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
5793,ERR1955208,ERX2020800,ERS1697077,ERP017053,PRJEB15333,Transposon driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution,ena-STUDY-EMBL EUROPEAN BIOINFORMATICS INSTITUTE-07-09-2016-10:25:55:499-247,Other,In order to better understand the features associated with male germline transcription we profiled the RNA expression in a number of germline cell types. These include spermatogonial stem cells  spermatocytes and round spermatids in mouse and spermatocytes in rat. We also profiled the transcription in zebrafish testes. As a consequence it became apparent that transposable elements are driving considerable lncRNA expression in the later stages of spermatogenesis. This is particularly apparent in the case of endogenous retroviruses in rodents.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 05 08,,,Transcriptional profiling of zebrafish testes for analysis of conserved repeat element associations,SAMEA104033184,EMBL EUROPEAN BIOINFORMATICS INSTITUTE,ENA FIRST PUBLIC:2017 05 10T17:01:28Z|ENA LAST UPDATE:2017 04 28T10:34:37Z|External Id:SAMEA104033184|INSDC center name:EMBL EUROPEAN BIOINFORMATICS INSTITUTE|INSDC first public:2017 05 10T17:01:28Z|INSDC last update:2017 04 28T10:34:37Z|INSDC status:public|Submitter Id:Zebrafish.Testis 2|common name:zebrafish|sample name:Zebrafish.Testis 2|scientific name:Danio rerio|strain:AB|tissue type:testis,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 16,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP017053,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 05 10|ENA LAST UPDATE:2018 11 16,zebrafish_testis_2.conserved.1.fastq.gz zebrafish_testis_2.conserved.2.fastq.gz,fastq fastq,46555372886.0,230472143.0,ena RUN EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 16,0:101 1:101,A:12260062264;C:10888457642;G:11605642683;T:11637267744;N:163942553,101,101,,,12260062264,10888457642,11605642683,11637267744,163942553,ERX2020800,ERS1697077,ERA904389,EMBL EUROPEAN BIOINFORMATICS INSTITUTE|European Nucleotide Archive,EMBL EUROPEAN BIOINFORMATICS INSTITUTE,2,0.93165,0.92785,0.29822,0.32141,0.71386,0.71971,0.66173,0.63843,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2017-01-31,Undetermined,Undetermined,Gonad,Reproductive System
5794,ERR1955207,ERX2020799,ERS1697076,ERP017053,PRJEB15333,Transposon driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution,ena-STUDY-EMBL EUROPEAN BIOINFORMATICS INSTITUTE-07-09-2016-10:25:55:499-247,Other,In order to better understand the features associated with male germline transcription we profiled the RNA expression in a number of germline cell types. These include spermatogonial stem cells  spermatocytes and round spermatids in mouse and spermatocytes in rat. We also profiled the transcription in zebrafish testes. As a consequence it became apparent that transposable elements are driving considerable lncRNA expression in the later stages of spermatogenesis. This is particularly apparent in the case of endogenous retroviruses in rodents.,ENA FIRST PUBLIC:2017 01 31|ENA LAST UPDATE:2017 05 08,,,Transcriptional profiling of zebrafish testes for analysis of conserved repeat element associations,SAMEA104033183,EMBL EUROPEAN BIOINFORMATICS INSTITUTE,ENA FIRST PUBLIC:2017 05 10T17:01:28Z|ENA LAST UPDATE:2017 04 28T10:34:37Z|External Id:SAMEA104033183|INSDC center name:EMBL EUROPEAN BIOINFORMATICS INSTITUTE|INSDC first public:2017 05 10T17:01:28Z|INSDC last update:2017 04 28T10:34:37Z|INSDC status:public|Submitter Id:Zebrafish.Testis 1|common name:zebrafish|sample name:Zebrafish.Testis 1|scientific name:Danio rerio|strain:AB|tissue type:testis,,,,,,,,,Illumina HiSeq 2000 paired end sequencing,ena EXPERIMENT EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 15,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,ERP017053,Illumina HiSeq 2000 paired end sequencing,ENA FIRST PUBLIC:2017 05 10|ENA LAST UPDATE:2018 11 16,zebrafish_testis_1.conserved.1.fastq.gz zebrafish_testis_1.conserved.2.fastq.gz,fastq fastq,41056086708.0,203247954.0,ena RUN EMBL EUROPEAN BIOINFORMATICS INSTITUTE 03 05 2017 17:32:41:660 15,0:101 1:101,A:10675591750;C:9672762387;G:10139834713;T:10380949257;N:186948601,101,101,,,10675591750,9672762387,10139834713,10380949257,186948601,ERX2020799,ERS1697076,ERA904389,EMBL EUROPEAN BIOINFORMATICS INSTITUTE|European Nucleotide Archive,EMBL EUROPEAN BIOINFORMATICS INSTITUTE,2,0.92308,0.9157,0.30221,0.31293,0.68276,0.68836,0.56114,0.5857,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United Kingdom,2017-01-31,Undetermined,Undetermined,Gonad,Reproductive System
7949,ERR015566,ERX005931,ERS000090,ERP000263,PRJEB2208,Zebrafish gene three prime end pull down for genome annotation,E-MTAB-308,Transcriptome Analysis,,,,,ZF ovary sample1,SAMEA708832,Wellcome Sanger Institute,Alias:ZF ovary sample1|Description:RNA extracted from adult zebrafish ovary|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000090|Sample Name:ERS000090|Sex:female|Strain:Tuebingen|Title:Danio rerio,,,,,,,,,Illumina Genome Analyzer II paired end sequencing; Zebrafish gene 3 prime end pull down for genome annotation,E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish ovary dpf three prime pull down paired end 250 to 300 bp insert,Zebrafish adult ovary mRNA three prime end,Zebrafish gene three prime end pull down for genome annotation,20 ug of total RNA was fragmented using RNA Fragmentation Reagent Ambion for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl.   RNA was annealed to the oligo stBPM1polyT22 biotin GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN and bound to streptavidin  magnetic beads.   post washing by pull down on a magnet  the bound RNA was reverse transcribed with SuperScript II Invitrogen and a second strand synthesised with DNA polymerase I Promega and RNase H NEB.   post further washing  the double strand cDNA was released from the beads with BpmI NEB.   The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturer's protocol with a fragment size of 250 to 300 bp.,Experimental Factor: DEVELOPMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:ovary|Experimental Factor: SEX:female,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina Genome Analyzer II,,ERP000263,Illumina Genome Analyzer II paired end sequencing; Zebrafish gene three prime end pull down for genome annotation,ENA FIRST PUBLIC:2010 08 19|ENA LAST UPDATE:2018 11 16,3444_6.srf,srf,1150193272.0,7567061.0,E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish ovary dpf three prime pull down paired end 250 to 300 bp insert,0:76 1:76,A:280621121;C:291623460;G:285422205;T:273609496;N:18916990,76,76,,,280621121,291623460,285422205,273609496,18916990,ERX005931,ERS000090,ERA010603,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.96663,0.96605,0.0126,0.01249,0.82272,0.82548,0.45602,0.45286,76,76,B,B,biological fallback assumption,illumina,early_illumina,3prime,other,unknown,bulk,unknown,unknown,,United Kingdom,2010-02-26,Adult,Adult,Gonad,Reproductive System
9357,ERR2983451,ERX2986067,ERS2955655,ERP112513,PRJEB30097,RNA Seq of Danionine species,E-MTAB-7476,Transcriptome Analysis,Tissues specific transcriptomes of Danio rerio  Danio albolineatus and Danio aesculapii Brain  Liver and Gonads.,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,,Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,R2wG,SAMEA5147910,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology",ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147910|INSDC center name:University of Hamburg  Institute of Zoology  Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R2wG|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:2|organism part:gonad|sample name:E MTAB 7476:R2wG|scientific name:Danio rerio|sex:female|strain:tu,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species,E MTAB 7476:R2wG p,R2wG p,RNA Seq of Danionine species,Organs were sampled and snap frozen in liquid nitrogen   RNA was extracted using Trizol and standard silica membrane protocol  Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:gonad,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP112513,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,FCHNW2WBBXX_L6_HKZEBodsEAAFRAAPEI-209_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAAFRAAPEI-209_2.fq.gz,fastq fastq,4276100600.0,21380503.0,E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAAFRAAPEI 209 ,0:100 1:100,A:1108098396;C:1033423434;G:1019885778;T:1113782383;N:910609,100,100,,,1108098396,1033423434,1019885778,1113782383,910609,ERX2986067,ERS2955655,ERA1674470,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive","University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive",2,0.9444,0.94495,0.02624,0.02606,0.74959,0.7512,0.48453,0.48539,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2018-12-05,Adult,Adult,Gonad,Reproductive System
9359,ERR2983449,ERX2986065,ERS2955653,ERP112513,PRJEB30097,RNA Seq of Danionine species,E-MTAB-7476,Transcriptome Analysis,Tissues specific transcriptomes of Danio rerio  Danio albolineatus and Danio aesculapii Brain  Liver and Gonads.,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,,Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,R1wG,SAMEA5147908,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology",ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147908|INSDC center name:University of Hamburg  Institute of Zoology  Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R1wG|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:1|organism part:gonad|sample name:E MTAB 7476:R1wG|scientific name:Danio rerio|sex:female|strain:tu,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species,E MTAB 7476:R1wG p,R1wG p,RNA Seq of Danionine species,Organs were sampled and snap frozen in liquid nitrogen   RNA was extracted using Trizol and standard silica membrane protocol  Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers.,Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:gonad,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP112513,Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species,ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05,FCHNW2WBBXX_L6_HKZEBodsEAAERAAPEI-208_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAAERAAPEI-208_2.fq.gz,fastq fastq,3574419200.0,17872096.0,E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAAERAAPEI 208 ,0:100 1:100,A:927454175;C:863033369;G:844910972;T:938253904;N:766780,100,100,,,927454175,863033369,844910972,938253904,766780,ERX2986065,ERS2955653,ERA1674470,"University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive","University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive",2,0.93851,0.93973,0.02799,0.02809,0.72701,0.72914,0.48827,0.48841,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2018-12-05,Adult,Adult,Gonad,Reproductive System
25267,SRR25744342,SRX21467662,SRS18702380,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish  we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad eif4e1b 3,GSM7730282,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b  / |geo loc name:missing|collection date:missing,Gonad eif4e1b 3,RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts  subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b  / ,GSM7730282,GSM7730282: Gonad eif4e1b 3; Danio rerio; ssRNA seq,GSM7730282 r1,GSM7730282,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_HOM3_1.fastq.gz Ovary_HOM3_2.fastq.gz,fastq fastq,2170738056.0,10746228.0,GSM7730282 r1,0:101 1:101,A:531993767;C:520631008;G:565772072;T:552334154;N:7055,101,101,,,531993767,520631008,565772072,552334154,7055,SRX21467662,SRS18702380,SRA1698764,IMP,IMP,2,0.77665,0.7702,0.14988,0.14284,0.66716,0.66957,0.49991,0.47425,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25268,SRR25744343,SRX21467661,SRS18702379,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish  we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad eif4e1b 2,GSM7730281,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b  / |geo loc name:missing|collection date:missing,Gonad eif4e1b 2,RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts  subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b  / ,GSM7730281,GSM7730281: Gonad eif4e1b 2; Danio rerio; ssRNA seq,GSM7730281 r1,GSM7730281,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_HOM2_1.fastq.gz Ovary_HOM2_2.fastq.gz,fastq fastq,3459149000.0,17124500.0,GSM7730281 r1,0:101 1:101,A:876732239;C:796603142;G:882912604;T:902886783;N:14232,101,101,,,876732239,796603142,882912604,902886783,14232,SRX21467661,SRS18702379,SRA1698764,IMP,IMP,2,0.81761,0.79589,0.26282,0.24746,0.70607,0.7039,0.50658,0.49236,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25269,SRR25744344,SRX21467660,SRS18702381,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish  we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad eif4e1b 1,GSM7730280,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b  / |geo loc name:missing|collection date:missing,Gonad eif4e1b 1,RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts  subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b  / ,GSM7730280,GSM7730280: Gonad eif4e1b 1; Danio rerio; ssRNA seq,GSM7730280 r1,GSM7730280,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_HOM1_1.fastq.gz Ovary_HOM1_2.fastq.gz,fastq fastq,2189781202.0,10840501.0,GSM7730280 r1,0:101 1:101,A:537591255;C:525448020;G:568979980;T:557754770;N:7177,101,101,,,537591255,525448020,568979980,557754770,7177,SRX21467660,SRS18702381,SRA1698764,IMP,IMP,2,0.7459,0.74191,0.15778,0.15291,0.65543,0.65841,0.48578,0.48291,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25270,SRR25744345,SRX21467659,SRS18702378,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish  we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad WT 3,GSM7730279,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b +/+|geo loc name:missing|collection date:missing,Gonad WT 3,RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts  subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b +/+,GSM7730279,GSM7730279: Gonad WT 3; Danio rerio; ssRNA seq,GSM7730279 r1,GSM7730279,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_WT3_1.fastq.gz Ovary_WT3_2.fastq.gz,fastq fastq,3674041448.0,18188324.0,GSM7730279 r1,0:101 1:101,A:910831144;C:876967044;G:953299105;T:932928913;N:15242,101,101,,,910831144,876967044,953299105,932928913,15242,SRX21467659,SRS18702378,SRA1698764,IMP,IMP,2,0.89093,0.89038,0.09253,0.09348,0.73892,0.73858,0.47115,0.47218,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25271,SRR25744346,SRX21467658,SRS18702377,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish  we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad WT 2,GSM7730278,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b +/+|geo loc name:missing|collection date:missing,Gonad WT 2,RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts  subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b +/+,GSM7730278,GSM7730278: Gonad WT 2; Danio rerio; ssRNA seq,GSM7730278 r1,GSM7730278,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_WT2_1.fastq.gz Ovary_WT2_2.fastq.gz,fastq fastq,3024886370.0,14974685.0,GSM7730278 r1,0:101 1:101,A:744374909;C:727299396;G:782294774;T:770904797;N:12494,101,101,,,744374909,727299396,782294774,770904797,12494,SRX21467658,SRS18702377,SRA1698764,IMP,IMP,2,0.91806,0.91689,0.06949,0.07178,0.74458,0.74474,0.47548,0.47338,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25272,SRR25744347,SRX21467657,SRS18702376,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish  we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad WT 1,GSM7730277,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b +/+|geo loc name:missing|collection date:missing,Gonad WT 1,RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts  subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP  eif4e1b +/+,GSM7730277,GSM7730277: Gonad WT 1; Danio rerio; ssRNA seq,GSM7730277 r1,GSM7730277,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_WT1_2.fastq.gz Ovary_WT1_1.fastq.gz,fastq fastq,3571638356.0,17681378.0,GSM7730277 r1,0:101 1:101,A:876280472;C:856417516;G:935896746;T:903028845;N:14777,101,101,,,876280472,856417516,935896746,903028845,14777,SRX21467657,SRS18702376,SRA1698764,IMP,IMP,2,0.89559,0.89353,0.09223,0.09423,0.73052,0.73012,0.47772,0.47408,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
26542,SRR28370185,SRX23975270,SRS20773688,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,L13 2 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 27|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E27,E27,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,L13-2_1.fq.gz L13-2_2.fq.gz,fastq fastq,6912432900.0,23041443.0,L13 2 1.fq.gz,0:150 1:150,A:1784119910;C:1650041348;G:1690584500;T:1787634630;N:52512,150,150,,,1784119910,1650041348,1690584500,1787634630,52512,SRX23975270,SRS20773688,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26543,SRR28370183,SRX23975269,SRS20773687,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,L13 3 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 29|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E29,E29,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,L13-3_1.fq.gz L13-3_2.fq.gz,fastq fastq,6353525700.0,21178419.0,L13 3 1.fq.gz,0:150 1:150,A:1642863679;C:1514378445;G:1549765145;T:1646469683;N:48748,150,150,,,1642863679,1514378445,1549765145,1646469683,48748,SRX23975269,SRS20773687,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26544,SRR28370186,SRX23975268,SRS20773685,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,L13 4 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 31|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E31,E31,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,L13-4_1.fq.gz L13-4_2.fq.gz,fastq fastq,6026853600.0,20089512.0,L13 4 1.fq.gz,0:150 1:150,A:1557631540;C:1437822618;G:1472097382;T:1559255786;N:46274,150,150,,,1557631540,1437822618,1472097382,1559255786,46274,SRX23975268,SRS20773685,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26545,SRR28370187,SRX23975267,SRS20773686,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,H27 3 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 5|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E5,E5,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,H27-3_1.fq.gz H27-3_2.fq.gz,fastq fastq,6437512500.0,21458375.0,H27 3 1.fq.gz,0:150 1:150,A:1664818485;C:1534913781;G:1570911516;T:1666819538;N:49180,150,150,,,1664818485,1534913781,1570911516,1666819538,49180,SRX23975267,SRS20773686,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26546,SRR28370188,SRX23975266,SRS20773684,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,H27 4 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 7|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E7,E7,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,H27-4_1.fq.gz H27-4_2.fq.gz,fastq fastq,6583604100.0,21945347.0,H27 4 1.fq.gz,0:150 1:150,A:1701207657;C:1570727535;G:1607990863;T:1703626924;N:51121,150,150,,,1701207657,1570727535,1607990863,1703626924,51121,SRX23975266,SRS20773684,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26547,SRR28370189,SRX23975265,SRS20773683,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,M20 1 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 9|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E9,E9,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,M20-1_1.fq.gz M20-1_2.fq.gz,fastq fastq,7048815900.0,23496053.0,M20 1 1.fq.gz,0:150 1:150,A:1818915133;C:1681912688;G:1724222526;T:1823711995;N:53558,150,150,,,1818915133,1681912688,1724222526,1823711995,53558,SRX23975265,SRS20773683,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26548,SRR28370190,SRX23975264,SRS20773682,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,M22 2 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 19|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E19,E19,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,M22-2_1.fq.gz M22-2_2.fq.gz,fastq fastq,6844400100.0,22814667.0,M22 2 1.fq.gz,0:150 1:150,A:1770073015;C:1631597148;G:1666105661;T:1776572883;N:51393,150,150,,,1770073015,1631597148,1666105661,1776572883,51393,SRX23975264,SRS20773682,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26549,SRR28370191,SRX23975263,SRS20773681,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,H27 2 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E3,E3,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,H27-2_1.fq.gz H27-2_2.fq.gz,fastq fastq,6803741100.0,22679137.0,H27 2 1.fq.gz,0:150 1:150,A:1759471720;C:1621328873;G:1660379342;T:1762509905;N:51260,150,150,,,1759471720,1621328873,1660379342,1762509905,51260,SRX23975263,SRS20773681,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26550,SRR28370184,SRX23975262,SRS20773680,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,M22 3 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 21|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E21,E21,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,M22-3_1.fq.gz M22-3_2.fq.gz,fastq fastq,6312346800.0,21041156.0,M22 3 1.fq.gz,0:150 1:150,A:1638152183;C:1500304435;G:1533591340;T:1640250617;N:48225,150,150,,,1638152183,1500304435,1533591340,1640250617,48225,SRX23975262,SRS20773680,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26551,SRR28370192,SRX23975261,SRS20773679,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,M22 4 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 23|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E23,E23,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,M22-4_1.fq.gz M22-4_2.fq.gz,fastq fastq,7163095500.0,23876985.0,M22 4 1.fq.gz,0:150 1:150,A:1851012240;C:1707016293;G:1748790263;T:1856222899;N:53805,150,150,,,1851012240,1707016293,1748790263,1856222899,53805,SRX23975261,SRS20773679,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26552,SRR28370193,SRX23975260,SRS20773678,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,L13 1 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 25|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E25,E25,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,L13-1_1.fq.gz L13-1_2.fq.gz,fastq fastq,6191424300.0,20638081.0,L13 1 1.fq.gz,0:150 1:150,A:1605753886;C:1471890545;G:1506901769;T:1606830995;N:47105,150,150,,,1605753886,1471890545,1506901769,1606830995,47105,SRX23975260,SRS20773678,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26553,SRR28370194,SRX23975259,SRS20773677,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,M22 1 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 17|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E17,E17,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,M22-1_1.fq.gz M22-1_2.fq.gz,fastq fastq,6102383400.0,20341278.0,M22 1 1.fq.gz,0:150 1:150,A:1577012976;C:1455984420;G:1487747979;T:1581590987;N:47038,150,150,,,1577012976,1455984420,1487747979,1581590987,47038,SRX23975259,SRS20773677,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26554,SRR28370195,SRX23975258,SRS20773676,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,M20 4 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 15|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E15,E15,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,M20-4_1.fq.gz M20-4_2.fq.gz,fastq fastq,6636566100.0,22121887.0,M20 4 1.fq.gz,0:150 1:150,A:1715667953;C:1580553403;G:1620418612;T:1719875870;N:50262,150,150,,,1715667953,1580553403,1620418612,1719875870,50262,SRX23975258,SRS20773676,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26555,SRR28370196,SRX23975257,SRS20773675,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,M20 3 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 13|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E13,E13,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,M20-3_1.fq.gz M20-3_2.fq.gz,fastq fastq,6761256900.0,22537523.0,M20 3 1.fq.gz,0:150 1:150,A:1758917520;C:1603264927;G:1642146940;T:1756875822;N:51691,150,150,,,1758917520,1603264927,1642146940,1756875822,51691,SRX23975257,SRS20773675,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26556,SRR28370197,SRX23975256,SRS20773674,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,M20 2 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 11|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E11,E11,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,M20-2_1.fq.gz M20-2_2.fq.gz,fastq fastq,6746623800.0,22488746.0,M20 2 1.fq.gz,0:150 1:150,A:1744481110;C:1606775717;G:1646048497;T:1749267538;N:50938,150,150,,,1744481110,1606775717,1646048497,1749267538,50938,SRX23975256,SRS20773674,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
26557,SRR28370198,SRX23975255,SRS20773673,SRP496008,PRJNA1020641,Danio rerio strain:AB strain Raw sequence reads,PRJNA1020641,Whole Genome Sequencing,post different low temperature treatments for 14 days  transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.,,,,,H27 1 1,,strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of ovary: adult female zebrafish,E1,E1,Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech  China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters  followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP496008,,,H27-1_1.fq.gz H27-1_2.fq.gz,fastq fastq,6713598900.0,22378663.0,H27 1 1.fq.gz,0:150 1:150,A:1734915716;C:1602520747;G:1639382442;T:1736729508;N:50487,150,150,,,1734915716,1602520747,1639382442,1736729508,50487,SRX23975255,SRS20773673,SRA1825755,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-18,Adult,Adult,Gonad,Reproductive System
28800,SRR26744390,SRX22443207,SRS19460925,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TL1,AWG21KI956,,strain:AB wild type|age:4 mpf|collection date:2021 10 20|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,LM,LM,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TL1_2.clean.fq.gz TL1_1.clean.fq.gz,fastq fastq,5699083800.0,18996946.0,TL1 1.clean.fq.gz,0:150 1:150,A:1551237534;C:1296027828;G:1322262120;T:1529547653;N:8665,150,150,,,1551237534,1296027828,1322262120,1529547653,8665,SRX22443207,SRS19460925,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92378,0.91959,0.10498,0.1026,0.6299,0.64319,0.49163,0.48651,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28801,SRR26744391,SRX22443206,SRS19460924,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OL3,AWG21KN131,,strain:AB wild type|age:4 mpf|collection date:2021 10 19|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,LF3,LF3,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OL3_2.clean.fq.gz OL3_1.clean.fq.gz,fastq fastq,6314250900.0,21047503.0,OL3 1.clean.fq.gz,0:150 1:150,A:1645668992;C:1501216557;G:1526087917;T:1641268461;N:8973,150,150,,,1645668992,1501216557,1526087917,1641268461,8973,SRX22443206,SRS19460924,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92555,0.92469,0.01845,0.01818,0.75146,0.75298,0.4697,0.47119,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28802,SRR26744392,SRX22443205,SRS19460920,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OL2,AWG21KN130,,strain:AB wild type|age:4 mpf|collection date:2021 10 18|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,LF2,LF2,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OL2_1.clean.fq.gz OL2_2.clean.fq.gz,fastq fastq,5723391300.0,19077971.0,OL2 1.clean.fq.gz,0:150 1:150,A:1493997463;C:1358589750;G:1376156813;T:1494638946;N:8328,150,150,,,1493997463,1358589750,1376156813,1494638946,8328,SRX22443205,SRS19460920,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92147,0.92251,0.0187,0.01891,0.75077,0.75156,0.46983,0.46864,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28803,SRR26744393,SRX22443204,SRS19460923,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OL1,AWG21KI955,,strain:AB wild type|age:4 mpf|collection date:2021 10 17|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,LF,LF,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OL1_1.clean.fq.gz OL1_2.clean.fq.gz,fastq fastq,5769588600.0,19231962.0,OL1 1.clean.fq.gz,0:150 1:150,A:1506564191;C:1368903119;G:1393174106;T:1500937757;N:9427,150,150,,,1506564191,1368903119,1393174106,1500937757,9427,SRX22443204,SRS19460923,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92622,0.92542,0.01753,0.01714,0.75694,0.7596,0.47038,0.46862,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28804,SRR26744394,SRX22443203,SRS19460921,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TC3,AWG21KN129,,strain:AB wild type|age:4 mpf|collection date:2021 10 16|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,CM3,CM3,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TC3_2.clean.fq.gz TC3_1.clean.fq.gz,fastq fastq,5849082900.0,19496943.0,TC3 1.clean.fq.gz,0:150 1:150,A:1588589470;C:1336193891;G:1355933296;T:1568357820;N:8423,150,150,,,1588589470,1336193891,1355933296,1568357820,8423,SRX22443203,SRS19460921,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.9259,0.92501,0.09579,0.09483,0.62501,0.6266,0.49341,0.49677,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28805,SRR26744395,SRX22443202,SRS19460922,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TC2,AWG21KN128,,strain:AB wild type|age:4 mpf|collection date:2021 10 15|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,CM2,CM2,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TC2_2.clean.fq.gz TC2_1.clean.fq.gz,fastq fastq,6060182100.0,20200607.0,TC2 1.clean.fq.gz,0:150 1:150,A:1640267244;C:1389270827;G:1407872392;T:1622763112;N:8525,150,150,,,1640267244,1389270827,1407872392,1622763112,8525,SRX22443202,SRS19460922,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92414,0.9235,0.0895,0.08929,0.62528,0.62682,0.48981,0.48954,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28806,SRR26744396,SRX22443201,SRS19460918,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TC1,AWG21KI954,,strain:AB wild type|age:4 mpf|collection date:2021 10 14|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,CM,CM,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TC1_1.clean.fq.gz TC1_2.clean.fq.gz,fastq fastq,5990926200.0,19969754.0,TC1 1.clean.fq.gz,0:150 1:150,A:1624594580;C:1370442060;G:1389854623;T:1606025586;N:9351,150,150,,,1624594580,1370442060,1389854623,1606025586,9351,SRX22443201,SRS19460918,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92373,0.92279,0.09865,0.09887,0.62568,0.62889,0.49516,0.49165,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28807,SRR26744397,SRX22443200,SRS19460914,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OC3,AWG21KN127,,strain:AB wild type|age:4 mpf|collection date:2021 10 13|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,CF3,CF3,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OC3_1.clean.fq.gz OC3_2.clean.fq.gz,fastq fastq,6016914600.0,20056382.0,OC3 1.clean.fq.gz,0:150 1:150,A:1568359804;C:1431107464;G:1450792678;T:1566645836;N:8818,150,150,,,1568359804,1431107464,1450792678,1566645836,8818,SRX22443200,SRS19460914,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92534,0.92528,0.01718,0.017,0.75201,0.753,0.47491,0.48041,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28808,SRR26744398,SRX22443199,SRS19460915,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TL3,AWG21KN137,,strain:AB wild type|age:4 mpf|collection date:2021 10 28|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,HM3,HM3,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TH3_1.clean.fq.gz TH3_2.clean.fq.gz,fastq fastq,5656023900.0,18853413.0,TH3 1.clean.fq.gz,0:150 1:150,A:1543170407;C:1285816998;G:1307460034;T:1519567327;N:9134,150,150,,,1543170407,1285816998,1307460034,1519567327,9134,SRX22443199,SRS19460915,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92316,0.92166,0.10167,0.10105,0.61546,0.61712,0.482,0.4844,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28809,SRR26744399,SRX22443198,SRS19460919,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TL2,AWG21KN136,,strain:AB wild type|age:4 mpf|collection date:2021 10 27|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,HM2,HM2,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TH2_2.clean.fq.gz TH2_1.clean.fq.gz,fastq fastq,6625748400.0,22085828.0,TH2 1.clean.fq.gz,0:150 1:150,A:1808454203;C:1505432915;G:1526482662;T:1785369099;N:9521,150,150,,,1808454203,1505432915,1526482662,1785369099,9521,SRX22443198,SRS19460919,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92273,0.92286,0.09974,0.09973,0.62043,0.62203,0.48636,0.48603,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28810,SRR26744400,SRX22443197,SRS19460917,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TL1,AWG21KI958,,strain:AB wild type|age:4 mpf|collection date:2021 10 26|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,HM,HM,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TH1_1.clean.fq.gz TH1_2.clean.fq.gz,fastq fastq,6588309600.0,21961032.0,TH1 1.clean.fq.gz,0:150 1:150,A:1793735270;C:1500551703;G:1518029671;T:1775983548;N:9408,150,150,,,1793735270,1500551703,1518029671,1775983548,9408,SRX22443197,SRS19460917,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92046,0.91969,0.10181,0.10206,0.61505,0.61477,0.48395,0.48957,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28811,SRR26744401,SRX22443196,SRS19460916,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OL3,AWG21KN135,,strain:AB wild type|age:4 mpf|collection date:2021 10 25|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,HF3,HF3,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OH3_1.clean.fq.gz OH3_2.clean.fq.gz,fastq fastq,5690890500.0,18969635.0,OH3 1.clean.fq.gz,0:150 1:150,A:1485585756;C:1351021989;G:1373539521;T:1480733791;N:9443,150,150,,,1485585756,1351021989,1373539521,1480733791,9443,SRX22443196,SRS19460916,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92616,0.9273,0.01843,0.01865,0.74793,0.74925,0.4724,0.47202,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28812,SRR26744402,SRX22443195,SRS19460912,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OL2,AWG21KN134,,strain:AB wild type|age:4 mpf|collection date:2021 10 24|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,HF2,HF2,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OH2_2.clean.fq.gz OH2_1.clean.fq.gz,fastq fastq,6047756700.0,20159189.0,OH2 1.clean.fq.gz,0:150 1:150,A:1577825068;C:1435108510;G:1458998347;T:1575814993;N:9782,150,150,,,1577825068,1435108510,1458998347,1575814993,9782,SRX22443195,SRS19460912,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.9233,0.92363,0.01923,0.01923,0.74474,0.74686,0.46918,0.46911,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28813,SRR26744403,SRX22443194,SRS19460913,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OL1,AWG21KI957,,strain:AB wild type|age:4 mpf|collection date:2021 10 23|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,HF,HF,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OH1_1.clean.fq.gz OH1_2.clean.fq.gz,fastq fastq,5756713800.0,19189046.0,OH1 1.clean.fq.gz,0:150 1:150,A:1501851096;C:1366577079;G:1382910165;T:1505367292;N:8168,150,150,,,1501851096,1366577079,1382910165,1505367292,8168,SRX22443194,SRS19460913,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92555,0.92628,0.0184,0.01828,0.74968,0.7512,0.47643,0.4776,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28814,SRR26744404,SRX22443193,SRS19460908,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TL3,AWG21KN133,,strain:AB wild type|age:4 mpf|collection date:2021 10 22|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,LM3,LM3,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TL3_1.clean.fq.gz TL3_2.clean.fq.gz,fastq fastq,5675551800.0,18918506.0,TL3 1.clean.fq.gz,0:150 1:150,A:1544159251;C:1294658828;G:1308831043;T:1527894467;N:8211,150,150,,,1544159251,1294658828,1308831043,1527894467,8211,SRX22443193,SRS19460908,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92069,0.92047,0.10371,0.10354,0.62741,0.62954,0.48923,0.48839,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28815,SRR26744405,SRX22443192,SRS19460909,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,TL2,AWG21KN132,,strain:AB wild type|age:4 mpf|collection date:2021 10 21|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,LM2,LM2,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,TL2_1.clean.fq.gz TL2_2.clean.fq.gz,fastq fastq,5834343300.0,19447811.0,TL2 1.clean.fq.gz,0:150 1:150,A:1583809689;C:1333511774;G:1345919597;T:1571093925;N:8315,150,150,,,1583809689,1333511774,1345919597,1571093925,8315,SRX22443192,SRS19460909,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.91878,0.92054,0.10134,0.10105,0.62708,0.62759,0.48763,0.48708,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28816,SRR26744406,SRX22443191,SRS19460911,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OC2,AWG21KN126,,strain:AB wild type|age:4 mpf|collection date:2021 10 12|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,CF2,CF2,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OC2_2.clean.fq.gz OC2_1.clean.fq.gz,fastq fastq,6462335700.0,21541119.0,OC2 1.clean.fq.gz,0:150 1:150,A:1684794140;C:1535771967;G:1553892063;T:1687868172;N:9358,150,150,,,1684794140,1535771967,1553892063,1687868172,9358,SRX22443191,SRS19460911,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92236,0.92263,0.01803,0.01777,0.74945,0.75081,0.47372,0.47191,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
28817,SRR26744407,SRX22443190,SRS19460907,SRP470937,PRJNA1036532,Danio rerio Raw sequence reads,PRJNA1036532,Whole Genome Sequencing,normal RNAseq of zebrafish,,,,OC1,AWG21KI953,,strain:AB wild type|age:4 mpf|collection date:2021 10 11|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,CF,CF,normal RNAseq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP470937,,,OC1_1.clean.fq.gz OC1_2.clean.fq.gz,fastq fastq,5719061700.0,19063539.0,OC1 1.clean.fq.gz,0:150 1:150,A:1489404392;C:1360123113;G:1386373369;T:1483151708;N:9118,150,150,,,1489404392,1360123113,1386373369,1483151708,9118,SRX22443190,SRS19460907,SRA1747895,Fujian Agriculture and Forestry University|College of Marine Sciences,Fujian Agriculture and Forestry University,2,0.92595,0.92513,0.0166,0.0163,0.75187,0.75503,0.47431,0.47637,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-09,Adult,Adult,Gonad,Reproductive System
29746,SRR27467679,SRX23139227,SRS20090270,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary BS R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  BS  rep2,EV02003,EV02003,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,SRP482074,,,EV02003.R1.fastq.gz EV02003.R2.fastq.gz,fastq fastq,1031891720.0,3416860.0,EV02003.R1.fastq.gz,0:151 1:151,A:264464363;C:153440613;G:408557241;T:205367487;N:62016,151,151,,,264464363,153440613,408557241,205367487,62016,SRX23139227,SRS20090270,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,2,0.0,0.00019,0.0,0.00015,1.0,0.99993,,1.0,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Adult,Adult,Gonad,Reproductive System
29755,SRR27467688,SRX23139218,SRS20090261,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary DM R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  DM  rep2,EV02002,EV02002,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,SRP482074,,,EV02002.R1.fastq.gz EV02002.R2.fastq.gz,fastq fastq,861320308.0,2852054.0,EV02002.R1.fastq.gz,0:151 1:151,A:205625519;C:162178974;G:334206312;T:159256900;N:52603,151,151,,,205625519,162178974,334206312,159256900,52603,SRX23139218,SRS20090261,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,2,2e-05,0.00049,0.0,0.00027,1.0,0.99947,,0.44444,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Adult,Adult,Gonad,Reproductive System
29756,SRR27467689,SRX23139217,SRS20090260,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,ovary mock R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal,,,,,,,,,tRAM seq of zebrafish: ovary  mock  rep2,EV02001,EV02001,RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.,,,OTHER,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,SRP482074,,,EV02001.R1.fastq.gz EV02001.R2.fastq.gz,fastq fastq,520371066.0,1723083.0,EV02001.R1.fastq.gz,0:151 1:151,A:116107273;C:90896560;G:218652568;T:94682244;N:32421,151,151,,,116107273,90896560,218652568,94682244,32421,SRX23139217,SRS20090260,SRA1781872,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,2,2e-05,0.00086,0.0,0.00078,0.99995,0.99981,0.0,0.61538,151,151,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,size_fractionation,nebnext,bulk,unknown,unknown,,Austria,2024-01-09,Adult,Adult,Gonad,Reproductive System
31721,SRR28537217,SRX24137319,SRS20921922,SRP499426,PRJNA1095659,lsm14b ko zebrafish RNA seq,PRJNA1095659,Other,Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation  however  the specific translational regulatory mechanisms remain unclear. Here  our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR  which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes  which ensures that the mRNA synthesized and stored during the growth stage of oocytes  is necessary for the normal growth and development of oocytes.,,,,,ko3,,strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,ko3,ko3,ko3,ko ovary,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP499426,,,ko3_1.fq.gz ko3_2.fq.gz,fastq fastq,8310654000.0,27702180.0,ko3 1.fq.gz,0:150 1:150,A:2164758632;C:1964255570;G:1984514973;T:2197073890;N:50935,150,150,,,2164758632,1964255570,1984514973,2197073890,50935,SRX24137319,SRS20921922,,,Shenzhen Second People's Hospital,2,0.9472,0.94617,0.02506,0.02527,0.74286,0.74535,0.45316,0.45662,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-04-03,Adult,Adult,Gonad,Reproductive System
31722,SRR28537218,SRX24137318,SRS20921924,SRP499426,PRJNA1095659,lsm14b ko zebrafish RNA seq,PRJNA1095659,Other,Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation  however  the specific translational regulatory mechanisms remain unclear. Here  our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR  which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes  which ensures that the mRNA synthesized and stored during the growth stage of oocytes  is necessary for the normal growth and development of oocytes.,,,,,ko2,,strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,ko2,ko2,ko2,ko ovary,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP499426,,,ko2_1.fq.gz ko2_2.fq.gz,fastq fastq,8095711800.0,26985706.0,ko2 1.fq.gz,0:150 1:150,A:2117986563;C:1909094084;G:1931885806;T:2136732639;N:12708,150,150,,,2117986563,1909094084,1931885806,2136732639,12708,SRX24137318,SRS20921924,,,Shenzhen Second People's Hospital,2,0.9483,0.94443,0.02385,0.02347,0.74266,0.74686,0.45568,0.45676,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-04-03,Adult,Adult,Gonad,Reproductive System
31723,SRR28537219,SRX24137317,SRS20921925,SRP499426,PRJNA1095659,lsm14b ko zebrafish RNA seq,PRJNA1095659,Other,Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation  however  the specific translational regulatory mechanisms remain unclear. Here  our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR  which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes  which ensures that the mRNA synthesized and stored during the growth stage of oocytes  is necessary for the normal growth and development of oocytes.,,,,,ko1,,strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,ko1,ko1,ko1,ko ovary,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP499426,,,ko1_1.fq.gz ko1_2.fq.gz,fastq fastq,9904629000.0,33015430.0,ko1 1.fq.gz,0:150 1:150,A:2565332092;C:2354153391;G:2380645312;T:2604437822;N:60383,150,150,,,2565332092,2354153391,2380645312,2604437822,60383,SRX24137317,SRS20921925,,,Shenzhen Second People's Hospital,2,0.94565,0.94416,0.01943,0.01956,0.7559,0.75739,0.456,0.45903,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-04-03,Adult,Adult,Gonad,Reproductive System
31724,SRR28537220,SRX24137316,SRS20921923,SRP499426,PRJNA1095659,lsm14b ko zebrafish RNA seq,PRJNA1095659,Other,Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation  however  the specific translational regulatory mechanisms remain unclear. Here  our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR  which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes  which ensures that the mRNA synthesized and stored during the growth stage of oocytes  is necessary for the normal growth and development of oocytes.,,,,,wt3,,strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,wt3,wt3,wt3,wt ovary,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP499426,,,wt3_1.fq.gz wt3_2.fq.gz,fastq fastq,10079485500.0,33598285.0,wt3 1.fq.gz,0:150 1:150,A:2607822943;C:2396994959;G:2427407078;T:2647197813;N:62707,150,150,,,2607822943,2396994959,2427407078,2647197813,62707,SRX24137316,SRS20921923,,,Shenzhen Second People's Hospital,2,0.94735,0.94594,0.01733,0.01743,0.75635,0.75712,0.44042,0.46348,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-04-03,Adult,Adult,Gonad,Reproductive System
31725,SRR28537221,SRX24137315,SRS20921920,SRP499426,PRJNA1095659,lsm14b ko zebrafish RNA seq,PRJNA1095659,Other,Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation  however  the specific translational regulatory mechanisms remain unclear. Here  our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR  which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes  which ensures that the mRNA synthesized and stored during the growth stage of oocytes  is necessary for the normal growth and development of oocytes.,,,,,wt2,,strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,wt2,wt2,wt2,wt ovary,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP499426,,,wt2_2.fq.gz wt2_1.fq.gz,fastq fastq,8980086900.0,29933623.0,wt2 1.fq.gz,0:150 1:150,A:2333474507;C:2131182397;G:2149144543;T:2366230132;N:55321,150,150,,,2333474507,2131182397,2149144543,2366230132,55321,SRX24137315,SRS20921920,,,Shenzhen Second People's Hospital,2,0.94182,0.94004,0.0187,0.01854,0.75077,0.75132,0.46271,0.46384,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-04-03,Adult,Adult,Gonad,Reproductive System
31726,SRR28537222,SRX24137314,SRS20921921,SRP499426,PRJNA1095659,lsm14b ko zebrafish RNA seq,PRJNA1095659,Other,Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation  however  the specific translational regulatory mechanisms remain unclear. Here  our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR  which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes  which ensures that the mRNA synthesized and stored during the growth stage of oocytes  is necessary for the normal growth and development of oocytes.,,,,,wt1,,strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,wt1,wt1,wt1,wt ovary,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP499426,,,wt1_1.fq.gz wt1_2.fq.gz,fastq fastq,5436554400.0,18121848.0,wt1 1.fq.gz,0:150 1:150,A:1418897733;C:1287256771;G:1297629578;T:1432736726;N:33592,150,150,,,1418897733,1287256771,1297629578,1432736726,33592,SRX24137314,SRS20921921,,,Shenzhen Second People's Hospital,2,0.9407,0.94657,0.02199,0.02152,0.74655,0.74679,0.47086,0.47165,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-04-03,Adult,Adult,Gonad,Reproductive System
31837,SRR28709001,SRX24276192,SRS21041156,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs  member 9  an extracellular matrix ECM metalloprotease  participates in primordial germ cell PGC migration and necessary for female fertility. In this study  we found that adamts9 knockout KO led to reduced body size  and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however  primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation  significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO  and arrested development at Stage IB follicles in mid  or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq  we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together  our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish  and loss of adamts9 in zebrafish leads to ovarian follicle arrest  female infertility  and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence  we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf61 Ov mt 3,GSM8212808,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing,dpf61 Ov mt 3,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod  lights on at 8:30am  lights off at 10:30pm; at water temperature of 28.5°C  pH of approximately 7.2  and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 61|genotype:mutant,GSM8212808,GSM8212808: dpf61 Ov mt 3; Danio rerio; RNA Seq,GSM8212808 r1,GSM8212808,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.M43_20230510_103430.L001.1.fastq.gz NS51397.M43_20230510_103430.L001.2.fastq.gz,fastq fastq,9024444634.0,29882267.0,GSM8212808 r1,0:151 1:151,A:2471288260;C:1931225512;G:2256742565;T:2363378475;N:1809822,151,151,,,2471288260,1931225512,2256742565,2363378475,1809822,SRX24276192,SRS21041156,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31838,SRR28709002,SRX24276191,SRS21041154,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs  member 9  an extracellular matrix ECM metalloprotease  participates in primordial germ cell PGC migration and necessary for female fertility. In this study  we found that adamts9 knockout KO led to reduced body size  and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however  primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation  significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO  and arrested development at Stage IB follicles in mid  or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq  we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together  our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish  and loss of adamts9 in zebrafish leads to ovarian follicle arrest  female infertility  and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence  we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf61 Ov mt 2,GSM8212807,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing,dpf61 Ov mt 2,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod  lights on at 8:30am  lights off at 10:30pm; at water temperature of 28.5°C  pH of approximately 7.2  and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 61|genotype:mutant,GSM8212807,GSM8212807: dpf61 Ov mt 2; Danio rerio; RNA Seq,GSM8212807 r1,GSM8212807,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.M41_20230510_103430.L001.1.fastq.gz NS51397.M41_20230510_103430.L001.2.fastq.gz,fastq fastq,13553131538.0,44877919.0,GSM8212807 r1,0:151 1:151,A:3707129145;C:2878818514;G:3433054125;T:3531357698;N:2772056,151,151,,,3707129145,2878818514,3433054125,3531357698,2772056,SRX24276191,SRS21041154,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31839,SRR28709003,SRX24276190,SRS21041155,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs  member 9  an extracellular matrix ECM metalloprotease  participates in primordial germ cell PGC migration and necessary for female fertility. In this study  we found that adamts9 knockout KO led to reduced body size  and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however  primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation  significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO  and arrested development at Stage IB follicles in mid  or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq  we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together  our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish  and loss of adamts9 in zebrafish leads to ovarian follicle arrest  female infertility  and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence  we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf61 Ov mt 1,GSM8212806,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing,dpf61 Ov mt 1,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod  lights on at 8:30am  lights off at 10:30pm; at water temperature of 28.5°C  pH of approximately 7.2  and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 61|genotype:mutant,GSM8212806,GSM8212806: dpf61 Ov mt 1; Danio rerio; RNA Seq,GSM8212806 r1,GSM8212806,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.M32_20230510_103430.L001.1.fastq.gz NS51397.M32_20230510_103430.L001.2.fastq.gz,fastq fastq,11752803234.0,38916567.0,GSM8212806 r1,0:151 1:151,A:3199511211;C:2525248103;G:2947698766;T:3077964367;N:2380787,151,151,,,3199511211,2525248103,2947698766,3077964367,2380787,SRX24276190,SRS21041155,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31840,SRR28709004,SRX24276189,SRS21041153,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs  member 9  an extracellular matrix ECM metalloprotease  participates in primordial germ cell PGC migration and necessary for female fertility. In this study  we found that adamts9 knockout KO led to reduced body size  and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however  primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation  significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO  and arrested development at Stage IB follicles in mid  or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq  we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together  our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish  and loss of adamts9 in zebrafish leads to ovarian follicle arrest  female infertility  and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence  we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf61 Ov wt 3,GSM8212805,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:wildtype|geo loc name:missing|collection date:missing,dpf61 Ov wt 3,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod  lights on at 8:30am  lights off at 10:30pm; at water temperature of 28.5°C  pH of approximately 7.2  and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 61|genotype:wildtype,GSM8212805,GSM8212805: dpf61 Ov wt 3; Danio rerio; RNA Seq,GSM8212805 r1,GSM8212805,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.M17_20230510_103430.L001.1.fastq.gz NS51397.M17_20230510_103430.L001.2.fastq.gz,fastq fastq,16726684646.0,55386373.0,GSM8212805 r1,0:151 1:151,A:4912874254;C:2935821083;G:3844206542;T:5030341800;N:3440967,151,151,,,4912874254,2935821083,3844206542,5030341800,3440967,SRX24276189,SRS21041153,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31841,SRR28709005,SRX24276188,SRS21041152,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs  member 9  an extracellular matrix ECM metalloprotease  participates in primordial germ cell PGC migration and necessary for female fertility. In this study  we found that adamts9 knockout KO led to reduced body size  and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however  primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation  significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO  and arrested development at Stage IB follicles in mid  or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq  we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together  our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish  and loss of adamts9 in zebrafish leads to ovarian follicle arrest  female infertility  and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence  we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf61 Ov wt 2,GSM8212804,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:wildtype|geo loc name:missing|collection date:missing,dpf61 Ov wt 2,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod  lights on at 8:30am  lights off at 10:30pm; at water temperature of 28.5°C  pH of approximately 7.2  and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 61|genotype:wildtype,GSM8212804,GSM8212804: dpf61 Ov wt 2; Danio rerio; RNA Seq,GSM8212804 r1,GSM8212804,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.M14_20230510_103430.L001.1.fastq.gz NS51397.M14_20230510_103430.L001.2.fastq.gz,fastq fastq,11600612146.0,38412623.0,GSM8212804 r1,0:151 1:151,A:3087038432;C:2559546168;G:3029729871;T:2921939557;N:2358118,151,151,,,3087038432,2559546168,3029729871,2921939557,2358118,SRX24276188,SRS21041152,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31842,SRR28709006,SRX24276187,SRS21041151,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs  member 9  an extracellular matrix ECM metalloprotease  participates in primordial germ cell PGC migration and necessary for female fertility. In this study  we found that adamts9 knockout KO led to reduced body size  and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however  primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation  significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO  and arrested development at Stage IB follicles in mid  or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq  we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together  our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish  and loss of adamts9 in zebrafish leads to ovarian follicle arrest  female infertility  and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence  we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf61 Ov wt 1,GSM8212803,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:wildtype|geo loc name:missing|collection date:missing,dpf61 Ov wt 1,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod  lights on at 8:30am  lights off at 10:30pm; at water temperature of 28.5°C  pH of approximately 7.2  and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 61|genotype:wildtype,GSM8212803,GSM8212803: dpf61 Ov wt 1; Danio rerio; RNA Seq,GSM8212803 r1,GSM8212803,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.M9_20230510_103430.L001.1.fastq.gz NS51397.M9_20230510_103430.L001.2.fastq.gz,fastq fastq,19081987478.0,63185389.0,GSM8212803 r1,0:151 1:151,A:5188307750;C:4048527738;G:4868706940;T:4972575432;N:3869618,151,151,,,5188307750,4048527738,4868706940,4972575432,3869618,SRX24276187,SRS21041151,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31843,SRR28709007,SRX24276186,SRS21041150,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs  member 9  an extracellular matrix ECM metalloprotease  participates in primordial germ cell PGC migration and necessary for female fertility. In this study  we found that adamts9 knockout KO led to reduced body size  and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however  primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation  significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO  and arrested development at Stage IB follicles in mid  or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq  we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together  our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish  and loss of adamts9 in zebrafish leads to ovarian follicle arrest  female infertility  and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence  we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf47 Ov mt 3,GSM8212802,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:mutant|geo loc name:missing|collection date:missing,dpf47 Ov mt 3,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod  lights on at 8:30am  lights off at 10:30pm; at water temperature of 28.5°C  pH of approximately 7.2  and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 47|genotype:mutant,GSM8212802,GSM8212802: dpf47 Ov mt 3; Danio rerio; RNA Seq,GSM8212802 r1,GSM8212802,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.C33_20230510_103430.L001.1.fastq.gz NS51397.C33_20230510_103430.L001.2.fastq.gz,fastq fastq,8256087174.0,27338037.0,GSM8212802 r1,0:151 1:151,A:2217123657;C:1857924925;G:2109544983;T:2069850323;N:1643286,151,151,,,2217123657,1857924925,2109544983,2069850323,1643286,SRX24276186,SRS21041150,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31844,SRR28709008,SRX24276185,SRS21041149,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs  member 9  an extracellular matrix ECM metalloprotease  participates in primordial germ cell PGC migration and necessary for female fertility. In this study  we found that adamts9 knockout KO led to reduced body size  and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however  primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation  significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO  and arrested development at Stage IB follicles in mid  or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq  we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together  our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish  and loss of adamts9 in zebrafish leads to ovarian follicle arrest  female infertility  and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence  we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf47 Ov mt 2,GSM8212801,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:mutant|geo loc name:missing|collection date:missing,dpf47 Ov mt 2,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod  lights on at 8:30am  lights off at 10:30pm; at water temperature of 28.5°C  pH of approximately 7.2  and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 47|genotype:mutant,GSM8212801,GSM8212801: dpf47 Ov mt 2; Danio rerio; RNA Seq,GSM8212801 r1,GSM8212801,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.C32_20230510_103430.L001.1.fastq.gz NS51397.C32_20230510_103430.L001.2.fastq.gz,fastq fastq,14985320634.0,49620267.0,GSM8212801 r1,0:151 1:151,A:4058920258;C:3245799385;G:3815485722;T:3862070151;N:3045118,151,151,,,4058920258,3245799385,3815485722,3862070151,3045118,SRX24276185,SRS21041149,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31845,SRR28709009,SRX24276184,SRS21041147,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs  member 9  an extracellular matrix ECM metalloprotease  participates in primordial germ cell PGC migration and necessary for female fertility. In this study  we found that adamts9 knockout KO led to reduced body size  and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however  primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation  significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO  and arrested development at Stage IB follicles in mid  or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq  we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together  our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish  and loss of adamts9 in zebrafish leads to ovarian follicle arrest  female infertility  and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence  we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf47 Ov mt 1,GSM8212800,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:mutant|geo loc name:missing|collection date:missing,dpf47 Ov mt 1,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod  lights on at 8:30am  lights off at 10:30pm; at water temperature of 28.5°C  pH of approximately 7.2  and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 47|genotype:mutant,GSM8212800,GSM8212800: dpf47 Ov mt 1; Danio rerio; RNA Seq,GSM8212800 r1,GSM8212800,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.C29_20230510_103430.L001.1.fastq.gz NS51397.C29_20230510_103430.L001.2.fastq.gz,fastq fastq,11177741176.0,37012388.0,GSM8212800 r1,0:151 1:151,A:3060199842;C:2374800912;G:2799391711;T:2941063533;N:2285178,151,151,,,3060199842,2374800912,2799391711,2941063533,2285178,SRX24276184,SRS21041147,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31846,SRR28709010,SRX24276183,SRS21041146,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs  member 9  an extracellular matrix ECM metalloprotease  participates in primordial germ cell PGC migration and necessary for female fertility. In this study  we found that adamts9 knockout KO led to reduced body size  and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however  primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation  significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO  and arrested development at Stage IB follicles in mid  or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq  we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together  our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish  and loss of adamts9 in zebrafish leads to ovarian follicle arrest  female infertility  and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence  we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf47 Ov wt 3,GSM8212799,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:wildtype|geo loc name:missing|collection date:missing,dpf47 Ov wt 3,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod  lights on at 8:30am  lights off at 10:30pm; at water temperature of 28.5°C  pH of approximately 7.2  and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 47|genotype:wildtype,GSM8212799,GSM8212799: dpf47 Ov wt 3; Danio rerio; RNA Seq,GSM8212799 r1,GSM8212799,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.C21_20230510_103430.L001.1.fastq.gz NS51397.C21_20230510_103430.L001.2.fastq.gz,fastq fastq,13599817718.0,45032509.0,GSM8212799 r1,0:151 1:151,A:3724782410;C:2835413438;G:3575258078;T:3461647906;N:2715886,151,151,,,3724782410,2835413438,3575258078,3461647906,2715886,SRX24276183,SRS21041146,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31847,SRR28709011,SRX24276182,SRS21041148,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs  member 9  an extracellular matrix ECM metalloprotease  participates in primordial germ cell PGC migration and necessary for female fertility. In this study  we found that adamts9 knockout KO led to reduced body size  and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however  primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation  significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO  and arrested development at Stage IB follicles in mid  or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq  we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together  our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish  and loss of adamts9 in zebrafish leads to ovarian follicle arrest  female infertility  and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence  we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf47 Ov wt 2,GSM8212798,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:wildtype|geo loc name:missing|collection date:missing,dpf47 Ov wt 2,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod  lights on at 8:30am  lights off at 10:30pm; at water temperature of 28.5°C  pH of approximately 7.2  and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 47|genotype:wildtype,GSM8212798,GSM8212798: dpf47 Ov wt 2; Danio rerio; RNA Seq,GSM8212798 r1,GSM8212798,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.C20_20230510_103430.L001.1.fastq.gz NS51397.C20_20230510_103430.L001.2.fastq.gz,fastq fastq,13632935642.0,45142171.0,GSM8212798 r1,0:151 1:151,A:3708965267;C:2903664830;G:3492295019;T:3525245989;N:2764537,151,151,,,3708965267,2903664830,3492295019,3525245989,2764537,SRX24276182,SRS21041148,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31848,SRR28709012,SRX24276181,SRS21041145,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs  member 9  an extracellular matrix ECM metalloprotease  participates in primordial germ cell PGC migration and necessary for female fertility. In this study  we found that adamts9 knockout KO led to reduced body size  and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however  primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation  significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO  and arrested development at Stage IB follicles in mid  or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq  we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together  our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish  and loss of adamts9 in zebrafish leads to ovarian follicle arrest  female infertility  and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence  we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf47 Ov wt 1,GSM8212797,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:wildtype|geo loc name:missing|collection date:missing,dpf47 Ov wt 1,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod  lights on at 8:30am  lights off at 10:30pm; at water temperature of 28.5°C  pH of approximately 7.2  and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 47|genotype:wildtype,GSM8212797,GSM8212797: dpf47 Ov wt 1; Danio rerio; RNA Seq,GSM8212797 r1,GSM8212797,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at  800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.C4_20230510_103430.L001.1.fastq.gz NS51397.C4_20230510_103430.L001.2.fastq.gz,fastq fastq,12378485324.0,40988362.0,GSM8212797 r1,0:151 1:151,A:3378421522;C:2638098449;G:3108553273;T:3250895048;N:2517032,151,151,,,3378421522,2638098449,3108553273,3250895048,2517032,SRX24276181,SRS21041145,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
32362,SRR29157958,SRX24679082,SRS21413713,SRP509709,PRJNA1115529,Danio rerio Raw sequence reads of gonadal tissue,PRJNA1115529,Whole Genome Sequencing,Evaluation of gene expression changes in zebrafish gonads following a full life cycle exposure to the non steroidal anti inflammatory drug naproxen NPX in order to evaluate the main pathways affected,,,The current study assessed the long term effects of environmentally relevant concentrations of NPX ng/L to low g/L on zebrafish ovary,Model organism or animal sample from Danio rerio,Ovary NPX,,strain:AB|age:4 month|dev stage:Adult|collection date:2021 03|geo loc name:Portugal: Matosinhos|sex:female|tissue:Ovary|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish ovary RNA seq from NPX,Ovary NPX,Ovary NPX,The current study assessed the long term effects of environmentally relevant concentrations of NPX ng/L to low g/L on parental zebrafish ovary,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP509709,,,H4_2.fq.gz H4_1.fq.gz H3_2.fq.gz H3_1.fq.gz H2_2.fq.gz H2_1.fq.gz H1_2.fq.gz H1_1.fq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,37288126200.0,124293754.0,H1 1.fq.gz,0:150 1:150,A:9870906480;C:8895442858;G:8761667172;T:9759826428;N:283262,150,150,,,9870906480,8895442858,8761667172,9759826428,283262,SRX24679082,SRS21413713,SRA1876810,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research,2,0.93451,0.93482,0.01992,0.01985,0.75966,0.75943,0.45469,0.4556,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Portugal,2024-05-24,Adult,Adult,Gonad,Reproductive System
32363,SRR29157959,SRX24679081,SRS21413712,SRP509709,PRJNA1115529,Danio rerio Raw sequence reads of gonadal tissue,PRJNA1115529,Whole Genome Sequencing,Evaluation of gene expression changes in zebrafish gonads following a full life cycle exposure to the non steroidal anti inflammatory drug naproxen NPX in order to evaluate the main pathways affected,,,The current study assessed the long term effects of environmentally relevant concentrations of NPX ng/L to low g/L on zebrafish ovary,Model organism or animal sample from Danio rerio,Ovary Ctrl,,strain:AB|age:4 month|dev stage:Adult|collection date:2021 03|geo loc name:Portugal: Matosinhos|sex:female|tissue:Ovary|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish ovary RNA seq from Control,Ovary CTRL,Ovary CTRL,The current study assessed the long term effects of environmentally relevant concentrations of NPX ng/L to low g/L on parental zebrafish ovary,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP509709,,,D4_2.fq.gz D4_1.fq.gz D3_2.fq.gz D3_1.fq.gz D2_2.fq.gz D2_1.fq.gz D1_2.fq.gz D1_1.fq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,48240351600.0,160801172.0,D1 1.fq.gz,0:150 1:150,A:12507813252;C:11711256340;G:11706267844;T:12313668932;N:1345232,150,150,,,12507813252,11711256340,11706267844,12313668932,1345232,SRX24679081,SRS21413712,SRA1876810,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research,2,0.93217,0.93303,0.01595,0.01634,0.75948,0.75998,0.46158,0.46061,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Portugal,2024-05-24,Adult,Adult,Gonad,Reproductive System
32364,SRR29157960,SRX24679080,SRS21413711,SRP509709,PRJNA1115529,Danio rerio Raw sequence reads of gonadal tissue,PRJNA1115529,Whole Genome Sequencing,Evaluation of gene expression changes in zebrafish gonads following a full life cycle exposure to the non steroidal anti inflammatory drug naproxen NPX in order to evaluate the main pathways affected,,,The current study assessed the long term effects of environmentally relevant concentrations of NPX ng/L to low g/L on zebrafish testis,Model organism or animal sample from Danio rerio,Testis NPX,,strain:AB|age:4 month|dev stage:Adult|collection date:2021 03|geo loc name:Portugal: Matosinhos|sex:male|tissue:Testis|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish testis RNA seq from NPX,Testis NPX,Testis NPX,The current study assessed the long term effects of environmentally relevant concentrations of NPX ng/L to low g/L on parental zebrafish testis,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP509709,,,G4_2.fq.gz G4_1.fq.gz G3_2.fq.gz G3_1.fq.gz G2_2.fq.gz G2_1.fq.gz G1_2.fq.gz G1_1.fq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,48293186700.0,160977289.0,G1 1.fq.gz,0:150 1:150,A:12737664564;C:11515099418;G:11506913376;T:12532403181;N:1106161,150,150,,,12737664564,11515099418,11506913376,12532403181,1106161,SRX24679080,SRS21413711,SRA1876810,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research,2,0.93531,0.93628,0.04883,0.04847,0.66707,0.66728,0.47213,0.47226,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Portugal,2024-05-24,Adult,Adult,Gonad,Reproductive System
32365,SRR29157961,SRX24679079,SRS21413710,SRP509709,PRJNA1115529,Danio rerio Raw sequence reads of gonadal tissue,PRJNA1115529,Whole Genome Sequencing,Evaluation of gene expression changes in zebrafish gonads following a full life cycle exposure to the non steroidal anti inflammatory drug naproxen NPX in order to evaluate the main pathways affected,,,The current study assessed the long term effects of environmentally relevant concentrations of NPX ng/L to low g/L on parental zebrafish testis,Model organism or animal sample from Danio rerio,Testis CTRL,,strain:AB|age:4 month|dev stage:Adult|collection date:2021 03|geo loc name:Portugal: Matosinhos|sex:male|tissue:Testis|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish testis RNA seq from Control,Testis CTRL,Testis CTRL,The current study assessed the long term effects of environmentally relevant concentrations of NPX ng/L to low g/L on parental zebrafish testis,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP509709,,,C4_2.fq.gz C4_1.fq.gz C3_2.fq.gz C3_1.fq.gz C2_2.fq.gz C2_1.fq.gz C1_2.fq.gz C1_1.fq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,47457731100.0,158192437.0,C1 1.fq.gz,0:150 1:150,A:12817545225;C:10993554835;G:10941137146;T:12704995076;N:498818,150,150,,,12817545225,10993554835,10941137146,12704995076,498818,SRX24679079,SRS21413710,SRA1876810,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research,2,0.93023,0.9282,0.0889,0.08851,0.63106,0.63098,0.4869,0.48618,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Portugal,2024-05-24,Adult,Adult,Gonad,Reproductive System
33663,SRR30502664,SRX25926478,SRS22513929,SRP529840,PRJNA1154960,Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries,GSE276129,Transcriptome Analysis,Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study  using the ddx4 L knockout zebrafish model  we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified  of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization  sperm egg recognition process  and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore  we found that Sycp1  a synaptonemal complex protein involved in meiosis and fertility  was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover  the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons  a subclass of transposable elements  in zebrafish ovaries. In conclusion  the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality  possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf  respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.,,pubmed:39765722,,ddx4E4Δ ovary rep3,GSM8491761,,source name:Ovary|tissue:Ovary|genotype:ddx4E4{delta}|geo loc name:missing|collection date:missing,ddx4E4Δ ovary rep3,The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish  the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially  differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples.,Ovary,,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,tissue:Ovary|genotype:ddx4E4{delta},GSM8491761,GSM8491761: ddx4E4Δ ovary rep3; Danio rerio; RNA Seq,GSM8491761 r1,GSM8491761,1,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP529840,,,D3_R1.fastq.gz D3_R2.fastq.gz,fastq fastq,8532086786.0,28251943.0,GSM8491761 r1,0:151 1:151,A:2175886107;C:2065104971;G:2109654211;T:2181416846;N:24651,151,151,,,2175886107,2065104971,2109654211,2181416846,24651,SRX25926478,SRS22513929,SRA1960397,"Institute of Hydrobiology, Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2024-08-31,Adult,Adult,Gonad,Reproductive System
33664,SRR30502665,SRX25926477,SRS22513928,SRP529840,PRJNA1154960,Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries,GSE276129,Transcriptome Analysis,Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study  using the ddx4 L knockout zebrafish model  we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified  of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization  sperm egg recognition process  and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore  we found that Sycp1  a synaptonemal complex protein involved in meiosis and fertility  was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover  the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons  a subclass of transposable elements  in zebrafish ovaries. In conclusion  the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality  possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf  respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.,,pubmed:39765722,,ddx4E4Δ ovary rep2,GSM8491760,,source name:Ovary|tissue:Ovary|genotype:ddx4E4{delta}|geo loc name:missing|collection date:missing,ddx4E4Δ ovary rep2,The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish  the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially  differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples.,Ovary,,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,tissue:Ovary|genotype:ddx4E4{delta},GSM8491760,GSM8491760: ddx4E4Δ ovary rep2; Danio rerio; RNA Seq,GSM8491760 r1,GSM8491760,1,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP529840,,,D2_R1.fastq.gz D2_R2.fastq.gz,fastq fastq,8420834516.0,27883558.0,GSM8491760 r1,0:151 1:151,A:2130607193;C:2053627459;G:2099203008;T:2137372997;N:23859,151,151,,,2130607193,2053627459,2099203008,2137372997,23859,SRX25926477,SRS22513928,SRA1960397,"Institute of Hydrobiology, Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2024-08-31,Adult,Adult,Gonad,Reproductive System
33665,SRR30502666,SRX25926476,SRS22513927,SRP529840,PRJNA1154960,Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries,GSE276129,Transcriptome Analysis,Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study  using the ddx4 L knockout zebrafish model  we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified  of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization  sperm egg recognition process  and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore  we found that Sycp1  a synaptonemal complex protein involved in meiosis and fertility  was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover  the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons  a subclass of transposable elements  in zebrafish ovaries. In conclusion  the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality  possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf  respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.,,pubmed:39765722,,ddx4E4Δ ovary rep1,GSM8491759,,source name:Ovary|tissue:Ovary|genotype:ddx4E4{delta}|geo loc name:missing|collection date:missing,ddx4E4Δ ovary rep1,The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish  the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially  differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples.,Ovary,,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,tissue:Ovary|genotype:ddx4E4{delta},GSM8491759,GSM8491759: ddx4E4Δ ovary rep1; Danio rerio; RNA Seq,GSM8491759 r1,GSM8491759,1,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP529840,,,D1_R1.fastq.gz D1_R2.fastq.gz,fastq fastq,8478573292.0,28074746.0,GSM8491759 r1,0:151 1:151,A:2141904837;C:2071392554;G:2116256871;T:2148995183;N:23847,151,151,,,2141904837,2071392554,2116256871,2148995183,23847,SRX25926476,SRS22513927,SRA1960397,"Institute of Hydrobiology, Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2024-08-31,Adult,Adult,Gonad,Reproductive System
33666,SRR30502667,SRX25926475,SRS22513926,SRP529840,PRJNA1154960,Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries,GSE276129,Transcriptome Analysis,Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study  using the ddx4 L knockout zebrafish model  we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified  of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization  sperm egg recognition process  and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore  we found that Sycp1  a synaptonemal complex protein involved in meiosis and fertility  was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover  the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons  a subclass of transposable elements  in zebrafish ovaries. In conclusion  the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality  possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf  respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.,,pubmed:39765722,,WT ovary rep3,GSM8491758,,source name:Ovary|tissue:Ovary|genotype:WT|geo loc name:missing|collection date:missing,WT ovary rep3,The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish  the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially  differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples.,Ovary,,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,tissue:Ovary|genotype:WT,GSM8491758,GSM8491758: WT ovary rep3; Danio rerio; RNA Seq,GSM8491758 r1,GSM8491758,1,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP529840,,,W3_R1.fastq.gz W3_R2.fastq.gz,fastq fastq,9507568228.0,31482014.0,GSM8491758 r1,0:151 1:151,A:2403365632;C:2318225719;G:2368354059;T:2417595791;N:27027,151,151,,,2403365632,2318225719,2368354059,2417595791,27027,SRX25926475,SRS22513926,SRA1960397,"Institute of Hydrobiology, Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2024-08-31,Adult,Adult,Gonad,Reproductive System
33667,SRR30502668,SRX25926474,SRS22513925,SRP529840,PRJNA1154960,Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries,GSE276129,Transcriptome Analysis,Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study  using the ddx4 L knockout zebrafish model  we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified  of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization  sperm egg recognition process  and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore  we found that Sycp1  a synaptonemal complex protein involved in meiosis and fertility  was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover  the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons  a subclass of transposable elements  in zebrafish ovaries. In conclusion  the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality  possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf  respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.,,pubmed:39765722,,WT ovary rep2,GSM8491757,,source name:Ovary|tissue:Ovary|genotype:WT|geo loc name:missing|collection date:missing,WT ovary rep2,The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish  the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially  differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples.,Ovary,,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,tissue:Ovary|genotype:WT,GSM8491757,GSM8491757: WT ovary rep2; Danio rerio; RNA Seq,GSM8491757 r1,GSM8491757,1,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP529840,,,W2_R1.fastq.gz W2_R2.fastq.gz,fastq fastq,8515265084.0,28196242.0,GSM8491757 r1,0:151 1:151,A:2152677268;C:2074877248;G:2122308956;T:2165377885;N:23727,151,151,,,2152677268,2074877248,2122308956,2165377885,23727,SRX25926474,SRS22513925,SRA1960397,"Institute of Hydrobiology, Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2024-08-31,Adult,Adult,Gonad,Reproductive System
33668,SRR30502669,SRX25926473,SRS22513924,SRP529840,PRJNA1154960,Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries,GSE276129,Transcriptome Analysis,Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study  using the ddx4 L knockout zebrafish model  we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified  of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization  sperm egg recognition process  and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore  we found that Sycp1  a synaptonemal complex protein involved in meiosis and fertility  was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover  the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons  a subclass of transposable elements  in zebrafish ovaries. In conclusion  the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality  possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf  respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.,,pubmed:39765722,,WT ovary rep1,GSM8491756,,source name:Ovary|tissue:Ovary|genotype:WT|geo loc name:missing|collection date:missing,WT ovary rep1,The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish  the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially  differential expression analysis was performed using the DESeq2 software. DEGs with |log2FC|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples.,Ovary,,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,tissue:Ovary|genotype:WT,GSM8491756,GSM8491756: WT ovary rep1; Danio rerio; RNA Seq,GSM8491756 r1,GSM8491756,1,Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina  San Diego  CA. About 1μg of high quality total RNA samples OD260/280=1.82.2  RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP529840,,,W1_R1.fastq.gz W1_R2.fastq.gz,fastq fastq,8347159200.0,27639600.0,GSM8491756 r1,0:151 1:151,A:2109928092;C:2033967699;G:2079802211;T:2123438464;N:22734,151,151,,,2109928092,2033967699,2079802211,2123438464,22734,SRX25926473,SRS22513924,SRA1960397,"Institute of Hydrobiology, Chinese Academy of Sciences","Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2024-08-31,Adult,Adult,Gonad,Reproductive System
33916,SRR30920839,SRX26323786,SRS22850830,SRP537366,PRJNA1169999,Danio rerio Raw sequence reads,PRJNA1169999,Other,Transcriptional analysis of zebrafish,,,,,PF iv 1,,strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,PF iv 1,PF iv 1,PF iv 1,the primary follicles of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP537366,,,PF_iv_1_1.fq.gz PF_iv_1_2.fq.gz,fastq fastq,7070670900.0,23568903.0,PF iv 1 1.fq.gz,0:150 1:150,A:1943964885;C:1626486936;G:1603332965;T:1896802175;N:83939,150,150,,,1943964885,1626486936,1603332965,1896802175,83939,SRX26323786,SRS22850830,SRA1988616,Hunan Normal University|School of Life Sciences,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-10-09,Adult,Adult,Gonad,Reproductive System
33917,SRR30920840,SRX26323785,SRS22850828,SRP537366,PRJNA1169999,Danio rerio Raw sequence reads,PRJNA1169999,Other,Transcriptional analysis of zebrafish,,,,,PF iii 3,,strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,PF iii 3,PF iii 3,PF iii 3,the primary follicles of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP537366,,,PF_iii_3_1.fq.gz PF_iii_3_2.fq.gz,fastq fastq,6934323600.0,23114412.0,PF iii 3 1.fq.gz,0:150 1:150,A:1813397404;C:1659011482;G:1680744429;T:1781143700;N:26585,150,150,,,1813397404,1659011482,1680744429,1781143700,26585,SRX26323785,SRS22850828,SRA1988616,Hunan Normal University|School of Life Sciences,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-10-09,Adult,Adult,Gonad,Reproductive System
33918,SRR30920841,SRX26323784,SRS22850835,SRP537366,PRJNA1169999,Danio rerio Raw sequence reads,PRJNA1169999,Other,Transcriptional analysis of zebrafish,,,,,PF iii 2,,strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,PF iii 2,PF iii 2,PF iii 2,the primary follicles of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP537366,,,PF_iii_2_1.fq.gz PF_iii_2_2.fq.gz,fastq fastq,7255113000.0,24183710.0,PF iii 2 1.fq.gz,0:150 1:150,A:1877711956;C:1751268862;G:1779105498;T:1846998314;N:28370,150,150,,,1877711956,1751268862,1779105498,1846998314,28370,SRX26323784,SRS22850835,SRA1988616,Hunan Normal University|School of Life Sciences,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-10-09,Adult,Adult,Gonad,Reproductive System
33919,SRR30920842,SRX26323783,SRS22850829,SRP537366,PRJNA1169999,Danio rerio Raw sequence reads,PRJNA1169999,Other,Transcriptional analysis of zebrafish,,,,,PF iii 1,,strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,PF iii 1,PF iii 1,PF iii 1,the primary follicles of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP537366,,,PF_iii_1_1.fq.gz PF_iii_1_2.fq.gz,fastq fastq,7367112000.0,24557040.0,PF iii 1 1.fq.gz,0:150 1:150,A:1943591568;C:1745588879;G:1774109048;T:1903793252;N:29253,150,150,,,1943591568,1745588879,1774109048,1903793252,29253,SRX26323783,SRS22850829,SRA1988616,Hunan Normal University|School of Life Sciences,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-10-09,Adult,Adult,Gonad,Reproductive System
33920,SRR30920843,SRX26323782,SRS22850827,SRP537366,PRJNA1169999,Danio rerio Raw sequence reads,PRJNA1169999,Other,Transcriptional analysis of zebrafish,,,,,PF ii 3,,strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China:Changsha|sex:female|tissue:ovary|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,PF ii 3,PF ii 3,PF ii 3,the primary follicles of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP537366,,,PF_ii_3_1.fq.gz PF_ii_3_2.fq.gz,fastq fastq,7076391300.0,23587971.0,PF ii 3 1.fq.gz,0:150 1:150,A:1894076667;C:1654017021;G:1661713202;T:1866530077;N:54333,150,150,,,1894076667,1654017021,1661713202,1866530077,54333,SRX26323782,SRS22850827,SRA1988616,Hunan Normal University|School of Life Sciences,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-10-09,Adult,Adult,Gonad,Reproductive System
33921,SRR30920844,SRX26323781,SRS22850824,SRP537366,PRJNA1169999,Danio rerio Raw sequence reads,PRJNA1169999,Other,Transcriptional analysis of zebrafish,,,,,PF ii 2,,strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China:Changsha|sex:female|tissue:ovary|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,PF ii 2,PF ii 2,PF ii 2,the primary follicles of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP537366,,,PF_ii_2_1.fq.gz PF_ii_2_2.fq.gz,fastq fastq,7019128200.0,23397094.0,PF ii 2 1.fq.gz,0:150 1:150,A:1864708472;C:1652262592;G:1662746794;T:1839356863;N:53479,150,150,,,1864708472,1652262592,1662746794,1839356863,53479,SRX26323781,SRS22850824,SRA1988616,Hunan Normal University|School of Life Sciences,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-10-09,Adult,Adult,Gonad,Reproductive System
33922,SRR30920845,SRX26323780,SRS22850826,SRP537366,PRJNA1169999,Danio rerio Raw sequence reads,PRJNA1169999,Other,Transcriptional analysis of zebrafish,,,,,PF ii 1,,strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China:Changsha|sex:female|tissue:ovary|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,PF ii 1,PF ii 1,PF ii 1,the primary follicles of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP537366,,,PF_ii_1_1.fq.gz PF_ii_1_2.fq.gz,fastq fastq,8013867900.0,26712893.0,PF ii 1 1.fq.gz,0:150 1:150,A:2115645121;C:1898389790;G:1909480370;T:2090291064;N:61555,150,150,,,2115645121,1898389790,1909480370,2090291064,61555,SRX26323780,SRS22850826,SRA1988616,Hunan Normal University|School of Life Sciences,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-10-09,Adult,Adult,Gonad,Reproductive System
33923,SRR30920846,SRX26323779,SRS22850825,SRP537366,PRJNA1169999,Danio rerio Raw sequence reads,PRJNA1169999,Other,Transcriptional analysis of zebrafish,,,,,PF i 3,,strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,PF i 3,PF i 3,PF i 3,the primary follicles of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP537366,,,PF_i_3_1.fq.gz PF_i_3_2.fq.gz,fastq fastq,8319390000.0,27731300.0,PF i 3 1.fq.gz,0:150 1:150,A:2161188519;C:1997121516;G:2035390212;T:2125657588;N:32165,150,150,,,2161188519,1997121516,2035390212,2125657588,32165,SRX26323779,SRS22850825,SRA1988616,Hunan Normal University|School of Life Sciences,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-10-09,Adult,Adult,Gonad,Reproductive System
33924,SRR30920847,SRX26323778,SRS22850823,SRP537366,PRJNA1169999,Danio rerio Raw sequence reads,PRJNA1169999,Other,Transcriptional analysis of zebrafish,,,,,PF iv 3,,strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,PF iv 3,PF iv 3,PF iv 3,the primary follicles of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP537366,,,PF_iv_3_1.fq.gz PF_iv_3_2.fq.gz,fastq fastq,7173257700.0,23910859.0,PF iv 3 1.fq.gz,0:150 1:150,A:1875724697;C:1713434205;G:1745363776;T:1838706880;N:28142,150,150,,,1875724697,1713434205,1745363776,1838706880,28142,SRX26323778,SRS22850823,SRA1988616,Hunan Normal University|School of Life Sciences,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-10-09,Adult,Adult,Gonad,Reproductive System
33925,SRR30920848,SRX26323777,SRS22850821,SRP537366,PRJNA1169999,Danio rerio Raw sequence reads,PRJNA1169999,Other,Transcriptional analysis of zebrafish,,,,,PF iv 2,,strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,PF iv 2,PF iv 2,PF iv 2,the primary follicles of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP537366,,,PF_iv_2_1.fq.gz PF_iv_2_2.fq.gz,fastq fastq,7161631500.0,23872105.0,PF iv 2 1.fq.gz,0:150 1:150,A:1890379638;C:1697508923;G:1718050265;T:1855664701;N:27973,150,150,,,1890379638,1697508923,1718050265,1855664701,27973,SRX26323777,SRS22850821,SRA1988616,Hunan Normal University|School of Life Sciences,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-10-09,Adult,Adult,Gonad,Reproductive System
33926,SRR30920849,SRX26323776,SRS22850822,SRP537366,PRJNA1169999,Danio rerio Raw sequence reads,PRJNA1169999,Other,Transcriptional analysis of zebrafish,,,,,PF i 2,,strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,PF i 2,PF i 2,PF i 2,the primary follicles of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP537366,,,PF_i_2_1.fq.gz PF_i_2_2.fq.gz,fastq fastq,7036742700.0,23455809.0,PF i 2 1.fq.gz,0:150 1:150,A:1861224200;C:1662236616;G:1671149144;T:1842079812;N:52928,150,150,,,1861224200,1662236616,1671149144,1842079812,52928,SRX26323776,SRS22850822,SRA1988616,Hunan Normal University|School of Life Sciences,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-10-09,Adult,Adult,Gonad,Reproductive System
33927,SRR30920850,SRX26323775,SRS22850820,SRP537366,PRJNA1169999,Danio rerio Raw sequence reads,PRJNA1169999,Other,Transcriptional analysis of zebrafish,,,,,PF i 1,,strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,PF i 1,PF i 1,PF i 1,the primary follicles of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP537366,,,PF_i_1_1.fq.gz PF_i_1_2.fq.gz,fastq fastq,6977957400.0,23259858.0,PF i 1 1.fq.gz,0:150 1:150,A:1821299728;C:1674791787;G:1691820873;T:1790017865;N:27147,150,150,,,1821299728,1674791787,1691820873,1790017865,27147,SRX26323775,SRS22850820,SRA1988616,Hunan Normal University|School of Life Sciences,Hunan Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-10-09,Adult,Adult,Gonad,Reproductive System
34128,SRR31371655,SRX26745254,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PC3 R1.fq,PC3 R1.fq,CuNPs and melatonin treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PC3_R1.fq.gz PC3_R2.fq.gz,fastq fastq,8050557450.0,26657475.0,PC3 R1.fq.gz,,,,,,,,,,,,SRX26745254,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34129,SRR31371656,SRX26745253,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PC2 R1.fq,PC2 R1.fq,CuNPs and melatonin treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PC2_R1.fq.gz PC2_R2.fq.gz,fastq fastq,7072903722.0,23420211.0,PC2 R1.fq.gz,0:151 1:151,A:1848366962;C:1685927772;G:1702568524;T:1835518466;N:521998,151,151,,,1848366962,1685927772,1702568524,1835518466,521998,SRX26745253,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34130,SRR31371657,SRX26745252,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PC1 R1.fq,PC1 R1.fq,CuNPs and melatonin treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PC1_R1.fq.gz PC1_R2.fq.gz,fastq fastq,9551575668.0,31627734.0,PC1 R1.fq.gz,,,,,,,,,,,,SRX26745252,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34131,SRR31371658,SRX26745251,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PB3 R1.fq,PB3 R1.fq,CuNPs treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PB3_R1.fq.gz PB3_R2.fq.gz,fastq fastq,6839092000.0,22646000.0,PB3 R1.fq.gz,,,,,,,,,,,,SRX26745251,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34132,SRR31371659,SRX26745250,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PB2 R1.fq,PB2 R1.fq,CuNPs treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PB2_R1.fq.gz PB2_R2.fq.gz,fastq fastq,7582292558.0,25106929.0,PB2 R1.fq.gz,,,,,,,,,,,,SRX26745250,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34133,SRR31371660,SRX26745249,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PB1 R1.fq,PB1 R1.fq,CuNPs treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PB1_R1.fq.gz PB1_R2.fq.gz,fastq fastq,8122972218.0,26897259.0,PB1 R1.fq.gz,,,,,,,,,,,,SRX26745249,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34134,SRR31371661,SRX26745248,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,CA3 R1.fq,CA3 R1.fq,control,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,CA3_R1.fq.gz CA3_R2.fq.gz,fastq fastq,7638136586.0,25291843.0,CA3 R1.fq.gz,,,,,,,,,,,,SRX26745248,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34135,SRR31371662,SRX26745247,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,CA1 R1.fq,CA1 R1.fq,control,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,CA1_R1.fq.gz CA1_R2.fq.gz,fastq fastq,7499744784.0,24833592.0,CA1 R1.fq.gz,0:151 1:151,A:1951636355;C:1801626786;G:1812560367;T:1933366696;N:554580,151,151,,,1951636355,1801626786,1812560367,1933366696,554580,SRX26745247,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34136,SRR31371663,SRX26745246,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,CA2 R1.fq,CA2 R1.fq,control,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,CA2_R1.fq.gz CA2_R2.fq.gz,fastq fastq,6253035330.0,20705415.0,CA2 R1.fq.gz,,,,,,,,,,,,SRX26745246,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34425,SRR31754963,SRX27116846,SRS23574567,SRP552202,PRJNA1199694,Zebrafish ovarian RNA seq,PRJNA1199694,Other,Adult female zebrafish ovaries were taken for subsequent analyses.In this study  we used RNA seq results to uncover the key pathways involved in ovarian damage caused by single and combined exposure to EPO and AFB1.,,,,,ovary AFB2,,strain:not collected|isolate:ovary AFB2|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:ovary|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,transcriptomic sequencing,LRA172648,LRA172648,The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552202,,,AFB2_R2.fastq.gz AFB2_R1.fastq.gz,fastq fastq,8264268656.0,27365128.0,AFB2 R1.fastq.gz,0:151 1:151,A:2181967333;C:1933268479;G:1966876338;T:2182007880;N:148626,151,151,,,2181967333,1933268479,1966876338,2182007880,148626,SRX27116846,SRS23574567,SRA2036776,shandong university|School of Public Health,shandong university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-12-17,Adult,Adult,Gonad,Reproductive System
34426,SRR31754964,SRX27116845,SRS23574566,SRP552202,PRJNA1199694,Zebrafish ovarian RNA seq,PRJNA1199694,Other,Adult female zebrafish ovaries were taken for subsequent analyses.In this study  we used RNA seq results to uncover the key pathways involved in ovarian damage caused by single and combined exposure to EPO and AFB1.,,,,,ovary AFB1,,strain:not collected|isolate:ovary AFB1|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:ovary|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,transcriptomic sequencing,LRA172647,LRA172647,The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552202,,,AFB1_R1.fastq.gz AFB1_R2.fastq.gz,fastq fastq,8208094240.0,27179120.0,AFB1 R1.fastq.gz,0:151 1:151,A:2198424448;C:1899278946;G:1926174417;T:2184068899;N:147530,151,151,,,2198424448,1899278946,1926174417,2184068899,147530,SRX27116845,SRS23574566,SRA2036776,shandong university|School of Public Health,shandong university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-12-17,Adult,Adult,Gonad,Reproductive System
34427,SRR31754965,SRX27116844,SRS23574565,SRP552202,PRJNA1199694,Zebrafish ovarian RNA seq,PRJNA1199694,Other,Adult female zebrafish ovaries were taken for subsequent analyses.In this study  we used RNA seq results to uncover the key pathways involved in ovarian damage caused by single and combined exposure to EPO and AFB1.,,,,,ovary EPO4,,strain:not collected|isolate:ovary EPO4|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:ovary|replicate:biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,transcriptomic sequencing,LRA172655,LRA172655,The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552202,,,EPO4_R1.fastq.gz EPO4_R2.fastq.gz,fastq fastq,6421073868.0,21261834.0,EPO4 R1.fastq.gz,0:151 1:151,A:1714628675;C:1485463411;G:1507815048;T:1712492241;N:674493,151,151,,,1714628675,1485463411,1507815048,1712492241,674493,SRX27116844,SRS23574565,SRA2036776,shandong university|School of Public Health,shandong university,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-12-17,Adult,Adult,Gonad,Reproductive System