.gz CF_7i_3_R1.fastq.gz CF_7i_3_R2.fastq.gz CF_7i_4_R1.fastq.gz CF_7i_4_R2.fastq.gz CF_7ii_1_R1.fastq.gz CF_7ii_1_R2.fastq.gz CF_7ii_2_R1.fastq.gz CF_7ii_2_R2.fastq.gz CF_7ii_3_R1.fastq.gz CF_7ii_3_R2.fastq.gz CF_7ii_4_R1.fastq.gz CF_7ii_4_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,1747909200.0,2913182.0,CF 7i 1 R1.fastq.gz,0:300 1:300,A:483225545;C:364529202;G:366375323;T:532231673;N:1547457,300,300,,,483225545,364529202,366375323,532231673,1547457,SRX16843128,SRS14446943,SRA1468943,Max Planck Institut|Boehm,Max Planck Institut,2,0.11826,4e-05,0.00019,3e-05,0.99939,1.0,0.0663,,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70877,SRR20823556,SRX16843127,SRS14446942,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,,CF 6,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 6|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,CF 25 6,CF 25 6,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,CF_6i_1_R1.fastq.gz CF_6i_1_R2.fastq.gz CF_6i_2_R1.fastq.gz CF_6i_2_R2.fastq.gz CF_6i_3_R1.fastq.gz CF_6i_3_R2.fastq.gz CF_6i_4_R1.fastq.gz CF_6i_4_R2.fastq.gz CF_6ii_1_R1.fastq.gz CF_6ii_1_R2.fastq.gz CF_6ii_2_R1.fastq.gz CF_6ii_2_R2.fastq.gz CF_6ii_3_R1.fastq.gz CF_6ii_3_R2.fastq.gz CF_6ii_4_R1.fastq.gz CF_6ii_4_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,2113688400.0,3522814.0,CF 6i 1 R1.fastq.gz,0:300 1:300,A:584272199;C:441403541;G:441691655;T:644543652;N:1777353,300,300,,,584272199,441403541,441691655,644543652,1777353,SRX16843127,SRS14446942,SRA1468943,Max Planck Institut|Boehm,Max Planck Institut,2,0.11642,4e-05,0.00012,1e-05,0.99955,0.99997,0.05908,0.0,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70878,SRR20823557,SRX16843126,SRS14446941,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,,CF 5,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 5|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,CF 25 5,CF 25 5,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,CF_5i_1_R1.fastq.gz CF_5i_1_R2.fastq.gz CF_5i_2_R1.fastq.gz CF_5i_2_R2.fastq.gz CF_5i_3_R1.fastq.gz CF_5i_3_R2.fastq.gz CF_5i_4_R1.fastq.gz CF_5i_4_R2.fastq.gz CF_5ii_1_R1.fastq.gz CF_5ii_1_R2.fastq.gz CF_5ii_2_R1.fastq.gz CF_5ii_2_R2.fastq.gz CF_5ii_3_R1.fastq.gz CF_5ii_3_R2.fastq.gz CF_5ii_4_R1.fastq.gz CF_5ii_4_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,1563231600.0,2605386.0,CF 5i 1 R1.fastq.gz,0:300 1:300,A:431285088;C:326876454;G:326380744;T:477247162;N:1442152,300,300,,,431285088,326876454,326380744,477247162,1442152,SRX16843126,SRS14446941,SRA1468943,Max Planck Institut|Boehm,Max Planck Institut,2,0.11826,4e-05,0.00024,2e-05,0.99928,0.99997,0.20833,0.0,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70879,SRR20823558,SRX16843125,SRS14446939,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,,CF 4,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 4|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,CF 25 4,CF 25 4,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,CF_4i_1_R1.fastq.gz CF_4i_1_R2.fastq.gz CF_4i_2_R1.fastq.gz CF_4i_2_R2.fastq.gz CF_4i_3_R1.fastq.gz CF_4i_3_R2.fastq.gz CF_4i_4_R1.fastq.gz CF_4i_4_R2.fastq.gz CF_4ii_1_R1.fastq.gz CF_4ii_1_R2.fastq.gz CF_4ii_2_R1.fastq.gz CF_4ii_2_R2.fastq.gz CF_4ii_3_R1.fastq.gz CF_4ii_3_R2.fastq.gz CF_4ii_4_R1.fastq.gz CF_4ii_4_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,2110654800.0,3517758.0,CF 4i 1 R1.fastq.gz,0:300 1:300,A:583907147;C:441977681;G:442168609;T:640843429;N:1757934,300,300,,,583907147,441977681,442168609,640843429,1757934,SRX16843125,SRS14446939,SRA1468943,Max Planck Institut|Boehm,Max Planck Institut,2,0.09992,3e-05,0.00029,2e-05,0.99922,1.0,0.06198,,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70880,SRR20823559,SRX16843124,SRS14446940,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,,CF 3,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 3|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,CF 25 3,CF 25 3,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,CF_3i_1_R1.fastq.gz CF_3i_1_R2.fastq.gz CF_3i_2_R1.fastq.gz CF_3i_2_R2.fastq.gz CF_3i_3_R1.fastq.gz CF_3i_3_R2.fastq.gz CF_3i_4_R1.fastq.gz CF_3i_4_R2.fastq.gz CF_3ii_1_R1.fastq.gz CF_3ii_1_R2.fastq.gz CF_3ii_2_R1.fastq.gz CF_3ii_2_R2.fastq.gz CF_3ii_3_R1.fastq.gz CF_3ii_3_R2.fastq.gz CF_3ii_4_R1.fastq.gz CF_3ii_4_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,1358656200.0,2264427.0,CF 3i 1 R1.fastq.gz,0:300 1:300,A:373530868;C:285820823;G:282903019;T:415201895;N:1199595,300,300,,,373530868,285820823,282903019,415201895,1199595,SRX16843124,SRS14446940,SRA1468943,Max Planck Institut|Boehm,Max Planck Institut,2,0.13469,7e-05,0.00024,4e-05,0.9992,0.99997,0.09944,0.0,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70881,SRR20823560,SRX16843123,SRS14446938,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,,CF 2,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 2|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,CF 25 2,CF 25 2,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,CF_1_2ii_5_R1.fastq.gz CF_1_2ii_5_R2.fastq.gz CF_1_2ii_6_R1.fastq.gz CF_1_2ii_6_R2.fastq.gz CF_1_2ii_7_R1.fastq.gz CF_1_2ii_7_R2.fastq.gz CF_1_2ii_8_R1.fastq.gz CF_1_2ii_8_R2.fastq.gz CF_2i_1_R1.fastq.gz CF_2i_1_R2.fastq.gz CF_2i_2_R1.fastq.gz CF_2i_2_R2.fastq.gz CF_2i_3_R1.fastq.gz CF_2i_3_R2.fastq.gz CF_2i_4_R1.fastq.gz CF_2i_4_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,1017871200.0,1696452.0,CF 1 2ii 5 R1.fastq.gz,0:300 1:300,A:281361148;C:213220413;G:212347028;T:310111745;N:830866,300,300,,,281361148,213220413,212347028,310111745,830866,SRX16843123,SRS14446938,SRA1468943,Max Planck Institut|Boehm,Max Planck Institut,2,0.13088,5e-05,0.00029,3e-05,0.99949,0.99997,0.11499,0.0,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70882,SRR20823561,SRX16843122,SRS14446937,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,,CF 1,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 1|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,CF 25 1,CF 25 1,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,CF_1_2ii_1_R1.fastq.gz CF_1_2ii_1_R2.fastq.gz CF_1_2ii_2_R1.fastq.gz CF_1_2ii_2_R2.fastq.gz CF_1_2ii_3_R1.fastq.gz CF_1_2ii_3_R2.fastq.gz CF_1_2ii_4_R1.fastq.gz CF_1_2ii_4_R2.fastq.gz CF_1i_1_R1.fastq.gz CF_1i_1_R2.fastq.gz CF_1i_2_R1.fastq.gz CF_1i_2_R2.fastq.gz CF_1i_3_R1.fastq.gz CF_1i_3_R2.fastq.gz CF_1i_4_R1.fastq.gz CF_1i_4_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,725888400.0,1209814.0,CF 1 2ii 1 R1.fastq.gz,0:300 1:300,A:200725177;C:151940953;G:151616803;T:220966635;N:638832,300,300,,,200725177,151940953,151616803,220966635,638832,SRX16843122,SRS14446937,SRA1468943,Max Planck Institut|Boehm,Max Planck Institut,2,0.12857,4e-05,0.0002,2e-05,0.99937,0.99995,0.05962,0.0,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70883,SRR20822140,SRX16841749,SRS14446944,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,,CF 8,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 8|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,CF 23 8,CF 23 8,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,CF_8i_1_R1.fastq.gz CF_8i_1_R2.fastq.gz CF_8i_2_R1.fastq.gz CF_8i_2_R2.fastq.gz CF_8i_3_R1.fastq.gz CF_8i_3_R2.fastq.gz CF_8i_4_R1.fastq.gz CF_8i_4_R2.fastq.gz CF_8ii_1_R1.fastq.gz CF_8ii_1_R2.fastq.gz CF_8ii_2_R1.fastq.gz CF_8ii_2_R2.fastq.gz CF_8ii_3_R1.fastq.gz CF_8ii_3_R2.fastq.gz CF_8ii_4_R1.fastq.gz CF_8ii_4_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,992400.0,1654.0,CF 8i 1 R1.fastq.gz,0:300 1:300,A:268792;C:212596;G:195943;T:315027;N:42,300,300,,,268792,212596,195943,315027,42,SRX16841749,SRS14446944,SRA1468924,Max Planck Institut|Boehm,Max Planck Institut,2,0.15462,0.04181,0.0,0.03858,0.99995,0.99997,0.62809,0.0,300,300,B,T,mate2 technical by mapping diff,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70884,SRR20822141,SRX16841748,SRS14446943,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,,CF 7,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 7|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,CF 23 7,CF 23 7,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,CF_7i_1_R1.fastq.gz CF_7i_1_R2.fastq.gz CF_7i_2_R1.fastq.gz CF_7i_2_R2.fastq.gz CF_7i_3_R1.fastq.gz CF_7i_3_R2.fastq.gz CF_7i_4_R1.fastq.gz CF_7i_4_R2.fastq.gz CF_7ii_1_R1.fastq.gz CF_7ii_1_R2.fastq.gz CF_7ii_2_R1.fastq.gz CF_7ii_2_R2.fastq.gz CF_7ii_3_R1.fastq.gz CF_7ii_3_R2.fastq.gz CF_7ii_4_R1.fastq.gz CF_7ii_4_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,90294000.0,150490.0,CF 7i 1 R1.fastq.gz,0:300 1:300,A:24528989;C:19392684;G:18743775;T:27623730;N:4822,300,300,,,24528989,19392684,18743775,27623730,4822,SRX16841748,SRS14446943,SRA1468924,Max Planck Institut|Boehm,Max Planck Institut,2,0.07466,2e-05,0.00014,1e-05,0.99979,1.0,0.07443,,300,300,T,T,mates < 9% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70885,SRR20822142,SRX16841747,SRS14446942,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,,CF 6,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 6|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,CF 23 6,CF 23 6,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,CF_6i_1_R1.fastq.gz CF_6i_1_R2.fastq.gz CF_6i_2_R1.fastq.gz CF_6i_2_R2.fastq.gz CF_6i_3_R1.fastq.gz CF_6i_3_R2.fastq.gz CF_6i_4_R1.fastq.gz CF_6i_4_R2.fastq.gz CF_6ii_1_R1.fastq.gz CF_6ii_1_R2.fastq.gz CF_6ii_2_R1.fastq.gz CF_6ii_2_R2.fastq.gz CF_6ii_3_R1.fastq.gz CF_6ii_3_R2.fastq.gz CF_6ii_4_R1.fastq.gz CF_6ii_4_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,88349400.0,147249.0,CF 6i 1 R1.fastq.gz,0:300 1:300,A:23979442;C:18990541;G:18286837;T:27088540;N:4040,300,300,,,23979442,18990541,18286837,27088540,4040,SRX16841747,SRS14446942,SRA1468924,Max Planck Institut|Boehm,Max Planck Institut,2,0.07,1e-05,0.00013,0.0,0.99967,1.0,0.08186,,300,300,T,T,mates < 9% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70886,SRR20822143,SRX16841746,SRS14446941,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,,CF 5,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 5|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,CF 23 5,CF 23 5,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,CF_5i_1_R1.fastq.gz CF_5i_1_R2.fastq.gz CF_5i_2_R1.fastq.gz CF_5i_2_R2.fastq.gz CF_5i_3_R1.fastq.gz CF_5i_3_R2.fastq.gz CF_5i_4_R1.fastq.gz CF_5i_4_R2.fastq.gz CF_5ii_1_R1.fastq.gz CF_5ii_1_R2.fastq.gz CF_5ii_2_R1.fastq.gz CF_5ii_2_R2.fastq.gz CF_5ii_3_R1.fastq.gz CF_5ii_3_R2.fastq.gz CF_5ii_4_R1.fastq.gz CF_5ii_4_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,64482600.0,107471.0,CF 5i 1 R1.fastq.gz,0:300 1:300,A:17454099;C:13879333;G:13325003;T:19821371;N:2794,300,300,,,17454099,13879333,13325003,19821371,2794,SRX16841746,SRS14446941,SRA1468924,Max Planck Institut|Boehm,Max Planck Institut,2,0.06999,4e-05,0.00066,3e-05,0.99971,1.0,0.34418,,300,300,T,T,mates < 9% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70887,SRR20822144,SRX16841745,SRS14446939,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,,CF 4,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 4|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,CF 23 4,CF 23 4,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,CF_4i_1_R1.fastq.gz CF_4i_1_R2.fastq.gz CF_4i_2_R1.fastq.gz CF_4i_2_R2.fastq.gz CF_4i_3_R1.fastq.gz CF_4i_3_R2.fastq.gz CF_4i_4_R1.fastq.gz CF_4i_4_R2.fastq.gz CF_4ii_1_R1.fastq.gz CF_4ii_1_R2.fastq.gz CF_4ii_2_R1.fastq.gz CF_4ii_2_R2.fastq.gz CF_4ii_3_R1.fastq.gz CF_4ii_3_R2.fastq.gz CF_4ii_4_R1.fastq.gz CF_4ii_4_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,89868600.0,149781.0,CF 4i 1 R1.fastq.gz,0:300 1:300,A:24387218;C:19355528;G:18593888;T:27527119;N:4847,300,300,,,24387218,19355528,18593888,27527119,4847,SRX16841745,SRS14446939,SRA1468924,Max Planck Institut|Boehm,Max Planck Institut,2,0.04754,1e-05,0.00033,0.0,0.99939,1.0,0.10674,,300,300,T,T,mates < 9% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70888,SRR20822145,SRX16841744,SRS14446940,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,,CF 3,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 3|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,CF 23 3,CF 23 3,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,CF_3i_1_R1.fastq.gz CF_3i_1_R2.fastq.gz CF_3i_2_R1.fastq.gz CF_3i_2_R2.fastq.gz CF_3i_3_R1.fastq.gz CF_3i_3_R2.fastq.gz CF_3i_4_R1.fastq.gz CF_3i_4_R2.fastq.gz CF_3ii_1_R1.fastq.gz CF_3ii_1_R2.fastq.gz CF_3ii_2_R1.fastq.gz CF_3ii_2_R2.fastq.gz CF_3ii_3_R1.fastq.gz CF_3ii_3_R2.fastq.gz CF_3ii_4_R1.fastq.gz CF_3ii_4_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,57636000.0,96060.0,CF 3i 1 R1.fastq.gz,0:300 1:300,A:15535821;C:12511228;G:11909225;T:17677153;N:2573,300,300,,,15535821,12511228,11909225,17677153,2573,SRX16841744,SRS14446940,SRA1468924,Max Planck Institut|Boehm,Max Planck Institut,2,0.08313,3e-05,0.00034,1e-05,0.99979,0.99997,0.14815,0.0,300,300,T,T,mates < 9% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70889,SRR20822146,SRX16841743,SRS14446938,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,,CF 2,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 2|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,CF 23 2,CF 23 2,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,CF_1_2ii_5_R1.fastq.gz CF_1_2ii_5_R2.fastq.gz CF_1_2ii_6_R1.fastq.gz CF_1_2ii_6_R2.fastq.gz CF_1_2ii_7_R1.fastq.gz CF_1_2ii_7_R2.fastq.gz CF_1_2ii_8_R1.fastq.gz CF_1_2ii_8_R2.fastq.gz CF_2i_1_R1.fastq.gz CF_2i_1_R2.fastq.gz CF_2i_2_R1.fastq.gz CF_2i_2_R2.fastq.gz CF_2i_3_R1.fastq.gz CF_2i_3_R2.fastq.gz CF_2i_4_R1.fastq.gz CF_2i_4_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,45198000.0,75330.0,CF 1 2ii 5 R1.fastq.gz,0:300 1:300,A:12248161;C:9753570;G:9327745;T:13866741;N:1783,300,300,,,12248161,9753570,9327745,13866741,1783,SRX16841743,SRS14446938,SRA1468924,Max Planck Institut|Boehm,Max Planck Institut,2,0.07225,0.0,0.00046,0.0,0.99981,1.0,0.19253,,300,300,T,T,mates < 9% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
70890,SRR20822147,SRX16841742,SRS14446937,SRP389887,PRJNA865921,Zebrafish mutant TCR alpha and beta lines,PRJNA865921,Other,Cas9 generated TCR alpha or beta Zebrafish lines,,pubmed:37344590,,,CF 1,,strain:TLEK|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:6 month|dev stage:adult|sex:missing|tissue:whole body|replicate:Zebrafish 1|BioSampleModel:Model organism or animal,,,,,,,,,TCRab zebrafish repertoire,CF 23 1,CF 23 1,Repertoire amplification from cDNA  with C specific primers for TCRa and TCRb,,,AMPLICON,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP389887,,,CF_1_2ii_1_R1.fastq.gz CF_1_2ii_1_R2.fastq.gz CF_1_2ii_2_R1.fastq.gz CF_1_2ii_2_R2.fastq.gz CF_1_2ii_3_R1.fastq.gz CF_1_2ii_3_R2.fastq.gz CF_1_2ii_4_R1.fastq.gz CF_1_2ii_4_R2.fastq.gz CF_1i_1_R1.fastq.gz CF_1i_1_R2.fastq.gz CF_1i_2_R1.fastq.gz CF_1i_2_R2.fastq.gz CF_1i_3_R1.fastq.gz CF_1i_3_R2.fastq.gz CF_1i_4_R1.fastq.gz CF_1i_4_R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,33274200.0,55457.0,CF 1 2ii 1 R1.fastq.gz,0:300 1:300,A:9021097;C:7171844;G:6860950;T:10218627;N:1682,300,300,,,9021097,7171844,6860950,10218627,1682,SRX16841742,SRS14446937,SRA1468924,Max Planck Institut|Boehm,Max Planck Institut,2,0.06705,3e-05,0.00012,2e-05,0.99987,1.0,0.11281,,300,300,T,T,mates < 9% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Germany,2022-08-04,Adult,Adult,Trunk,Surface Structure
76317,SRR24827620,SRX20592547,SRS17893040,SRP441132,PRJNA980117,Sex blind: bridging the gap between drug exposure and sex related gene expression in Danio rerio using next generation sequencing NGS data and a literature review to find the missing links in pharmaceutical and environmental toxicology studies,GSE234104,Transcriptome Analysis,Abstract: The sex of both humans and Danio rerio has previously been shown to affect the way individuals respond to drug exposure. Genes which allow identification of sex in juvenile zebrafish show potential to reveal these confounding variables between sex in toxicological and preclinical trials but the link between these is so far missing. These sex specific  early expressed genes where expression is not altered by drug exposure must be carefully selected for this purpose. We aimed to discover genes which can be used in pharmaceutical trials and environmental toxicology studies to uncover sex related variations in gene expression with drug application using the model organism Danio rerio. Previously published early sex determining genes from King et al. were evaluated as well as additional genes selected from our zebrafish Next generation sequencing NGS data which are known from previously published works not to be susceptible to changes in expression with drug exposure. NGS revealed a further ten female specific genes vtg1  cyp17a1  cyp19a1a  igf3  ftz f1  gdf9  foxl2a  Nr0b1  ipo4  lhcgr and five male related candidate genes FKBP5  apobb1  hbaa1  dmrt1  spata6 which are also expressed in juvenile zebrafish  28 dpf dpf. Following this  a literature review was performed to classify which of these early expressed sex specific genes are already known to be affected by drug exposure in order to determine candidate genes to be used in pharmaceutical trials or environmental toxicology testing studies. Discovery of these early sex determining genes in Danio rerio will allow identification of sex related responses to drug testing to improve sex specific healthcare and the medical treatment of human patients. Overall design: NGS RNA sequences were produced from two 28 dpf zebrafish which we classified as juvenile in this paper  two adult male and two adult female zebrafish using whole body tissue samples. Juveniles were tested to indicate whether sex was genetically visible at this stage of development. RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF  Basel  according to Illumina's standard protocol for RNA sequencing Illumina Inc.  San Diego  USA  Cat. # RS 100 0801. The NGS transcript data of the sampled zebrafish were compared to identify possible genes that contribute to sex determination as well as those which are expressed early in juvenile development  28dpf King et al.  2020. All data analyses steps were carried out using the Galaxy server usegalaxy.org Jalili et al.  2020. Data from transcript sequencing was mapped to the GRCz11 reference genome GCA 000002035.4 using HISAT2 Galaxy Version 2.1.0+galaxy4 Kim et al.  2019. Transcripts were assembled and merged from the mapped reads with StringTie Galaxy Version 1.3.4 Pertea et al.  2015. post determining gene expression with featureCount Galaxy Version 1.6.3+galaxy2  the NGS data was normalised and differential gene expression analysis of juvenile  male and female zebrafish was carried out using DESeq2 Galaxy Version 2.11.40.2 Love et al.  2014; King et al.  2020. Normalisation was based on the 'median of ratios'   the counts divided by sample specific size factors determined by median ratio of gene counts relative to geometric mean per gene  to account for sequencing depth and RNA composition. This allowed us to produce a table of gene expression which highlighted genes with the highest transcript count difference between males and females. From this data  genes expressed at juvenile stage 28dpf which were also expressed highly in male or female samples were selected as the best gene candidates for indicating early sex identity of zebrafish. Four male Sox9a  Gapdhs  atp1b1a and cyp26b1 and nine female genes gyg1a  rdh10b  pdia  KPNA2  ccnb1  ctsla  Chr4  bmp15 and zbp3 which were previously identified as an early sex determining marker in zebrafish King et al.  2020 were used within a literature search to access previous information as to whether their level of expression was known to be influenced by certain drugs. In this study a further ten female and five male genes  which could be used in early sex determination were selected from NGS data. A literature search was also carried out on these genes to discover if they were known to be affected by drug usage. Based on published literature from ScienceDirect in early 2021  we obtained information previous studies from the past twenty years by searching for the key terms; including the gene name  drug or pharmaceutical exposure  sex  or gender influence. Then  we eliminated irrelevant literature by reading the titles and abstracts and supplemented our literature database by reading the references of the selected studies. We used the selected literature to inform whether genes highlighted from our NGS data as early expressed within juveniles could be candidates in drug trials. Finally  we grouped early expressed genes from NGS data based on the literature search into three categories. If the study was shown to affect the expression of the selected genes  then they were deemed not good to use in pharmaceutical trials. Conversely  if it was not known from previous research that drugs affect the expression of a certain gene  it was included as a potential candidate for revealing how sex response differs with drug exposure and further investigation of its use in this area is necessary in future research.,,pubmed:37398910,,Adult female Danio rerio 1,GSM7445820,,source name:Whole body|tissue:Whole body|cell type:female|developmental stage:Adult|treatment:N/A|geo loc name:missing|collection date:missing,Adult female Danio rerio 1,All data analyses steps were carried out using the Galaxy server usegalaxy.org Jalili et al.  2020. Data from transcript sequencing was mapped to the GRCz11 reference genome GCA 000002035.4 using HISAT2 Galaxy Version 2.1.0+galaxy4 Kim et al.  2019. Transcripts were assembled and merged from the mapped reads with StringTie Galaxy Version 1.3.4 Pertea et al.  2015. post determining gene expression with featureCount Galaxy Version 1.6.3+galaxy2  the NGS data was normalised and differential gene expression analysis of juvenile  male and female zebrafish was carried out using DESeq2 Galaxy Version 2.11.40.2 Love et al.  2014; King et al.  2020. Normalisation was based on the ‘median of ratios’   the counts divided by sample specific size factors determined by median ratio of gene counts relative to geometric mean per gene  to account for sequencing depth and RNA composition. This allowed us to produce a table of gene expression which highlighted genes with the highest transcript count difference between males and females. From this data  genes expressed at juvenile stage 28dpf which were also expressed highly in male or female samples were selected as the best gene candidates for indicating early sex identity of zebrafish. Assembly: StringTie Galaxy Version 1.3.4 Pertea et al.  2015. Supplementary files format and content: Tables of gene expression,Whole body,No experiments were carried out with live adult nor subadult fish before euthanasia. Accordingly  animal welfare guidelines were followed while zebrafish were kept by the breeder.,RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF  Basel  according to Illumina’s standard protocol for RNA sequencing Illumina Inc.  San Diego  USA  Cat. # RS 100 0801. Galaxy server usegalaxy.org,NGS data was collected from 28 dpf and adult zebrafish  which had already been euthanised with Tricaine by the breeder.,tissue:Whole body|cell type:female|developmental stage:Adult|treatment:N/A,GSM7445820,GSM7445820: Adult female Danio rerio 1; Danio rerio; RNA Seq,GSM7445820 r1,GSM7445820,1,RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF  Basel  according to Illumina's standard protocol for RNA sequencing Illumina Inc.  San Diego  USA  Cat. # RS 100 0801. Galaxy server usegalaxy.org,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP441132,,loader:fastq load.py,adult_female1.trim.fastq.gz,fastq,6960942447.0,92399725.0,GSM7445820 r1,0:75.34,A:1696472126;C:1707300560;G:1688891841;T:1868259357;N:18563,75,,,,1696472126,1707300560,1688891841,1868259357,18563,SRX20592547,SRS17893040,SRA1649389,"Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland","Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland",1,0.96065,,0.03687,,0.70378,,0.4269,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Switzerland,2023-06-05,Adult,Adult,Trunk,Surface Structure
76318,SRR24827621,SRX20592546,SRS17893038,SRP441132,PRJNA980117,Sex blind: bridging the gap between drug exposure and sex related gene expression in Danio rerio using next generation sequencing NGS data and a literature review to find the missing links in pharmaceutical and environmental toxicology studies,GSE234104,Transcriptome Analysis,Abstract: The sex of both humans and Danio rerio has previously been shown to affect the way individuals respond to drug exposure. Genes which allow identification of sex in juvenile zebrafish show potential to reveal these confounding variables between sex in toxicological and preclinical trials but the link between these is so far missing. These sex specific  early expressed genes where expression is not altered by drug exposure must be carefully selected for this purpose. We aimed to discover genes which can be used in pharmaceutical trials and environmental toxicology studies to uncover sex related variations in gene expression with drug application using the model organism Danio rerio. Previously published early sex determining genes from King et al. were evaluated as well as additional genes selected from our zebrafish Next generation sequencing NGS data which are known from previously published works not to be susceptible to changes in expression with drug exposure. NGS revealed a further ten female specific genes vtg1  cyp17a1  cyp19a1a  igf3  ftz f1  gdf9  foxl2a  Nr0b1  ipo4  lhcgr and five male related candidate genes FKBP5  apobb1  hbaa1  dmrt1  spata6 which are also expressed in juvenile zebrafish  28 dpf dpf. Following this  a literature review was performed to classify which of these early expressed sex specific genes are already known to be affected by drug exposure in order to determine candidate genes to be used in pharmaceutical trials or environmental toxicology testing studies. Discovery of these early sex determining genes in Danio rerio will allow identification of sex related responses to drug testing to improve sex specific healthcare and the medical treatment of human patients. Overall design: NGS RNA sequences were produced from two 28 dpf zebrafish which we classified as juvenile in this paper  two adult male and two adult female zebrafish using whole body tissue samples. Juveniles were tested to indicate whether sex was genetically visible at this stage of development. RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF  Basel  according to Illumina's standard protocol for RNA sequencing Illumina Inc.  San Diego  USA  Cat. # RS 100 0801. The NGS transcript data of the sampled zebrafish were compared to identify possible genes that contribute to sex determination as well as those which are expressed early in juvenile development  28dpf King et al.  2020. All data analyses steps were carried out using the Galaxy server usegalaxy.org Jalili et al.  2020. Data from transcript sequencing was mapped to the GRCz11 reference genome GCA 000002035.4 using HISAT2 Galaxy Version 2.1.0+galaxy4 Kim et al.  2019. Transcripts were assembled and merged from the mapped reads with StringTie Galaxy Version 1.3.4 Pertea et al.  2015. post determining gene expression with featureCount Galaxy Version 1.6.3+galaxy2  the NGS data was normalised and differential gene expression analysis of juvenile  male and female zebrafish was carried out using DESeq2 Galaxy Version 2.11.40.2 Love et al.  2014; King et al.  2020. Normalisation was based on the 'median of ratios'   the counts divided by sample specific size factors determined by median ratio of gene counts relative to geometric mean per gene  to account for sequencing depth and RNA composition. This allowed us to produce a table of gene expression which highlighted genes with the highest transcript count difference between males and females. From this data  genes expressed at juvenile stage 28dpf which were also expressed highly in male or female samples were selected as the best gene candidates for indicating early sex identity of zebrafish. Four male Sox9a  Gapdhs  atp1b1a and cyp26b1 and nine female genes gyg1a  rdh10b  pdia  KPNA2  ccnb1  ctsla  Chr4  bmp15 and zbp3 which were previously identified as an early sex determining marker in zebrafish King et al.  2020 were used within a literature search to access previous information as to whether their level of expression was known to be influenced by certain drugs. In this study a further ten female and five male genes  which could be used in early sex determination were selected from NGS data. A literature search was also carried out on these genes to discover if they were known to be affected by drug usage. Based on published literature from ScienceDirect in early 2021  we obtained information previous studies from the past twenty years by searching for the key terms; including the gene name  drug or pharmaceutical exposure  sex  or gender influence. Then  we eliminated irrelevant literature by reading the titles and abstracts and supplemented our literature database by reading the references of the selected studies. We used the selected literature to inform whether genes highlighted from our NGS data as early expressed within juveniles could be candidates in drug trials. Finally  we grouped early expressed genes from NGS data based on the literature search into three categories. If the study was shown to affect the expression of the selected genes  then they were deemed not good to use in pharmaceutical trials. Conversely  if it was not known from previous research that drugs affect the expression of a certain gene  it was included as a potential candidate for revealing how sex response differs with drug exposure and further investigation of its use in this area is necessary in future research.,,pubmed:37398910,,Adult male Danio rerio 2,GSM7445819,,source name:Whole body|tissue:Whole body|cell type:male|developmental stage:Adult|treatment:N/A|geo loc name:missing|collection date:missing,Adult male Danio rerio 2,All data analyses steps were carried out using the Galaxy server usegalaxy.org Jalili et al.  2020. Data from transcript sequencing was mapped to the GRCz11 reference genome GCA 000002035.4 using HISAT2 Galaxy Version 2.1.0+galaxy4 Kim et al.  2019. Transcripts were assembled and merged from the mapped reads with StringTie Galaxy Version 1.3.4 Pertea et al.  2015. post determining gene expression with featureCount Galaxy Version 1.6.3+galaxy2  the NGS data was normalised and differential gene expression analysis of juvenile  male and female zebrafish was carried out using DESeq2 Galaxy Version 2.11.40.2 Love et al.  2014; King et al.  2020. Normalisation was based on the ‘median of ratios’   the counts divided by sample specific size factors determined by median ratio of gene counts relative to geometric mean per gene  to account for sequencing depth and RNA composition. This allowed us to produce a table of gene expression which highlighted genes with the highest transcript count difference between males and females. From this data  genes expressed at juvenile stage 28dpf which were also expressed highly in male or female samples were selected as the best gene candidates for indicating early sex identity of zebrafish. Assembly: StringTie Galaxy Version 1.3.4 Pertea et al.  2015. Supplementary files format and content: Tables of gene expression,Whole body,No experiments were carried out with live adult nor subadult fish before euthanasia. Accordingly  animal welfare guidelines were followed while zebrafish were kept by the breeder.,RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF  Basel  according to Illumina’s standard protocol for RNA sequencing Illumina Inc.  San Diego  USA  Cat. # RS 100 0801. Galaxy server usegalaxy.org,NGS data was collected from 28 dpf and adult zebrafish  which had already been euthanised with Tricaine by the breeder.,tissue:Whole body|cell type:male|developmental stage:Adult|treatment:N/A,GSM7445819,GSM7445819: Adult male Danio rerio 2; Danio rerio; RNA Seq,GSM7445819 r1,GSM7445819,1,RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF  Basel  according to Illumina's standard protocol for RNA sequencing Illumina Inc.  San Diego  USA  Cat. # RS 100 0801. Galaxy server usegalaxy.org,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP441132,,loader:fastq load.py,adult_male2.fastq.gz,fastq,6427348500.0,84570375.0,GSM7445819 r1,0:76,A:1545286842;C:1577518751;G:1546293475;T:1758222296;N:27136,76,,,,1545286842,1577518751,1546293475,1758222296,27136,SRX20592546,SRS17893038,SRA1649389,"Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland","Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland",1,0.96097,,0.05997,,0.67892,,0.50309,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Switzerland,2023-06-05,Adult,Adult,Trunk,Surface Structure
76319,SRR24827622,SRX20592545,SRS17893037,SRP441132,PRJNA980117,Sex blind: bridging the gap between drug exposure and sex related gene expression in Danio rerio using next generation sequencing NGS data and a literature review to find the missing links in pharmaceutical and environmental toxicology studies,GSE234104,Transcriptome Analysis,Abstract: The sex of both humans and Danio rerio has previously been shown to affect the way individuals respond to drug exposure. Genes which allow identification of sex in juvenile zebrafish show potential to reveal these confounding variables between sex in toxicological and preclinical trials but the link between these is so far missing. These sex specific  early expressed genes where expression is not altered by drug exposure must be carefully selected for this purpose. We aimed to discover genes which can be used in pharmaceutical trials and environmental toxicology studies to uncover sex related variations in gene expression with drug application using the model organism Danio rerio. Previously published early sex determining genes from King et al. were evaluated as well as additional genes selected from our zebrafish Next generation sequencing NGS data which are known from previously published works not to be susceptible to changes in expression with drug exposure. NGS revealed a further ten female specific genes vtg1  cyp17a1  cyp19a1a  igf3  ftz f1  gdf9  foxl2a  Nr0b1  ipo4  lhcgr and five male related candidate genes FKBP5  apobb1  hbaa1  dmrt1  spata6 which are also expressed in juvenile zebrafish  28 dpf dpf. Following this  a literature review was performed to classify which of these early expressed sex specific genes are already known to be affected by drug exposure in order to determine candidate genes to be used in pharmaceutical trials or environmental toxicology testing studies. Discovery of these early sex determining genes in Danio rerio will allow identification of sex related responses to drug testing to improve sex specific healthcare and the medical treatment of human patients. Overall design: NGS RNA sequences were produced from two 28 dpf zebrafish which we classified as juvenile in this paper  two adult male and two adult female zebrafish using whole body tissue samples. Juveniles were tested to indicate whether sex was genetically visible at this stage of development. RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF  Basel  according to Illumina's standard protocol for RNA sequencing Illumina Inc.  San Diego  USA  Cat. # RS 100 0801. The NGS transcript data of the sampled zebrafish were compared to identify possible genes that contribute to sex determination as well as those which are expressed early in juvenile development  28dpf King et al.  2020. All data analyses steps were carried out using the Galaxy server usegalaxy.org Jalili et al.  2020. Data from transcript sequencing was mapped to the GRCz11 reference genome GCA 000002035.4 using HISAT2 Galaxy Version 2.1.0+galaxy4 Kim et al.  2019. Transcripts were assembled and merged from the mapped reads with StringTie Galaxy Version 1.3.4 Pertea et al.  2015. post determining gene expression with featureCount Galaxy Version 1.6.3+galaxy2  the NGS data was normalised and differential gene expression analysis of juvenile  male and female zebrafish was carried out using DESeq2 Galaxy Version 2.11.40.2 Love et al.  2014; King et al.  2020. Normalisation was based on the 'median of ratios'   the counts divided by sample specific size factors determined by median ratio of gene counts relative to geometric mean per gene  to account for sequencing depth and RNA composition. This allowed us to produce a table of gene expression which highlighted genes with the highest transcript count difference between males and females. From this data  genes expressed at juvenile stage 28dpf which were also expressed highly in male or female samples were selected as the best gene candidates for indicating early sex identity of zebrafish. Four male Sox9a  Gapdhs  atp1b1a and cyp26b1 and nine female genes gyg1a  rdh10b  pdia  KPNA2  ccnb1  ctsla  Chr4  bmp15 and zbp3 which were previously identified as an early sex determining marker in zebrafish King et al.  2020 were used within a literature search to access previous information as to whether their level of expression was known to be influenced by certain drugs. In this study a further ten female and five male genes  which could be used in early sex determination were selected from NGS data. A literature search was also carried out on these genes to discover if they were known to be affected by drug usage. Based on published literature from ScienceDirect in early 2021  we obtained information previous studies from the past twenty years by searching for the key terms; including the gene name  drug or pharmaceutical exposure  sex  or gender influence. Then  we eliminated irrelevant literature by reading the titles and abstracts and supplemented our literature database by reading the references of the selected studies. We used the selected literature to inform whether genes highlighted from our NGS data as early expressed within juveniles could be candidates in drug trials. Finally  we grouped early expressed genes from NGS data based on the literature search into three categories. If the study was shown to affect the expression of the selected genes  then they were deemed not good to use in pharmaceutical trials. Conversely  if it was not known from previous research that drugs affect the expression of a certain gene  it was included as a potential candidate for revealing how sex response differs with drug exposure and further investigation of its use in this area is necessary in future research.,,pubmed:37398910,,Adult male Danio rerio 1,GSM7445818,,source name:Whole body|tissue:Whole body|cell type:male|developmental stage:Adult|treatment:N/A|geo loc name:missing|collection date:missing,Adult male Danio rerio 1,All data analyses steps were carried out using the Galaxy server usegalaxy.org Jalili et al.  2020. Data from transcript sequencing was mapped to the GRCz11 reference genome GCA 000002035.4 using HISAT2 Galaxy Version 2.1.0+galaxy4 Kim et al.  2019. Transcripts were assembled and merged from the mapped reads with StringTie Galaxy Version 1.3.4 Pertea et al.  2015. post determining gene expression with featureCount Galaxy Version 1.6.3+galaxy2  the NGS data was normalised and differential gene expression analysis of juvenile  male and female zebrafish was carried out using DESeq2 Galaxy Version 2.11.40.2 Love et al.  2014; King et al.  2020. Normalisation was based on the ‘median of ratios’   the counts divided by sample specific size factors determined by median ratio of gene counts relative to geometric mean per gene  to account for sequencing depth and RNA composition. This allowed us to produce a table of gene expression which highlighted genes with the highest transcript count difference between males and females. From this data  genes expressed at juvenile stage 28dpf which were also expressed highly in male or female samples were selected as the best gene candidates for indicating early sex identity of zebrafish. Assembly: StringTie Galaxy Version 1.3.4 Pertea et al.  2015. Supplementary files format and content: Tables of gene expression,Whole body,No experiments were carried out with live adult nor subadult fish before euthanasia. Accordingly  animal welfare guidelines were followed while zebrafish were kept by the breeder.,RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF  Basel  according to Illumina’s standard protocol for RNA sequencing Illumina Inc.  San Diego  USA  Cat. # RS 100 0801. Galaxy server usegalaxy.org,NGS data was collected from 28 dpf and adult zebrafish  which had already been euthanised with Tricaine by the breeder.,tissue:Whole body|cell type:male|developmental stage:Adult|treatment:N/A,GSM7445818,GSM7445818: Adult male Danio rerio 1; Danio rerio; RNA Seq,GSM7445818 r1,GSM7445818,1,RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF  Basel  according to Illumina's standard protocol for RNA sequencing Illumina Inc.  San Diego  USA  Cat. # RS 100 0801. Galaxy server usegalaxy.org,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP441132,,loader:fastq load.py,adult_male1.fastq.gz,fastq,5805719116.0,76391041.0,GSM7445818 r1,0:76,A:1411248618;C:1411955007;G:1394119941;T:1588372207;N:23343,76,,,,1411248618,1411955007,1394119941,1588372207,23343,SRX20592545,SRS17893037,SRA1649389,"Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland","Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland",1,0.95916,,0.06495,,0.67744,,0.50406,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Switzerland,2023-06-05,Adult,Adult,Trunk,Surface Structure
76322,SRR24827625,SRX20592542,SRS17893034,SRP441132,PRJNA980117,Sex blind: bridging the gap between drug exposure and sex related gene expression in Danio rerio using next generation sequencing NGS data and a literature review to find the missing links in pharmaceutical and environmental toxicology studies,GSE234104,Transcriptome Analysis,Abstract: The sex of both humans and Danio rerio has previously been shown to affect the way individuals respond to drug exposure. Genes which allow identification of sex in juvenile zebrafish show potential to reveal these confounding variables between sex in toxicological and preclinical trials but the link between these is so far missing. These sex specific  early expressed genes where expression is not altered by drug exposure must be carefully selected for this purpose. We aimed to discover genes which can be used in pharmaceutical trials and environmental toxicology studies to uncover sex related variations in gene expression with drug application using the model organism Danio rerio. Previously published early sex determining genes from King et al. were evaluated as well as additional genes selected from our zebrafish Next generation sequencing NGS data which are known from previously published works not to be susceptible to changes in expression with drug exposure. NGS revealed a further ten female specific genes vtg1  cyp17a1  cyp19a1a  igf3  ftz f1  gdf9  foxl2a  Nr0b1  ipo4  lhcgr and five male related candidate genes FKBP5  apobb1  hbaa1  dmrt1  spata6 which are also expressed in juvenile zebrafish  28 dpf dpf. Following this  a literature review was performed to classify which of these early expressed sex specific genes are already known to be affected by drug exposure in order to determine candidate genes to be used in pharmaceutical trials or environmental toxicology testing studies. Discovery of these early sex determining genes in Danio rerio will allow identification of sex related responses to drug testing to improve sex specific healthcare and the medical treatment of human patients. Overall design: NGS RNA sequences were produced from two 28 dpf zebrafish which we classified as juvenile in this paper  two adult male and two adult female zebrafish using whole body tissue samples. Juveniles were tested to indicate whether sex was genetically visible at this stage of development. RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF  Basel  according to Illumina's standard protocol for RNA sequencing Illumina Inc.  San Diego  USA  Cat. # RS 100 0801. The NGS transcript data of the sampled zebrafish were compared to identify possible genes that contribute to sex determination as well as those which are expressed early in juvenile development  28dpf King et al.  2020. All data analyses steps were carried out using the Galaxy server usegalaxy.org Jalili et al.  2020. Data from transcript sequencing was mapped to the GRCz11 reference genome GCA 000002035.4 using HISAT2 Galaxy Version 2.1.0+galaxy4 Kim et al.  2019. Transcripts were assembled and merged from the mapped reads with StringTie Galaxy Version 1.3.4 Pertea et al.  2015. post determining gene expression with featureCount Galaxy Version 1.6.3+galaxy2  the NGS data was normalised and differential gene expression analysis of juvenile  male and female zebrafish was carried out using DESeq2 Galaxy Version 2.11.40.2 Love et al.  2014; King et al.  2020. Normalisation was based on the 'median of ratios'   the counts divided by sample specific size factors determined by median ratio of gene counts relative to geometric mean per gene  to account for sequencing depth and RNA composition. This allowed us to produce a table of gene expression which highlighted genes with the highest transcript count difference between males and females. From this data  genes expressed at juvenile stage 28dpf which were also expressed highly in male or female samples were selected as the best gene candidates for indicating early sex identity of zebrafish. Four male Sox9a  Gapdhs  atp1b1a and cyp26b1 and nine female genes gyg1a  rdh10b  pdia  KPNA2  ccnb1  ctsla  Chr4  bmp15 and zbp3 which were previously identified as an early sex determining marker in zebrafish King et al.  2020 were used within a literature search to access previous information as to whether their level of expression was known to be influenced by certain drugs. In this study a further ten female and five male genes  which could be used in early sex determination were selected from NGS data. A literature search was also carried out on these genes to discover if they were known to be affected by drug usage. Based on published literature from ScienceDirect in early 2021  we obtained information previous studies from the past twenty years by searching for the key terms; including the gene name  drug or pharmaceutical exposure  sex  or gender influence. Then  we eliminated irrelevant literature by reading the titles and abstracts and supplemented our literature database by reading the references of the selected studies. We used the selected literature to inform whether genes highlighted from our NGS data as early expressed within juveniles could be candidates in drug trials. Finally  we grouped early expressed genes from NGS data based on the literature search into three categories. If the study was shown to affect the expression of the selected genes  then they were deemed not good to use in pharmaceutical trials. Conversely  if it was not known from previous research that drugs affect the expression of a certain gene  it was included as a potential candidate for revealing how sex response differs with drug exposure and further investigation of its use in this area is necessary in future research.,,pubmed:37398910,,Adult female Danio rerio 2,GSM7445821,,source name:Whole body|tissue:Whole body|cell type:female|developmental stage:Adult|treatment:N/A|geo loc name:missing|collection date:missing,Adult female Danio rerio 2,All data analyses steps were carried out using the Galaxy server usegalaxy.org Jalili et al.  2020. Data from transcript sequencing was mapped to the GRCz11 reference genome GCA 000002035.4 using HISAT2 Galaxy Version 2.1.0+galaxy4 Kim et al.  2019. Transcripts were assembled and merged from the mapped reads with StringTie Galaxy Version 1.3.4 Pertea et al.  2015. post determining gene expression with featureCount Galaxy Version 1.6.3+galaxy2  the NGS data was normalised and differential gene expression analysis of juvenile  male and female zebrafish was carried out using DESeq2 Galaxy Version 2.11.40.2 Love et al.  2014; King et al.  2020. Normalisation was based on the ‘median of ratios’   the counts divided by sample specific size factors determined by median ratio of gene counts relative to geometric mean per gene  to account for sequencing depth and RNA composition. This allowed us to produce a table of gene expression which highlighted genes with the highest transcript count difference between males and females. From this data  genes expressed at juvenile stage 28dpf which were also expressed highly in male or female samples were selected as the best gene candidates for indicating early sex identity of zebrafish. Assembly: StringTie Galaxy Version 1.3.4 Pertea et al.  2015. Supplementary files format and content: Tables of gene expression,Whole body,No experiments were carried out with live adult nor subadult fish before euthanasia. Accordingly  animal welfare guidelines were followed while zebrafish were kept by the breeder.,RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF  Basel  according to Illumina’s standard protocol for RNA sequencing Illumina Inc.  San Diego  USA  Cat. # RS 100 0801. Galaxy server usegalaxy.org,NGS data was collected from 28 dpf and adult zebrafish  which had already been euthanised with Tricaine by the breeder.,tissue:Whole body|cell type:female|developmental stage:Adult|treatment:N/A,GSM7445821,GSM7445821: Adult female Danio rerio 2; Danio rerio; RNA Seq,GSM7445821 r1,GSM7445821,1,RNA quality testing and NGS were performed at the Biocentre under the supervision of Philippe Demougin Life Sciences Training Facility LSTF  Basel  according to Illumina's standard protocol for RNA sequencing Illumina Inc.  San Diego  USA  Cat. # RS 100 0801. Galaxy server usegalaxy.org,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP441132,,loader:fastq load.py,adult_female2.fastq.gz,fastq,6198618444.0,81560769.0,GSM7445821 r1,0:76,A:1511391857;C:1515880388;G:1511198416;T:1660122547;N:25236,76,,,,1511391857,1515880388,1511198416,1660122547,25236,SRX20592542,SRS17893034,SRA1649389,"Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland","Zenker Lab, School of Life Sciences - Institute for Ecopreneurship, University of Applied Sciences and Arts Northwestern Switzerland",1,0.95993,,0.0372,,0.71242,,0.42265,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Switzerland,2023-06-05,Adult,Adult,Trunk,Surface Structure