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 39616,SRR1873564,SRX915244,SRS870230,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.,,pubmed:26694924,,45dpf,GSM1630508,,source name:45 dpf embryos|strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:45dpf,45dpf,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005 19:1288 1293 and a miRNA expression profile using identical number of reads for each sample was generated. The number of reads between samples was normalized as indicated below: Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs sequences and respective raw counts post data processing for each sample.,45 dpf embryos,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:45dpf,GSM1630508,GSM1630508: 45dpf; Danio rerio; miRNA Seq,GSM1630508,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.",GEO Accession:GSM1630508,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,123960.0,2248.0,GSM1630508 r1,0:4 1:51.14,A:38130;C:31332;G:30088;T:24223;N:187,4,51,,,38130,31332,30088,24223,187,SRX915244,SRS870230,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,52,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Juvenile,Juvenile,Trunk,Surface Structure 50908,SRR8377208,SRX5187249,SRS4193651,SRP174644,PRJNA512103,Danio rerio amh mutant RNA Seq,PRJNA512103,Other,For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,pubmed:31399485,,,WT2 35d,,strain:AB|age:35 dpf determined|tissue:trunk|biomaterial provider:Zebrafish Facility at the University of Oregon|collected by:Yilin Yan|replicate:biological replicate 2 wild type 35 dpf organism or animal,,,,,,,,,Danio rerio amh mutant RNA seq,WT2 35d,WT2 35d,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following Amores 2011. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP174644,,,WT2_35d_R1.fq.gz WT2_35d_R2.fq.gz,fastq fastq,571893714.0,2831157.0,WT2 35d R1.fq.gz,0:101 1:101,A:145166622;C:135811176;G:137506724;T:151978871;N:1430321,101,101,,,145166622,135811176,137506724,151978871,1430321,SRX5187249,SRS4193651,SRA827573,University of Oregon|Biology,University of Oregon,2,0.78867,0.8064,0.09492,0.07075,0.7558,0.7626,0.49842,0.62539,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-09-06,Juvenile,Juvenile,Trunk,Surface Structure 50910,SRR8377210,SRX5187247,SRS4193649,SRP174644,PRJNA512103,Danio rerio amh mutant RNA Seq,PRJNA512103,Other,For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,pubmed:31399485,,,WT1 35d,,strain:AB|age:35 dpf determined|tissue:trunk|biomaterial provider:Zebrafish Facility at the University of Oregon|collected by:Yilin Yan|replicate:biological replicate 1 wild type 35 dpf organism or animal,,,,,,,,,Danio rerio amh mutant RNA seq,WT1 35d,WT1 35d,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following Amores 2011. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP174644,,,WT1_35d_R1.fq.gz WT1_35d_R2.fq.gz,fastq fastq,1155741586.0,5721493.0,WT1 35d R1.fq.gz,0:101 1:101,A:292356993;C:274928333;G:278712623;T:306842252;N:2901385,101,101,,,292356993,274928333,278712623,306842252,2901385,SRX5187247,SRS4193649,SRA827573,University of Oregon|Biology,University of Oregon,2,0.76241,0.80051,0.10558,0.07532,0.75211,0.75266,0.4642,0.64552,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-09-06,Juvenile,Juvenile,Trunk,Surface Structure 50916,SRR8377216,SRX5187241,SRS4193643,SRP174644,PRJNA512103,Danio rerio amh mutant RNA Seq,PRJNA512103,Other,For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,pubmed:31399485,,,WT3 35d,,strain:AB|age:35 dpf determined|tissue:trunk|biomaterial provider:Zebrafish Facility at the University of Oregon|collected by:Yilin Yan|replicate:biological replicate 3 wild type 35 dpf organism or animal,,,,,,,,,Danio rerio amh mutant RNA seq,WT3 35d,WT3 35d,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following Amores 2011. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP174644,,,WT3_35d_R1.fq.gz WT3_35d_R2.fq.gz,fastq fastq,2213899396.0,10959898.0,WT3 35d R1.fq.gz,0:101 1:101,A:554041965;C:532710862;G:540276530;T:581316693;N:5553346,101,101,,,554041965,532710862,540276530,581316693,5553346,SRX5187241,SRS4193643,SRA827573,University of Oregon|Biology,University of Oregon,2,0.79591,0.83174,0.09578,0.06681,0.7302,0.73026,0.44297,0.62741,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-09-06,Juvenile,Juvenile,Trunk,Surface Structure 50918,SRR8377218,SRX5187239,SRS4193641,SRP174644,PRJNA512103,Danio rerio amh mutant RNA Seq,PRJNA512103,Other,For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,pubmed:31399485,,,Mut4 35d,,strain:AB|age:35 dpf determined|tissue:trunk|biomaterial provider:Zebrafish Facility at the University of Oregon|collected by:Yilin Yan|replicate:biological replicate 4 mutant 35 dpf organism or animal,,,,,,,,,Danio rerio amh mutant RNA seq,Mut4 35d,Mut4 35d,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following {Amores 2011 #69}. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP174644,,,Mut4_35d_R2.fq.gz Mut4_35d_R1.fq.gz,fastq fastq,513244832.0,2540816.0,Mut4 35d R1.fq.gz,0:101 1:101,A:129206304;C:122668650;G:124118336;T:135960922;N:1290620,101,101,,,129206304,122668650,124118336,135960922,1290620,SRX5187239,SRS4193641,SRA827573,University of Oregon|Biology,University of Oregon,2,0.75977,0.79881,0.08292,0.05843,0.73821,0.73841,0.46109,0.63029,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-09-06,Juvenile,Juvenile,Trunk,Surface Structure 50920,SRR8377220,SRX5187237,SRS4193639,SRP174644,PRJNA512103,Danio rerio amh mutant RNA Seq,PRJNA512103,Other,For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,pubmed:31399485,,,Mut3 35d,,strain:AB|age:35 dpf determined|tissue:trunk|biomaterial provider:Zebrafish Facility at the University of Oregon|collected by:Yilin Yan|replicate:biological replicate 3 mutant 35 dpf organism or animal,,,,,,,,,Danio rerio amh mutant RNA seq,Mut3 35d,Mut3 35d,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following {Amores 2011 #69}. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP174644,,,Mut3_35d_R2.fq.gz Mut3_35d_R1.fq.gz,fastq fastq,538713800.0,2666900.0,Mut3 35d R1.fq.gz,0:101 1:101,A:137960428;C:126697441;G:128931488;T:143775732;N:1348711,101,101,,,137960428,126697441,128931488,143775732,1348711,SRX5187237,SRS4193639,SRA827573,University of Oregon|Biology,University of Oregon,2,0.74719,0.78839,0.09758,0.07078,0.74243,0.74552,0.41904,0.61805,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-12-28,Juvenile,Juvenile,Trunk,Surface Structure 50922,SRR8377222,SRX5187235,SRS4193637,SRP174644,PRJNA512103,Danio rerio amh mutant RNA Seq,PRJNA512103,Other,For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,pubmed:31399485,,,Mut2 35d,,strain:AB|age:35 dpf determined|tissue:trunk|biomaterial provider:Zebrafish Facility at the University of Oregon|collected by:Yilin Yan|replicate:biological replicate 2 mutant 35 dpf organism or animal,,,,,,,,,Danio rerio amh mutant RNA seq,Mut2 35d,Mut2 35d,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following {Amores 2011 #69}. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP174644,,,Mut2_35d_R1.fq.gz Mut2_35d_R2.fq.gz,fastq fastq,477929374.0,2365987.0,Mut2 35d R1.fq.gz,0:101 1:101,A:120800666;C:113959321;G:115434316;T:126536893;N:1198178,101,101,,,120800666,113959321,115434316,126536893,1198178,SRX5187235,SRS4193637,SRA827573,University of Oregon|Biology,University of Oregon,2,0.78113,0.82359,0.11386,0.07902,0.76357,0.764,0.45261,0.57374,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-09-06,Juvenile,Juvenile,Trunk,Surface Structure 50924,SRR8377224,SRX5187233,SRS4193635,SRP174644,PRJNA512103,Danio rerio amh mutant RNA Seq,PRJNA512103,Other,For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,pubmed:31399485,,,Mut1 35d,,strain:AB|age:35 dpf determined|tissue:trunk|biomaterial provider:Zebrafish Facility at the University of Oregon|collected by:Yilin Yan|replicate:biological replicate 1 mutant 35 dpf organism or animal,,,,,,,,,Danio rerio amh mutant RNA seq,Mut1 35d,Mut1 35d,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following {Amores 2011 #69}. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP174644,,,Mut1_35d_R1.fq.gz Mut1_35d_R2.fq.gz,fastq fastq,763890068.0,3781634.0,Mut1 35d R1.fq.gz,0:101 1:101,A:193272679;C:181852990;G:185455955;T:201399437;N:1909007,101,101,,,193272679,181852990,185455955,201399437,1909007,SRX5187233,SRS4193635,SRA827573,University of Oregon|Biology,University of Oregon,2,0.76966,0.81108,0.1208,0.08422,0.76558,0.76674,0.42645,0.59374,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-09-06,Juvenile,Juvenile,Trunk,Surface Structure 50926,SRR8377226,SRX5187231,SRS4193633,SRP174644,PRJNA512103,Danio rerio amh mutant RNA Seq,PRJNA512103,Other,For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,pubmed:31399485,,,Mut5 35d,,strain:AB|age:35 dpf determined|tissue:trunk|biomaterial provider:Zebrafish Facility at the University of Oregon|collected by:Yilin Yan|replicate:biological replicate 5 mutant 35 dpf organism or animal,,,,,,,,,Danio rerio amh mutant RNA seq,Mut5 35d,Mut5 35d,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following {Amores 2011 #69}. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP174644,,,Mut5_35d_R1.fq.gz Mut5_35d_R2.fq.gz,fastq fastq,409858808.0,2029004.0,Mut5 35d R1.fq.gz,0:101 1:101,A:103983021;C:97241865;G:98716378;T:108891565;N:1025979,101,101,,,103983021,97241865,98716378,108891565,1025979,SRX5187231,SRS4193633,SRA827573,University of Oregon|Biology,University of Oregon,2,0.76655,0.80882,0.0977,0.06882,0.74233,0.74308,0.45426,0.64072,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-09-06,Juvenile,Juvenile,Trunk,Surface Structure 50932,SRR8377232,SRX5187225,SRS4193627,SRP174644,PRJNA512103,Danio rerio amh mutant RNA Seq,PRJNA512103,Other,For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,pubmed:31399485,,,Mut8 35d,,strain:AB|age:35 dpf determined|tissue:trunk|biomaterial provider:Zebrafish Facility at the University of Oregon|collected by:Yilin Yan|replicate:biological replicate 8 mutant 35 dpf organism or animal,,,,,,,,,Danio rerio amh mutant RNA seq,Mut8 35d,Mut8 35d,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following {Amores 2011 #69}. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP174644,,,Mut8_35d_R2.fq.gz Mut8_35d_R1.fq.gz,fastq fastq,45854.0,227.0,Mut8 35d R1.fq.gz,0:101 1:101,A:11862;C:10838;G:11042;T:11991;N:121,101,101,,,11862,10838,11042,11991,121,SRX5187225,SRS4193627,SRA827573,University of Oregon|Biology,University of Oregon,2,0.69908,0.68966,0.08333,0.0862,0.99782,0.99827,0.54198,0.61538,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-12-28,Juvenile,Juvenile,Trunk,Surface Structure 50934,SRR8377234,SRX5187223,SRS4193625,SRP174644,PRJNA512103,Danio rerio amh mutant RNA Seq,PRJNA512103,Other,For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,pubmed:31399485,,,Mut7 35d,,strain:AB|age:35 dpf determined|tissue:trunk|biomaterial provider:Zebrafish Facility at the University of Oregon|collected by:Yilin Yan|replicate:biological replicate 7 mutant 35 dpf organism or animal,,,,,,,,,Danio rerio amh mutant RNA seq,Mut7 35d,Mut7 35d,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following {Amores 2011 #69}. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP174644,,,Mut7_35d_R1.fq.gz Mut7_35d_R2.fq.gz,fastq fastq,482025328.0,2386264.0,Mut7 35d R1.fq.gz,0:101 1:101,A:121726092;C:114765680;G:117176132;T:127153823;N:1203601,101,101,,,121726092,114765680,117176132,127153823,1203601,SRX5187223,SRS4193625,SRA827573,University of Oregon|Biology,University of Oregon,2,0.7944,0.81981,0.09158,0.06615,0.73868,0.74286,0.48604,0.60293,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-09-06,Juvenile,Juvenile,Trunk,Surface Structure 50936,SRR8377236,SRX5187221,SRS4193623,SRP174644,PRJNA512103,Danio rerio amh mutant RNA Seq,PRJNA512103,Other,For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,pubmed:31399485,,,Mut6 35d,,strain:AB|age:35 dpf determined|tissue:trunk|biomaterial provider:Zebrafish Facility at the University of Oregon|collected by:Yilin Yan|replicate:biological replicate 6 mutant 35 dpf organism or animal,,,,,,,,,Danio rerio amh mutant RNA seq,Mut6 35d,Mut6 35d,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following {Amores 2011 #69}. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP174644,,,Mut6_35d_R2.fq.gz Mut6_35d_R1.fq.gz,fastq fastq,547559178.0,2710689.0,Mut6 35d R1.fq.gz,0:101 1:101,A:142088966;C:126584543;G:128466439;T:149044813;N:1374417,101,101,,,142088966,126584543,128466439,149044813,1374417,SRX5187221,SRS4193623,SRA827573,University of Oregon|Biology,University of Oregon,2,0.68203,0.72897,0.0848,0.06405,0.75982,0.75948,0.46606,0.62979,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-12-28,Juvenile,Juvenile,Trunk,Surface Structure 50937,SRR8377237,SRX5187220,SRS4193622,SRP174644,PRJNA512103,Danio rerio amh mutant RNA Seq,PRJNA512103,Other,For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,pubmed:31399485,,,WT4 35d,,strain:AB|age:35 dpf determined|tissue:trunk|biomaterial provider:Zebrafish Facility at the University of Oregon|collected by:Yilin Yan|replicate:biological replicate 4 wild type 35 dpf organism or animal,,,,,,,,,Danio rerio amh mutant RNA seq,WT4 35d,WT4 35d,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following Amores 2011. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP174644,,,WT4_35d_R1.fq.gz WT4_35d_R2.fq.gz,fastq fastq,739057804.0,3658702.0,WT4 35d R1.fq.gz,0:101 1:101,A:180459808;C:181418460;G:184830579;T:190499000;N:1849957,101,101,,,180459808,181418460,184830579,190499000,1849957,SRX5187220,SRS4193622,SRA827573,University of Oregon|Biology,University of Oregon,2,0.80755,0.83958,0.08323,0.05532,0.73251,0.73115,0.43394,0.59528,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-09-06,Juvenile,Juvenile,Trunk,Surface Structure 50939,SRR8377239,SRX5187218,SRS4193620,SRP174644,PRJNA512103,Danio rerio amh mutant RNA Seq,PRJNA512103,Other,For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,pubmed:31399485,,,WT5 35d,,strain:AB|age:35 dpf determined|tissue:trunk|biomaterial provider:Zebrafish Facility at the University of Oregon|collected by:Yilin Yan|replicate:biological replicate 5 wild type 35 dpf organism or animal,,,,,,,,,Danio rerio amh mutant RNA seq,WT5 35d,WT5 35d,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following Amores 2011. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP174644,,,WT5_35d_R2.fq.gz WT5_35d_R1.fq.gz,fastq fastq,2566933786.0,12707593.0,WT5 35d R1.fq.gz,0:101 1:101,A:633536222;C:624684514;G:640292815;T:661995540;N:6424695,101,101,,,633536222,624684514,640292815,661995540,6424695,SRX5187218,SRS4193620,SRA827573,University of Oregon|Biology,University of Oregon,2,0.78006,0.81406,0.09856,0.06416,0.76246,0.76548,0.44739,0.61325,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-09-06,Juvenile,Juvenile,Trunk,Surface Structure 50941,SRR8377241,SRX5187216,SRS4193618,SRP174644,PRJNA512103,Danio rerio amh mutant RNA Seq,PRJNA512103,Other,For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,pubmed:31399485,,,WT6 35d,,strain:AB|age:35 dpf determined|tissue:trunk|biomaterial provider:Zebrafish Facility at the University of Oregon|collected by:Yilin Yan|replicate:biological replicate 6 wild type 35 dpf organism or animal,,,,,,,,,Danio rerio amh mutant RNA seq,WT6 35d,WT6 35d,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following Amores 2011. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP174644,,,WT6_35d_R1.fq.gz WT6_35d_R2.fq.gz,fastq fastq,3854126670.0,19079835.0,WT6 35d R1.fq.gz,0:101 1:101,A:954892191;C:939940975;G:950682732;T:998987524;N:9623248,101,101,,,954892191,939940975,950682732,998987524,9623248,SRX5187216,SRS4193618,SRA827573,University of Oregon|Biology,University of Oregon,2,0.79771,0.83006,0.08571,0.06024,0.75984,0.76319,0.46268,0.60806,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-09-06,Juvenile,Juvenile,Trunk,Surface Structure 50943,SRR8377243,SRX5187214,SRS4193616,SRP174644,PRJNA512103,Danio rerio amh mutant RNA Seq,PRJNA512103,Other,For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,pubmed:31399485,,,WT7 35d,,strain:AB|age:35 dpf determined|tissue:trunk|biomaterial provider:Zebrafish Facility at the University of Oregon|collected by:Yilin Yan|replicate:biological replicate 7 wild type 35 dpf organism or animal,,,,,,,,,Danio rerio amh mutant RNA seq,WT7 35d,WT7 35d,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following Amores 2011. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP174644,,,WT7_35d_R1.fq.gz WT7_35d_R2.fq.gz,fastq fastq,2039843268.0,10098234.0,WT7 35d R1.fq.gz,0:101 1:101,A:509345773;C:493700254;G:500220571;T:531465526;N:5111144,101,101,,,509345773,493700254,500220571,531465526,5111144,SRX5187214,SRS4193616,SRA827573,University of Oregon|Biology,University of Oregon,2,0.80902,0.83668,0.09137,0.0654,0.75499,0.75763,0.44568,0.61746,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-09-06,Juvenile,Juvenile,Trunk,Surface Structure 50945,SRR8377245,SRX5187212,SRS4193614,SRP174644,PRJNA512103,Danio rerio amh mutant RNA Seq,PRJNA512103,Other,For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,pubmed:31399485,,,WT8 35d,,strain:AB|age:35 dpf determined|tissue:trunk|biomaterial provider:Zebrafish Facility at the University of Oregon|collected by:Yilin Yan|replicate:biological replicate 8 wild type 35 dpf organism or animal,,,,,,,,,Danio rerio amh mutant RNA seq,WT8 35d,WT8 35d,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following Amores 2011. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP174644,,,WT8_35d_R1.fq.gz WT8_35d_R2.fq.gz,fastq fastq,1932194842.0,9565321.0,WT8 35d R1.fq.gz,0:101 1:101,A:482699320;C:469072746;G:471446663;T:504153836;N:4822277,101,101,,,482699320,469072746,471446663,504153836,4822277,SRX5187212,SRS4193614,SRA827573,University of Oregon|Biology,University of Oregon,2,0.78256,0.81142,0.09076,0.0636,0.76343,0.76808,0.4583,0.63397,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-09-06,Juvenile,Juvenile,Trunk,Surface Structure 51081,SRR8526653,SRX5329488,SRS4324064,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,EM+E2 64 rep1 [M+E 64 2],GSM3589622,,source name:EM+E2 64d whole body|strain:AB|age:64d|treatment:EM 10μg/L+E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,EM+E2 64 rep1 [M+E 64 2],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,EM+E2 64d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:64d|treatment:EM 10μg/L+E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589622,GSM3589622: EM+E2 64 rep1 [M+E 64 2]; Danio rerio; RNA Seq,GSM3589622,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589622,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4408273800.0,14694246.0,GSM3589622 r1,0:150 1:150,A:1158156249;C:1028455616;G:1053939888;T:1167688241;N:33806,150,150,,,1158156249,1028455616,1053939888,1167688241,33806,SRX5329488,SRS4324064,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.9185,0.92133,0.05255,0.05163,0.67955,0.68387,0.51677,0.52282,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51082,SRR8526652,SRX5329487,SRS4324063,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,EM+E2 64 rep2 [M+E 64 1],GSM3589621,,source name:EM+E2 64d whole body|strain:AB|age:64d|treatment:EM 10μg/L+E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,EM+E2 64 rep2 [M+E 64 1],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,EM+E2 64d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:64d|treatment:EM 10μg/L+E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589621,GSM3589621: EM+E2 64 rep2 [M+E 64 1]; Danio rerio; RNA Seq,GSM3589621,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589621,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4231228200.0,14104094.0,GSM3589621 r1,0:150 1:150,A:1119319333;C:981695616;G:1004397500;T:1125753427;N:62324,150,150,,,1119319333,981695616,1004397500,1125753427,62324,SRX5329487,SRS4324063,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.94234,0.94739,0.05704,0.05559,0.66718,0.6734,0.51908,0.52775,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51083,SRR8526651,SRX5329486,SRS4324062,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,EM+E2 32 rep3 [M+E 32 3],GSM3589620,,source name:EM+E2 32d whole body|strain:AB|age:32d|treatment:EM 10μg/L+E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,EM+E2 32 rep3 [M+E 32 3],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,EM+E2 32d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:32d|treatment:EM 10μg/L+E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589620,GSM3589620: EM+E2 32 rep3 [M+E 32 3]; Danio rerio; RNA Seq,GSM3589620,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589620,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4414833300.0,14716111.0,GSM3589620 r1,0:150 1:150,A:1180860829;C:1013214793;G:1033100558;T:1187620240;N:36880,150,150,,,1180860829,1013214793,1033100558,1187620240,36880,SRX5329486,SRS4324062,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.86173,0.86377,0.05737,0.05481,0.68404,0.68572,0.52052,0.5167,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51084,SRR8526650,SRX5329485,SRS4324061,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,EM+E2 32 rep2 [M+E 32 2],GSM3589619,,source name:EM+E2 32d whole body|strain:AB|age:32d|treatment:EM 10μg/L+E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,EM+E2 32 rep2 [M+E 32 2],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,EM+E2 32d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:32d|treatment:EM 10μg/L+E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589619,GSM3589619: EM+E2 32 rep2 [M+E 32 2]; Danio rerio; RNA Seq,GSM3589619,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589619,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4674416400.0,15581388.0,GSM3589619 r1,0:150 1:150,A:1260695580;C:1068785088;G:1077861274;T:1267060585;N:13873,150,150,,,1260695580,1068785088,1077861274,1267060585,13873,SRX5329485,SRS4324061,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93759,0.94218,0.08109,0.07874,0.6604,0.66651,0.51003,0.50793,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51085,SRR8526649,SRX5329484,SRS4324060,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,EM+E2 32 rep1 [M+E 32 1],GSM3589618,,source name:EM+E2 32d whole body|strain:AB|age:32d|treatment:EM 10μg/L+E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,EM+E2 32 rep1 [M+E 32 1],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,EM+E2 32d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:32d|treatment:EM 10μg/L+E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589618,GSM3589618: EM+E2 32 rep1 [M+E 32 1]; Danio rerio; RNA Seq,GSM3589618,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589618,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4630710300.0,15435701.0,GSM3589618 r1,0:150 1:150,A:1246579792;C:1059793670;G:1070299106;T:1254024919;N:12813,150,150,,,1246579792,1059793670,1070299106,1254024919,12813,SRX5329484,SRS4324060,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93697,0.94101,0.07994,0.07816,0.6588,0.66336,0.49468,0.50073,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51095,SRR8526639,SRX5329474,SRS4324050,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,EM 64 rep2 [M 64 2],GSM3589608,,source name:EM 64d whole body|strain:AB|age:64d|treatment:EM 10μg/L|tissue:whole body|library type:fr firststrand dUTP,EM 64 rep2 [M 64 2],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,EM 64d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:64d|treatment:EM 10μg/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589608,GSM3589608: EM 64 rep2 [M 64 2]; Danio rerio; RNA Seq,GSM3589608,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589608,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4509884100.0,15032947.0,GSM3589608 r1,0:150 1:150,A:1197321068;C:1040350609;G:1065890520;T:1206284935;N:36968,150,150,,,1197321068,1040350609,1065890520,1206284935,36968,SRX5329474,SRS4324050,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93937,0.94378,0.06389,0.06288,0.66667,0.66985,0.5442,0.5472,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51096,SRR8526638,SRX5329473,SRS4324049,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,EM 64 rep1 [M 64 1],GSM3589607,,source name:EM 64d whole body|strain:AB|age:64d|treatment:EM 10μg/L|tissue:whole body|library type:fr firststrand dUTP,EM 64 rep1 [M 64 1],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,EM 64d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:64d|treatment:EM 10μg/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589607,GSM3589607: EM 64 rep1 [M 64 1]; Danio rerio; RNA Seq,GSM3589607,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589607,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4707130500.0,15690435.0,GSM3589607 r1,0:150 1:150,A:1222987625;C:1112814040;G:1142401391;T:1228887490;N:39954,150,150,,,1222987625,1112814040,1142401391,1228887490,39954,SRX5329473,SRS4324049,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93804,0.94119,0.04875,0.04736,0.67939,0.68235,0.51007,0.50467,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51097,SRR8526637,SRX5329472,SRS4324048,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,EM 32 rep3 [M 32 3],GSM3589606,,source name:EM 32d whole body|strain:AB|age:32d|treatment:EM 10μg/L|tissue:whole body|library type:fr firststrand dUTP,EM 32 rep3 [M 32 3],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,EM 32d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:32d|treatment:EM 10μg/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589606,GSM3589606: EM 32 rep3 [M 32 3]; Danio rerio; RNA Seq,GSM3589606,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589606,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4435488900.0,14784963.0,GSM3589606 r1,0:150 1:150,A:1186018762;C:1020745541;G:1027377398;T:1201231860;N:115339,150,150,,,1186018762,1020745541,1027377398,1201231860,115339,SRX5329472,SRS4324048,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.94303,0.93634,0.06437,0.06339,0.66371,0.6702,0.52638,0.52007,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51098,SRR8526636,SRX5329471,SRS4324047,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,EM 32 rep2 [M 32 2],GSM3589605,,source name:EM 32d whole body|strain:AB|age:32d|treatment:EM 10μg/L|tissue:whole body|library type:fr firststrand dUTP,EM 32 rep2 [M 32 2],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,EM 32d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:32d|treatment:EM 10μg/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589605,GSM3589605: EM 32 rep2 [M 32 2]; Danio rerio; RNA Seq,GSM3589605,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589605,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4700869500.0,15669565.0,GSM3589605 r1,0:150 1:150,A:1259665516;C:1078177861;G:1088412868;T:1274486581;N:126674,150,150,,,1259665516,1078177861,1088412868,1274486581,126674,SRX5329471,SRS4324047,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93845,0.93424,0.0745,0.07436,0.66229,0.66699,0.51076,0.50948,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51099,SRR8526635,SRX5329470,SRS4324046,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,EM 32 rep1 [M 32 1],GSM3589604,,source name:EM 32d whole body|strain:AB|age:32d|treatment:EM 10μg/L|tissue:whole body|library type:fr firststrand dUTP,EM 32 rep1 [M 32 1],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,EM 32d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:32d|treatment:EM 10μg/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589604,GSM3589604: EM 32 rep1 [M 32 1]; Danio rerio; RNA Seq,GSM3589604,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589604,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4625748600.0,15419162.0,GSM3589604 r1,0:150 1:150,A:1244970811;C:1059169068;G:1069448326;T:1252147187;N:13208,150,150,,,1244970811,1059169068,1069448326,1252147187,13208,SRX5329470,SRS4324046,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93913,0.94313,0.07757,0.07478,0.65559,0.65993,0.50881,0.50895,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51109,SRR8526625,SRX5329460,SRS4324036,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,E2 64 rep2 [E 64 2],GSM3589594,,source name:E2 64d whole body|strain:AB|age:64d|treatment:E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,E2 64 rep2 [E 64 2],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,E2 64d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:64d|treatment:E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589594,GSM3589594: E2 64 rep2 [E 64 2]; Danio rerio; RNA Seq,GSM3589594,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589594,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4639704000.0,15465680.0,GSM3589594 r1,0:150 1:150,A:1218277330;C:1082926119;G:1111774567;T:1226688362;N:37622,150,150,,,1218277330,1082926119,1111774567,1226688362,37622,SRX5329460,SRS4324036,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.94135,0.94584,0.04867,0.04744,0.66523,0.66831,0.51157,0.51455,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51110,SRR8526624,SRX5329459,SRS4324035,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,E2 64 rep1 [E 64 1],GSM3589593,,source name:E2 64d whole body|strain:AB|age:64d|treatment:E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,E2 64 rep1 [E 64 1],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,E2 64d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:64d|treatment:E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589593,GSM3589593: E2 64 rep1 [E 64 1]; Danio rerio; RNA Seq,GSM3589593,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589593,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4732263300.0,15774211.0,GSM3589593 r1,0:150 1:150,A:1231004806;C:1113939736;G:1147783646;T:1239495429;N:39683,150,150,,,1231004806,1113939736,1147783646,1239495429,39683,SRX5329459,SRS4324035,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.94551,0.94929,0.05467,0.05373,0.66728,0.67083,0.47358,0.50808,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51111,SRR8526623,SRX5329458,SRS4324034,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,E2 32 rep3 [E 32 3],GSM3589592,,source name:E2 32d whole body|strain:AB|age:32d|treatment:E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,E2 32 rep3 [E 32 3],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,E2 32d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:32d|treatment:E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589592,GSM3589592: E2 32 rep3 [E 32 3]; Danio rerio; RNA Seq,GSM3589592,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589592,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4647897000.0,15492990.0,GSM3589592 r1,0:150 1:150,A:1227159647;C:1081854173;G:1090501348;T:1248211334;N:170498,150,150,,,1227159647,1081854173,1090501348,1248211334,170498,SRX5329458,SRS4324034,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.95191,0.95363,0.0492,0.0482,0.68028,0.68473,0.48667,0.53187,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51112,SRR8526622,SRX5329457,SRS4324033,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,E2 32 rep2 [E 32 2],GSM3589591,,source name:E2 32d whole body|strain:AB|age:32d|treatment:E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,E2 32 rep2 [E 32 2],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,E2 32d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:32d|treatment:E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589591,GSM3589591: E2 32 rep2 [E 32 2]; Danio rerio; RNA Seq,GSM3589591,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589591,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4462305900.0,14874353.0,GSM3589591 r1,0:150 1:150,A:1204720253;C:1015665856;G:1033297425;T:1208585776;N:36590,150,150,,,1204720253,1015665856,1033297425,1208585776,36590,SRX5329457,SRS4324033,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93912,0.94377,0.08007,0.07896,0.70045,0.70212,0.54534,0.53964,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51113,SRR8526621,SRX5329456,SRS4324032,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,E2 32 rep1 [E 32 1],GSM3589590,,source name:E2 32d whole body|strain:AB|age:32d|treatment:E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,E2 32 rep1 [E 32 1],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,E2 32d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:32d|treatment:E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589590,GSM3589590: E2 32 rep1 [E 32 1]; Danio rerio; RNA Seq,GSM3589590,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589590,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4680208800.0,15600696.0,GSM3589590 r1,0:150 1:150,A:1252438304;C:1077819873;G:1091296955;T:1258640326;N:13342,150,150,,,1252438304,1077819873,1091296955,1258640326,13342,SRX5329456,SRS4324032,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93967,0.94482,0.07548,0.0737,0.66101,0.66576,0.49463,0.5128,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51123,SRR8526611,SRX5329446,SRS4324022,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,DMSO 64 rep3 [D 64 3],GSM3589580,,source name:DMSO 64d whole body|strain:AB|age:64d|treatment:DMSO 100μl/L|tissue:whole body|library type:fr firststrand dUTP,DMSO 64 rep3 [D 64 3],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,DMSO 64d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:64d|treatment:DMSO 100μl/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589580,GSM3589580: DMSO 64 rep3 [D 64 3]; Danio rerio; RNA Seq,GSM3589580,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589580,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4454267400.0,14847558.0,GSM3589580 r1,0:150 1:150,A:1156788124;C:1049364365;G:1081430974;T:1166645835;N:38102,150,150,,,1156788124,1049364365,1081430974,1166645835,38102,SRX5329446,SRS4324022,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.94309,0.9465,0.03899,0.03733,0.67675,0.68136,0.47449,0.4731,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51124,SRR8526610,SRX5329445,SRS4324021,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,DMSO 64 rep2 [D 64 2],GSM3589579,,source name:DMSO 64d whole body|strain:AB|age:64d|treatment:DMSO 100μl/L|tissue:whole body|library type:fr firststrand dUTP,DMSO 64 rep2 [D 64 2],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,DMSO 64d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:64d|treatment:DMSO 100μl/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589579,GSM3589579: DMSO 64 rep2 [D 64 2]; Danio rerio; RNA Seq,GSM3589579,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589579,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4455829500.0,14852765.0,GSM3589579 r1,0:150 1:150,A:1201138092;C:1013538556;G:1038336918;T:1202778351;N:37583,150,150,,,1201138092,1013538556,1038336918,1202778351,37583,SRX5329445,SRS4324021,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93522,0.94269,0.05454,0.05437,0.69053,0.69335,0.56003,0.56129,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51125,SRR8526609,SRX5329444,SRS4324020,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,DMSO 64 rep1 [D 64 1],GSM3589578,,source name:DMSO 64d whole body|strain:AB|age:64d|treatment:DMSO 100μl/L|tissue:whole body|library type:fr firststrand dUTP,DMSO 64 rep1 [D 64 1],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,DMSO 64d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:64d|treatment:DMSO 100μl/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589578,GSM3589578: DMSO 64 rep1 [D 64 1]; Danio rerio; RNA Seq,GSM3589578,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589578,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4616709600.0,15389032.0,GSM3589578 r1,0:150 1:150,A:1231335675;C:1068266196;G:1079962650;T:1237120219;N:24860,150,150,,,1231335675,1068266196,1079962650,1237120219,24860,SRX5329444,SRS4324020,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.9338,0.93816,0.0421,0.04056,0.68211,0.6883,0.51623,0.51659,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51126,SRR8526608,SRX5329443,SRS4324019,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,DMSO 32 rep3 [D 32 3],GSM3589577,,source name:DMSO 32d whole body|strain:AB|age:32d|treatment:DMSO 100μl/L|tissue:whole body|library type:fr firststrand dUTP,DMSO 32 rep3 [D 32 3],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,DMSO 32d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:32d|treatment:DMSO 100μl/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589577,GSM3589577: DMSO 32 rep3 [D 32 3]; Danio rerio; RNA Seq,GSM3589577,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589577,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4478415000.0,14928050.0,GSM3589577 r1,0:150 1:150,A:1201233049;C:1028615474;G:1041186349;T:1207367964;N:12164,150,150,,,1201233049,1028615474,1041186349,1207367964,12164,SRX5329443,SRS4324019,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93583,0.93985,0.08339,0.08039,0.65598,0.66076,0.49651,0.49792,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51127,SRR8526607,SRX5329442,SRS4324018,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,DMSO 32 rep2 [D 32 2],GSM3589576,,source name:DMSO 32d whole body|strain:AB|age:32d|treatment:DMSO 100μl/L|tissue:whole body|library type:fr firststrand dUTP,DMSO 32 rep2 [D 32 2],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,DMSO 32d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:32d|treatment:DMSO 100μl/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589576,GSM3589576: DMSO 32 rep2 [D 32 2]; Danio rerio; RNA Seq,GSM3589576,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589576,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,3968030700.0,13226769.0,GSM3589576 r1,0:150 1:150,A:1093313864;C:883373314;G:902351847;T:1088960460;N:31215,150,150,,,1093313864,883373314,902351847,1088960460,31215,SRX5329442,SRS4324018,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.9079,0.91139,0.07862,0.07857,0.74326,0.74947,0.54717,0.55944,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 51128,SRR8526606,SRX5329441,SRS4324017,SRP183448,PRJNA520845,mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development,GSE126039,Transcriptome Analysis,To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.,,,,DMSO 32 rep1 [D 32 1],GSM3589575,,source name:DMSO 32d whole body|strain:AB|age:32d|treatment:DMSO 100μl/L|tissue:whole body|library type:fr firststrand dUTP,DMSO 32 rep1 [D 32 1],High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,DMSO 32d whole body,Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.,strain:AB|age:32d|treatment:DMSO 100μl/L|tissue:whole body|library type:fr firststrand dUTP,GSM3589575,GSM3589575: DMSO 32 rep1 [D 32 1]; Danio rerio; RNA Seq,GSM3589575,,1,We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.,GEO Accession:GSM3589575,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP183448,,,,,4650824700.0,15502749.0,GSM3589575 r1,0:150 1:150,A:1238578411;C:1072241996;G:1095554001;T:1244415211;N:35081,150,150,,,1238578411,1072241996,1095554001,1244415211,35081,SRX5329441,SRS4324017,SRA843750,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.94552,0.94929,0.06662,0.06472,0.66486,0.66785,0.53342,0.52954,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-02-04,Juvenile,Juvenile,Trunk,Surface Structure 53654,SRR10010335,SRX6748603,SRS5298717,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1a nr5a1b,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b / |BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 11,35dpf nr5a1a nr5a1b double mutant 11,35dpf nr5a1a nr5a1b double mutant 11,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1ab35dmut-11_combined_R1.fq.gz nr5a1ab35dmut-11_combined_R2.fq.gz,fastq fastq,5464020164.0,18092782.0,nr5a1ab35dmut 11 combined R1.fq.gz,0:151 1:151,A:1417197935;C:1238763491;G:1264099371;T:1543026312;N:933055,151,151,,,1417197935,1238763491,1264099371,1543026312,933055,SRX6748603,SRS5298717,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.82573,0.85627,0.0768,0.06148,0.75704,0.76017,0.49566,0.58424,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53655,SRR10010336,SRX6748602,SRS5298716,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1b,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b / |BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1b mutant 7,35dpf nr5a1b mutant 7,35dpf nr5a1b mutant 7,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1b35dmut-7_combined_R1.fq.gz nr5a1b35dmut-7_combined_R2.fq.gz,fastq fastq,2116406940.0,7007970.0,nr5a1b35dmut 7 combined R1.fq.gz,0:151 1:151,A:534677619;C:494553805;G:503529167;T:583343323;N:303026,151,151,,,534677619,494553805,503529167,583343323,303026,SRX6748602,SRS5298716,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.89953,0.9204,0.08475,0.06359,0.75069,0.75615,0.5203,0.5919,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53656,SRR10010337,SRX6748601,SRS5298717,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1a nr5a1b,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b / |BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 10,35dpf nr5a1a nr5a1b double mutant 10,35dpf nr5a1a nr5a1b double mutant 10,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1ab35dmut-10_combined_R1.fq.gz nr5a1ab35dmut-10_combined_R2.fq.gz,fastq fastq,3016366034.0,9987967.0,nr5a1ab35dmut 10 combined R1.fq.gz,0:151 1:151,A:752733986;C:720025699;G:731849549;T:811247600;N:509200,151,151,,,752733986,720025699,731849549,811247600,509200,SRX6748601,SRS5298717,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.90615,0.91707,0.11046,0.07981,0.74651,0.74966,0.49676,0.60165,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53657,SRR10010338,SRX6748600,SRS5298717,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1a nr5a1b,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b / |BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 9,35dpf nr5a1a nr5a1b double mutant 9,35dpf nr5a1a nr5a1b double mutant 9,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1ab35dmut-9_combined_R1.fq.gz nr5a1ab35dmut-9_combined_R2.fq.gz,fastq fastq,3569050194.0,11818047.0,nr5a1ab35dmut 9 combined R1.fq.gz,0:151 1:151,A:899915774;C:849832234;G:859458329;T:959242263;N:601594,151,151,,,899915774,849832234,859458329,959242263,601594,SRX6748600,SRS5298717,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.88978,0.9004,0.09772,0.07218,0.74799,0.74968,0.51174,0.6088,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53658,SRR10010339,SRX6748599,SRS5298717,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1a nr5a1b,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b / |BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 2,35dpf nr5a1a nr5a1b double mutant 2,35dpf nr5a1a nr5a1b double mutant 2,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1ab35dmut-2_combined_R1.fq.gz nr5a1ab35dmut-2_combined_R2.fq.gz,fastq fastq,2828323922.0,9365311.0,nr5a1ab35dmut 2 combined R1.fq.gz,0:151 1:151,A:691090279;C:673032167;G:684529355;T:779155559;N:516562,151,151,,,691090279,673032167,684529355,779155559,516562,SRX6748599,SRS5298717,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.8834,0.9068,0.11546,0.07455,0.75503,0.75615,0.51068,0.61929,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53659,SRR10010340,SRX6748598,SRS5298717,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1a nr5a1b,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b / |BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 1,35dpf nr5a1a nr5a1b double mutant 1,35dpf nr5a1a nr5a1b double mutant 1,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1ab35dmut-1_combined_R1.fq.gz nr5a1ab35dmut-1_combined_R2.fq.gz,fastq fastq,3461567790.0,11462145.0,nr5a1ab35dmut 1 combined R1.fq.gz,0:151 1:151,A:863912807;C:826288038;G:844009627;T:926819831;N:537487,151,151,,,863912807,826288038,844009627,926819831,537487,SRX6748598,SRS5298717,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.90732,0.91778,0.10103,0.06771,0.74026,0.74619,0.50631,0.59632,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53660,SRR10010341,SRX6748597,SRS5298716,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1b,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b / |BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1b mutant 4,35dpf nr5a1b mutant 4,35dpf nr5a1b mutant 4,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1b35dmut-4_combined_R1.fq.gz nr5a1b35dmut-4_combined_R2.fq.gz,fastq fastq,2823289582.0,9348641.0,nr5a1b35dmut 4 combined R1.fq.gz,0:151 1:151,A:692918043;C:667773087;G:683991041;T:778117057;N:490354,151,151,,,692918043,667773087,683991041,778117057,490354,SRX6748597,SRS5298716,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.89649,0.92027,0.09415,0.06385,0.75463,0.75883,0.48098,0.58128,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53661,SRR10010342,SRX6748596,SRS5298717,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1a nr5a1b,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b / |BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 14,35dpf nr5a1a nr5a1b double mutant 14,35dpf nr5a1a nr5a1b double mutant 14,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1ab35dmut-14_combined_R1.fq.gz nr5a1ab35dmut-14_combined_R2.fq.gz,fastq fastq,2662720410.0,8816955.0,nr5a1ab35dmut 14 combined R1.fq.gz,0:151 1:151,A:665577500;C:635869780;G:647241076;T:713592928;N:439126,151,151,,,665577500,635869780,647241076,713592928,439126,SRX6748596,SRS5298717,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.90062,0.91305,0.1132,0.08326,0.75339,0.7555,0.49702,0.59781,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53664,SRR10010345,SRX6748593,SRS5298716,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1b,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b / |BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1b mutant 1,35dpf nr5a1b mutant 1,35dpf nr5a1b mutant 1,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1b35dmut-1_combined_R1.fq.gz nr5a1b35dmut-1_combined_R2.fq.gz,fastq fastq,3080371310.0,10199905.0,nr5a1b35dmut 1 combined R1.fq.gz,0:151 1:151,A:749979603;C:751889973;G:770422909;T:807597821;N:481004,151,151,,,749979603,751889973,770422909,807597821,481004,SRX6748593,SRS5298716,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.91959,0.93095,0.11586,0.07628,0.76187,0.76562,0.49454,0.57785,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53665,SRR10010346,SRX6748592,SRS5298716,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1b,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b / |BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1b mutant 2,35dpf nr5a1b mutant 2,35dpf nr5a1b mutant 2,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1b35dmut-2_combined_R1.fq.gz nr5a1b35dmut-2_combined_R2.fq.gz,fastq fastq,3633938820.0,12032910.0,nr5a1b35dmut 2 combined R1.fq.gz,0:151 1:151,A:905316417;C:865468187;G:876812140;T:985720508;N:621568,151,151,,,905316417,865468187,876812140,985720508,621568,SRX6748592,SRS5298716,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.8972,0.91027,0.11437,0.07781,0.74099,0.74446,0.4981,0.60461,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53676,SRR10010357,SRX6748581,SRS5298719,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1a,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b +/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1a mutant 7,35dpf nr5a1a mutant 7,35dpf nr5a1a mutant 7,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1a35dmut-7_combined_R1.fq.gz nr5a1a35dmut-7_combined_R2.fq.gz,fastq fastq,2969897294.0,9834097.0,nr5a1a35dmut 7 combined R1.fq.gz,0:151 1:151,A:752593200;C:695994377;G:707935979;T:812884925;N:488813,151,151,,,752593200,695994377,707935979,812884925,488813,SRX6748581,SRS5298719,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.89218,0.906,0.09342,0.07022,0.73795,0.73898,0.51281,0.5911,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53677,SRR10010358,SRX6748580,SRS5298719,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1a,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b +/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1a mutant 8,35dpf nr5a1a mutant 8,35dpf nr5a1a mutant 8,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1a35dmut-8_combined_R1.fq.gz nr5a1a35dmut-8_combined_R2.fq.gz,fastq fastq,6225038118.0,20612709.0,nr5a1a35dmut 8 combined R1.fq.gz,0:151 1:151,A:1559098665;C:1505493891;G:1534176065;T:1625255981;N:1013516,151,151,,,1559098665,1505493891,1534176065,1625255981,1013516,SRX6748580,SRS5298719,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.90023,0.90282,0.09369,0.06592,0.73525,0.73854,0.50906,0.59368,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53678,SRR10010359,SRX6748579,SRS5298721,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf wildtype,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b +/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf wild type 2,35dpf wild type 2,35dpf wild type 2,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1_35day_WT-2_combined_R1.fq.gz nr5a1_35day_WT-2_combined_R2.fq.gz,fastq fastq,4142275186.0,13716143.0,nr5a1 35day WT 2 combined R1.fq.gz,0:151 1:151,A:1055251193;C:967398418;G:984879234;T:1134062187;N:684154,151,151,,,1055251193,967398418,984879234,1134062187,684154,SRX6748579,SRS5298721,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.89791,0.91014,0.09157,0.06806,0.73927,0.74067,0.515,0.58656,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53679,SRR10010360,SRX6748578,SRS5298721,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf wildtype,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b +/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf wild type 3,35dpf wild type 3,35dpf wild type 3,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1_35day_WT-3_combined_R2.fq.gz nr5a1_35day_WT-3_combined_R1.fq.gz,fastq fastq,2471376532.0,8183366.0,nr5a1 35day WT 3 combined R1.fq.gz,0:151 1:151,A:615088670;C:576161730;G:582945558;T:696743565;N:437009,151,151,,,615088670,576161730,582945558,696743565,437009,SRX6748578,SRS5298721,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.87753,0.90284,0.1111,0.07857,0.72563,0.72794,0.50927,0.59766,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53680,SRR10010361,SRX6748577,SRS5298721,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf wildtype,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b +/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf wild type 4,35dpf wild type 4,35dpf wild type 4,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1_35day_WT-4_combined_R1.fq.gz nr5a1_35day_WT-4_combined_R2.fq.gz,fastq fastq,2116363754.0,7007827.0,nr5a1 35day WT 4 combined R1.fq.gz,0:151 1:151,A:517886726;C:489788898;G:502421580;T:605882187;N:384363,151,151,,,517886726,489788898,502421580,605882187,384363,SRX6748577,SRS5298721,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.87446,0.91282,0.08961,0.06167,0.75325,0.75363,0.50444,0.58991,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53681,SRR10010362,SRX6748576,SRS5298721,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf wildtype,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b +/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf wild type 5,35dpf wild type 5,35dpf wild type 5,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1_35day_WT-5_combined_R1.fq.gz nr5a1_35day_WT-5_combined_R2.fq.gz,fastq fastq,2730512464.0,9041432.0,nr5a1 35day WT 5 combined R1.fq.gz,0:151 1:151,A:676487187;C:641297195;G:648646413;T:763575356;N:506313,151,151,,,676487187,641297195,648646413,763575356,506313,SRX6748576,SRS5298721,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.87293,0.89776,0.08726,0.06177,0.7727,0.77402,0.47624,0.58994,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53682,SRR10010363,SRX6748575,SRS5298721,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf wildtype,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b +/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf wild type 6,35dpf wild type 6,35dpf wild type 6,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1_35day_WT-6_combined_R1.fq.gz nr5a1_35day_WT-6_combined_R2.fq.gz,fastq fastq,2539526758.0,8409029.0,nr5a1 35day WT 6 combined R1.fq.gz,0:151 1:151,A:654061696;C:592950317;G:606528343;T:685572585;N:413817,151,151,,,654061696,592950317,606528343,685572585,413817,SRX6748575,SRS5298721,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.88978,0.89645,0.09493,0.07075,0.73509,0.73965,0.53187,0.55068,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53683,SRR10010364,SRX6748574,SRS5298721,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf wildtype,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b +/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf wild type 9,35dpf wild type 9,35dpf wild type 9,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1_35day_WT-9_combined_R1.fq.gz nr5a1_35day_WT-9_combined_R2.fq.gz,fastq fastq,2585156844.0,8560122.0,nr5a1 35day WT 9 combined R1.fq.gz,0:151 1:151,A:659256640;C:603793032;G:616048994;T:705643382;N:414796,151,151,,,659256640,603793032,616048994,705643382,414796,SRX6748574,SRS5298721,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.90219,0.91318,0.11237,0.08413,0.74472,0.74799,0.52565,0.61427,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53688,SRR10010369,SRX6748569,SRS5298716,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1b,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b / |BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1b mutant 8,35dpf nr5a1b mutant 8,35dpf nr5a1b mutant 8,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1b35dmut-8_combined_R1.fq.gz nr5a1b35dmut-8_combined_R2.fq.gz,fastq fastq,3225498920.0,10680460.0,nr5a1b35dmut 8 combined R1.fq.gz,0:151 1:151,A:810589172;C:772659409;G:785398777;T:856326001;N:525561,151,151,,,810589172,772659409,785398777,856326001,525561,SRX6748569,SRS5298716,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.9048,0.9133,0.0825,0.05993,0.74627,0.74933,0.52212,0.58896,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53698,SRR10010379,SRX6748559,SRS5298721,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf wildtype,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b +/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf wild type 10,35dpf wild type 10,35dpf wild type 10,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1_35day_WT-10_combined_R1.fq.gz nr5a1_35day_WT-10_combined_R2.fq.gz,fastq fastq,3038724000.0,10062000.0,nr5a1 35day WT 10 combined R1.fq.gz,0:151 1:151,A:764571339;C:715912069;G:728730982;T:828987265;N:522345,151,151,,,764571339,715912069,728730982,828987265,522345,SRX6748559,SRS5298721,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.87838,0.89181,0.08908,0.06618,0.7484,0.7485,0.53115,0.59993,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53699,SRR10010380,SRX6748558,SRS5298721,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf wildtype,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b +/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf wild type 1,35dpf wild type 1,35dpf wild type 1,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1_35day_WT-1_combined_R1.fq.gz nr5a1_35day_WT-1_combined_R2.fq.gz,fastq fastq,3598780584.0,11916492.0,nr5a1 35day WT 1 combined R1.fq.gz,0:151 1:151,A:886857565;C:874550481;G:894991137;T:941808129;N:573272,151,151,,,886857565,874550481,894991137,941808129,573272,SRX6748558,SRS5298721,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.9139,0.92164,0.10525,0.06463,0.75057,0.75211,0.49642,0.57074,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53700,SRR10010381,SRX6748557,SRS5298716,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1b,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b / |BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1b mutant 6,35dpf nr5a1b mutant 6,35dpf nr5a1b mutant 6,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1b35dmut-6_combined_R1.fq.gz nr5a1b35dmut-6_combined_R2.fq.gz,fastq fastq,4476352418.0,14822359.0,nr5a1b35dmut 6 combined R1.fq.gz,0:151 1:151,A:1120206233;C:1067519728;G:1089929887;T:1197971503;N:725067,151,151,,,1120206233,1067519728,1089929887,1197971503,725067,SRX6748557,SRS5298716,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.91501,0.91912,0.08509,0.05807,0.74663,0.7488,0.51898,0.57667,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53701,SRR10010382,SRX6748556,SRS5298716,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1b,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b / |BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1b mutant 5,35dpf nr5a1b mutant 5,35dpf nr5a1b mutant 5,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1b35dmut-5_combined_R1.fq.gz nr5a1b35dmut-5_combined_R2.fq.gz,fastq fastq,4009328142.0,13275921.0,nr5a1b35dmut 5 combined R1.fq.gz,0:151 1:151,A:1067904920;C:901186174;G:923523205;T:1116013227;N:700616,151,151,,,1067904920,901186174,923523205,1116013227,700616,SRX6748556,SRS5298716,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.80761,0.83261,0.06793,0.05143,0.75911,0.76114,0.55479,0.61755,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53704,SRR10010385,SRX6748553,SRS5298719,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1a,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b +/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1a mutant 6,35dpf nr5a1a mutant 6,35dpf nr5a1a mutant 6,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1a35dmut-6_combined_R1.fq.gz nr5a1a35dmut-6_combined_R2.fq.gz,fastq fastq,3073492354.0,10177127.0,nr5a1a35dmut 6 combined R1.fq.gz,0:151 1:151,A:789160217;C:716824009;G:740200723;T:826797684;N:509721,151,151,,,789160217,716824009,740200723,826797684,509721,SRX6748553,SRS5298719,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.87516,0.88431,0.09065,0.07016,0.74588,0.74726,0.53057,0.60951,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53705,SRR10010386,SRX6748552,SRS5298719,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1a,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b +/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1a mutant 5,35dpf nr5a1a mutant 5,35dpf nr5a1a mutant 5,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1a35dmut-5_combined_R1.fq.gz nr5a1a35dmut-5_combined_R2.fq.gz,fastq fastq,3240379668.0,10729734.0,nr5a1a35dmut 5 combined R1.fq.gz,0:151 1:151,A:850546438;C:745212890;G:765395973;T:878658019;N:566348,151,151,,,850546438,745212890,765395973,878658019,566348,SRX6748552,SRS5298719,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.81872,0.83649,0.07435,0.05495,0.75225,0.75461,0.51257,0.58856,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53707,SRR10010388,SRX6748550,SRS5298719,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1a,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b +/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1a mutant 2,35dpf nr5a1a mutant 2,35dpf nr5a1a mutant 2,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1a35dmut-2_combined_R1.fq.gz nr5a1a35dmut-2_combined_R2.fq.gz,fastq fastq,1239380518.0,4103909.0,nr5a1a35dmut 2 combined R1.fq.gz,0:151 1:151,A:309089709;C:300159914;G:303434072;T:326498923;N:197900,151,151,,,309089709,300159914,303434072,326498923,197900,SRX6748550,SRS5298719,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.91546,0.92068,0.11935,0.07796,0.74397,0.7474,0.48962,0.61439,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53708,SRR10010389,SRX6748549,SRS5298719,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1a,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b +/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1a mutant 1,35dpf nr5a1a mutant 1,35dpf nr5a1a mutant 1,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1a35dmut-1_combined_R1.fq.gz nr5a1a35dmut-1_combined_R2.fq.gz,fastq fastq,2224834906.0,7367003.0,nr5a1a35dmut 1 combined R1.fq.gz,0:151 1:151,A:541266079;C:545117817;G:559850378;T:578249036;N:351596,151,151,,,541266079,545117817,559850378,578249036,351596,SRX6748549,SRS5298719,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.91337,0.9214,0.12797,0.08298,0.74961,0.75483,0.45923,0.54594,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53709,SRR10010390,SRX6748548,SRS5298719,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1a,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b +/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1a mutant 4,35dpf nr5a1a mutant 4,35dpf nr5a1a mutant 4,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1a35dmut-4_combined_R1.fq.gz nr5a1a35dmut-4_combined_R2.fq.gz,fastq fastq,2564347836.0,8491218.0,nr5a1a35dmut 4 combined R1.fq.gz,0:151 1:151,A:626506801;C:604109158;G:622843659;T:710461729;N:426489,151,151,,,626506801,604109158,622843659,710461729,426489,SRX6748548,SRS5298719,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.88743,0.91434,0.08038,0.05675,0.75562,0.75676,0.47736,0.57787,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53710,SRR10010391,SRX6748547,SRS5298719,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1a,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b +/+|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1a mutant 3,35dpf nr5a1a mutant 3,35dpf nr5a1a mutant 3,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1a35dmut-3_combined_R1.fq.gz nr5a1a35dmut-3_combined_R2.fq.gz,fastq fastq,2109532212.0,6985206.0,nr5a1a35dmut 3 combined R1.fq.gz,0:151 1:151,A:523059463;C:502631876;G:510494846;T:572988523;N:357504,151,151,,,523059463,502631876,510494846,572988523,357504,SRX6748547,SRS5298719,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.89446,0.90702,0.08692,0.06146,0.75049,0.75312,0.5212,0.57721,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53715,SRR10010396,SRX6748542,SRS5298717,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1a nr5a1b,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b / |BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 13,35dpf nr5a1a nr5a1b double mutant 13,35dpf nr5a1a nr5a1b double mutant 13,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1ab35dmut-13_combined_R1.fq.gz nr5a1ab35dmut-13_combined_R2.fq.gz,fastq fastq,4623122002.0,15308351.0,nr5a1ab35dmut 13 combined R1.fq.gz,0:151 1:151,A:1157235877;C:1116162876;G:1129874932;T:1219134272;N:714045,151,151,,,1157235877,1116162876,1129874932,1219134272,714045,SRX6748542,SRS5298717,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.91894,0.92533,0.11425,0.08034,0.75635,0.76023,0.50951,0.61492,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53716,SRR10010397,SRX6748541,SRS5298717,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1a nr5a1b,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a / ; nr5a1b / |BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1a nr5a1b double mutant 12,35dpf nr5a1a nr5a1b double mutant 12,35dpf nr5a1a nr5a1b double mutant 12,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1ab35dmut-12_combined_R1.fq.gz nr5a1ab35dmut-12_combined_R2.fq.gz,fastq fastq,2610452666.0,8643883.0,nr5a1ab35dmut 12 combined R1.fq.gz,0:151 1:151,A:648839778;C:629525229;G:642133919;T:689532605;N:421135,151,151,,,648839778,629525229,642133919,689532605,421135,SRX6748541,SRS5298717,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.90931,0.91675,0.11029,0.07732,0.74584,0.74937,0.48342,0.59544,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 53717,SRR10010398,SRX6748540,SRS5298716,SRP219014,PRJNA561212,RNA Seq of nr5a1a and nr5a1b mutant zebrafish,PRJNA561212,Transcriptome Analysis,Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of theanimals by removing the anterior of the fish from just posterior of the pectoral finand removing the caudal peduncle posterior to the anus. Trunks were individuallyhomogenized in 200ul Trizol. Total RNA was extracted using the Ribopure RNAPurification Kit ThermoFisher. Total RNA was enriched for mRNA using DynabeadsrOligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencinglibraries using the NEXTflextm qRNA seq kit BIOO Scientific. Libraryconcentrations were quantified using a Qubitr fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing wefurther evaluated the quality of the multiplexed library by quantitative real timePCR using the Kapa Library Quantification Kit Kapa Biosystems. Two lanes ofpaired end 150 base pair bp sequencing were performed on an Illumina HiSeq 4000.,,,,,35dpf nr5a1b,,strain:AB|age:35 dpf|sex:not applicable|tissue:trunk|biomaterial provider:Postlethwait lab University of Oregon|genotype:nr5a1a +/+ ; nr5a1b / |BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 35dpf nr5a1b mutant 3,35dpf nr5a1b mutant 3,35dpf nr5a1b mutant 3,Strand specific RNA seq library prepared with BIOO NEXTflex Rapid Directional qRNA Seq kit,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP219014,,,nr5a1b35dmut-3_combined_R1.fq.gz nr5a1b35dmut-3_combined_R2.fq.gz,fastq fastq,1943393556.0,6435078.0,nr5a1b35dmut 3 combined R1.fq.gz,0:151 1:151,A:475436905;C:468830275;G:477482918;T:521312410;N:331048,151,151,,,475436905,468830275,477482918,521312410,331048,SRX6748540,SRS5298716,SRA946180,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.90426,0.92131,0.09556,0.06323,0.75327,0.75292,0.50371,0.57748,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-08-21,Juvenile,Juvenile,Trunk,Surface Structure 55327,SRR10277634,SRX6990843,SRS5512852,SRP225662,PRJNA577580,Dynamic Properties of the Reissner Fiber and Implications on Scoliosis,GSE138842,Transcriptome Analysis,Background: RNASeq of a scospondin hypomorphic mutant at differnet time points Overall design: RNASeq of a scospondin hypomorphic mutant at differnet time points,,,,30dpf scospondin stl297 maternal zygotic mutant Library 3,GSM4120307,,tissue:30dpf scospondin stl297 maternal zygotic mutant Library 3|cell type:WHOLE BODY|iPSc source:N/A|passage:N/A,30dpf scospondin stl297 maternal zygotic mutant Library 3,Raw reads were trimmed with cutadapt to remove low quality bases Trimmed reads were aligned to danio rerio genome GRCz10 using STAR 2.5.4b with Ensembl v83 annotation Aligned reads were quantified using featureCounts 1.6.3 from the subreads package Genome build: GRCz10 Supplementary files format and content: gene counts text file,30dpf scospondin stl297 maternal zygotic mutant Library 3,None,Trizol isolation of RNA; Clean up on QIAGEN RNA column. Takara Clontech SMARTer prep,Typical,cell type:WHOLE BODY|iPSc source:N/A|passage:N/A,GSM4120307,GSM4120307: 30dpf scospondin stl297 maternal zygotic mutant Library 3; Danio rerio; RNA Seq,GSM4120307,,1,Trizol isolation of RNA; Clean up on QIAGEN RNA column. Takara Clontech SMARTer prep,GEO Accession:GSM4120307,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP225662,,,stl297_homoz_30d_r3_1.fastq.gz stl297_homoz_30d_r3_2.fastq.gz,fastq fastq,8251283260.0,27322130.0,GSM4120307 r1,0:151 1:151,A:2171660201;C:1843866593;G:2178007804;T:2057620716;N:127946,151,151,,,2171660201,1843866593,2178007804,2057620716,127946,SRX6990843,SRS5512852,SRA979154,GEO,"Zhang, Developmental Biology, Washington University School of Medicine",2,0.93766,0.94573,0.06206,0.06453,0.71086,0.71857,0.48398,0.48567,151,151,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2019-10-15,Juvenile,Juvenile,Trunk,Surface Structure 55328,SRR10277633,SRX6990842,SRS5512851,SRP225662,PRJNA577580,Dynamic Properties of the Reissner Fiber and Implications on Scoliosis,GSE138842,Transcriptome Analysis,Background: RNASeq of a scospondin hypomorphic mutant at differnet time points Overall design: RNASeq of a scospondin hypomorphic mutant at differnet time points,,,,30dpf scospondin stl297 maternal zygotic mutant Library 2,GSM4120306,,tissue:30dpf scospondin stl297 maternal zygotic mutant Library 2|cell type:WHOLE BODY|iPSc source:N/A|passage:N/A,30dpf scospondin stl297 maternal zygotic mutant Library 2,Raw reads were trimmed with cutadapt to remove low quality bases Trimmed reads were aligned to danio rerio genome GRCz10 using STAR 2.5.4b with Ensembl v83 annotation Aligned reads were quantified using featureCounts 1.6.3 from the subreads package Genome build: GRCz10 Supplementary files format and content: gene counts text file,30dpf scospondin stl297 maternal zygotic mutant Library 2,None,Trizol isolation of RNA; Clean up on QIAGEN RNA column. Takara Clontech SMARTer prep,Typical,cell type:WHOLE BODY|iPSc source:N/A|passage:N/A,GSM4120306,GSM4120306: 30dpf scospondin stl297 maternal zygotic mutant Library 2; Danio rerio; RNA Seq,GSM4120306,,1,Trizol isolation of RNA; Clean up on QIAGEN RNA column. Takara Clontech SMARTer prep,GEO Accession:GSM4120306,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP225662,,,stl297_homoz_30d_r2_1.fastq.gz stl297_homoz_30d_r2_2.fastq.gz,fastq fastq,7673449446.0,25408773.0,GSM4120306 r1,0:151 1:151,A:2015386792;C:1671817788;G:2059094247;T:1927029607;N:121012,151,151,,,2015386792,1671817788,2059094247,1927029607,121012,SRX6990842,SRS5512851,SRA979154,GEO,"Zhang, Developmental Biology, Washington University School of Medicine",2,0.92848,0.94225,0.05062,0.05321,0.72466,0.73428,0.48169,0.46873,151,151,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2019-10-15,Juvenile,Juvenile,Trunk,Surface Structure 55329,SRR10277632,SRX6990841,SRS5512850,SRP225662,PRJNA577580,Dynamic Properties of the Reissner Fiber and Implications on Scoliosis,GSE138842,Transcriptome Analysis,Background: RNASeq of a scospondin hypomorphic mutant at differnet time points Overall design: RNASeq of a scospondin hypomorphic mutant at differnet time points,,,,30dpf scospondin stl297 maternal zygotic mutant Library 1,GSM4120305,,tissue:30dpf scospondin stl297 maternal zygotic mutant Library 1|cell type:WHOLE BODY|iPSc source:N/A|passage:N/A,30dpf scospondin stl297 maternal zygotic mutant Library 1,Raw reads were trimmed with cutadapt to remove low quality bases Trimmed reads were aligned to danio rerio genome GRCz10 using STAR 2.5.4b with Ensembl v83 annotation Aligned reads were quantified using featureCounts 1.6.3 from the subreads package Genome build: GRCz10 Supplementary files format and content: gene counts text file,30dpf scospondin stl297 maternal zygotic mutant Library 1,None,Trizol isolation of RNA; Clean up on QIAGEN RNA column. Takara Clontech SMARTer prep,Typical,cell type:WHOLE BODY|iPSc source:N/A|passage:N/A,GSM4120305,GSM4120305: 30dpf scospondin stl297 maternal zygotic mutant Library 1; Danio rerio; RNA Seq,GSM4120305,,1,Trizol isolation of RNA; Clean up on QIAGEN RNA column. Takara Clontech SMARTer prep,GEO Accession:GSM4120305,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP225662,,,stl297_homoz_30d_r1_2.fastq.gz stl297_homoz_30d_r1_1.fastq.gz,fastq fastq,7400366550.0,24504525.0,GSM4120305 r1,0:151 1:151,A:1914229340;C:1635900358;G:2028975296;T:1821145683;N:115873,151,151,,,1914229340,1635900358,2028975296,1821145683,115873,SRX6990841,SRS5512850,SRA979154,GEO,"Zhang, Developmental Biology, Washington University School of Medicine",2,0.94017,0.94717,0.05269,0.05443,0.72553,0.736,0.48512,0.48244,151,151,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2019-10-15,Juvenile,Juvenile,Trunk,Surface Structure 55330,SRR10277631,SRX6990840,SRS5512849,SRP225662,PRJNA577580,Dynamic Properties of the Reissner Fiber and Implications on Scoliosis,GSE138842,Transcriptome Analysis,Background: RNASeq of a scospondin hypomorphic mutant at differnet time points Overall design: RNASeq of a scospondin hypomorphic mutant at differnet time points,,,,30dpf scospondin stl297 het Library 3,GSM4120304,,tissue:30dpf scospondin stl297 het Library 3|cell type:WHOLE BODY|iPSc source:N/A|passage:N/A,30dpf scospondin stl297 het Library 3,Raw reads were trimmed with cutadapt to remove low quality bases Trimmed reads were aligned to danio rerio genome GRCz10 using STAR 2.5.4b with Ensembl v83 annotation Aligned reads were quantified using featureCounts 1.6.3 from the subreads package Genome build: GRCz10 Supplementary files format and content: gene counts text file,30dpf scospondin stl297 het Library 3,None,Trizol isolation of RNA; Clean up on QIAGEN RNA column. Takara Clontech SMARTer prep,Typical,cell type:WHOLE BODY|iPSc source:N/A|passage:N/A,GSM4120304,GSM4120304: 30dpf scospondin stl297 het Library 3; Danio rerio; RNA Seq,GSM4120304,,1,Trizol isolation of RNA; Clean up on QIAGEN RNA column. Takara Clontech SMARTer prep,GEO Accession:GSM4120304,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP225662,,,stl297_ox_30d_r3_1.fastq.gz stl297_ox_30d_r3_2.fastq.gz,fastq fastq,8676086426.0,28728763.0,GSM4120304 r1,0:151 1:151,A:2248858827;C:1928904049;G:2330042871;T:2168143957;N:136722,151,151,,,2248858827,1928904049,2330042871,2168143957,136722,SRX6990840,SRS5512849,SRA979154,GEO,"Zhang, Developmental Biology, Washington University School of Medicine",2,0.94175,0.95226,0.05883,0.06161,0.71064,0.72263,0.49245,0.49067,151,151,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2019-10-15,Juvenile,Juvenile,Trunk,Surface Structure 55331,SRR10277630,SRX6990839,SRS5512848,SRP225662,PRJNA577580,Dynamic Properties of the Reissner Fiber and Implications on Scoliosis,GSE138842,Transcriptome Analysis,Background: RNASeq of a scospondin hypomorphic mutant at differnet time points Overall design: RNASeq of a scospondin hypomorphic mutant at differnet time points,,,,30dpf scospondin stl297 het Library 2,GSM4120303,,tissue:30dpf scospondin stl297 het Library 2|cell type:WHOLE BODY|iPSc source:N/A|passage:N/A,30dpf scospondin stl297 het Library 2,Raw reads were trimmed with cutadapt to remove low quality bases Trimmed reads were aligned to danio rerio genome GRCz10 using STAR 2.5.4b with Ensembl v83 annotation Aligned reads were quantified using featureCounts 1.6.3 from the subreads package Genome build: GRCz10 Supplementary files format and content: gene counts text file,30dpf scospondin stl297 het Library 2,None,Trizol isolation of RNA; Clean up on QIAGEN RNA column. Takara Clontech SMARTer prep,Typical,cell type:WHOLE BODY|iPSc source:N/A|passage:N/A,GSM4120303,GSM4120303: 30dpf scospondin stl297 het Library 2; Danio rerio; RNA Seq,GSM4120303,,1,Trizol isolation of RNA; Clean up on QIAGEN RNA column. Takara Clontech SMARTer prep,GEO Accession:GSM4120303,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP225662,,,stl297_ox_30d_r2_1.fastq.gz stl297_ox_30d_r2_2.fastq.gz,fastq fastq,7799129464.0,25824932.0,GSM4120303 r1,0:151 1:151,A:1995433056;C:1763290765;G:2118816746;T:1921467838;N:121059,151,151,,,1995433056,1763290765,2118816746,1921467838,121059,SRX6990839,SRS5512848,SRA979154,GEO,"Zhang, Developmental Biology, Washington University School of Medicine",2,0.95037,0.95916,0.05333,0.05571,0.7125,0.72328,0.48504,0.49362,151,151,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2019-10-15,Juvenile,Juvenile,Trunk,Surface Structure 55332,SRR10277629,SRX6990838,SRS5512847,SRP225662,PRJNA577580,Dynamic Properties of the Reissner Fiber and Implications on Scoliosis,GSE138842,Transcriptome Analysis,Background: RNASeq of a scospondin hypomorphic mutant at differnet time points Overall design: RNASeq of a scospondin hypomorphic mutant at differnet time points,,,,30dpf scospondin stl297 het Library 1,GSM4120302,,tissue:30dpf scospondin stl297 het Library 1|cell type:WHOLE BODY|iPSc source:N/A|passage:N/A,30dpf scospondin stl297 het Library 1,Raw reads were trimmed with cutadapt to remove low quality bases Trimmed reads were aligned to danio rerio genome GRCz10 using STAR 2.5.4b with Ensembl v83 annotation Aligned reads were quantified using featureCounts 1.6.3 from the subreads package Genome build: GRCz10 Supplementary files format and content: gene counts text file,30dpf scospondin stl297 het Library 1,None,Trizol isolation of RNA; Clean up on QIAGEN RNA column. Takara Clontech SMARTer prep,Typical,cell type:WHOLE BODY|iPSc source:N/A|passage:N/A,GSM4120302,GSM4120302: 30dpf scospondin stl297 het Library 1; Danio rerio; RNA Seq,GSM4120302,,1,Trizol isolation of RNA; Clean up on QIAGEN RNA column. Takara Clontech SMARTer prep,GEO Accession:GSM4120302,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP225662,,,stl297_ox_30d_r1_1.fastq.gz stl297_ox_30d_r1_2.fastq.gz,fastq fastq,7040145480.0,23311740.0,GSM4120302 r1,0:151 1:151,A:1825284012;C:1568860561;G:1907328477;T:1738562356;N:110074,151,151,,,1825284012,1568860561,1907328477,1738562356,110074,SRX6990838,SRS5512847,SRA979154,GEO,"Zhang, Developmental Biology, Washington University School of Medicine",2,0.68859,0.94895,0.04196,0.06081,0.73324,0.71384,0.48793,0.48024,151,151,B,B,mate1-mate2 similar by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2019-10-15,Juvenile,Juvenile,Trunk,Surface Structure 55729,SRR10741405,SRX7416889,SRS5863683,SRP238455,PRJNA596870,Transcriptome of juvenile zebrafish treated with the aromatase inhibitor exemestane and solvent control,GSE142353,Transcriptome Analysis,To reveal the transcriptomic changes during the sex differetiation in larval zebrafish we treated the lavarl fish with aromatase inhibitors EM CAS: 107868 30 4 100 µg/L as well as solvent as a control and sampled them post the exposure. Overall design: PolyA+ RNA seq were performed on 6 samples each of which was a mixture of 25 juvenile zebrafish. There are twor groups of larval zebrafish were exposed for two exposure treatments. Each group contained 3 replicates with 25 fish per replicate. The exposure treatments included 1 DMSO 10 µL/L 2 EM + DMSO. The exposure periods were 32 days for zebrafish.,parent bioproject:PRJNA596764,pubmed:31910818,,Zebrafish larva EM 32 rep3,GSM4226244,,source name:EM 32d replicates3|tissue:Whole body|strain:AB|treatment:EM10μg/L|age:32d|library type:fr firststrand dUTP,Zebrafish larva EM 32 rep3,High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 to evaluate the raw read quality statistics. Reads were mapped to the zebrafish genome Ensembl v95 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v95. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,EM 32d replicates3,The AI EM 6 methylenandrosta 1 4 diene 3 17 dione ≥ 98% purity Bervita used for juvenile zebrafish was dissolved in 10 μg/L DMSO. Two groups of juvenile zebrafish were also raised in continuous exposure to 10 μg/L EM or the solvent control for 32 days.,RNA samples from each individual were exacted using Trizol Invitrogen according to the manufacturer's protocol. We assessed the overall quality of extracted RNA by GEL RNA purity was checked using the NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the sequencing libraries were prepared at Annoroud Beijing Chinausing VAHTS Stranded mRNA seq Library Prep Kit Vazyme Biotech following the official protocol.,Zebrafish AB strain were obtained from China Zebrafish Resource Center and maintained at 28.5 oC with a light/dark cycle of 14/10 h. For each juvenile sample fifty embryos of zebrafish were maintained in a petri dish from 0 dpf and transferred to a three litter tank in the recirculation systems at 5 dpf. They were fed with paramecium at 5 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf twice a day.,tissue:Whole body|strain:AB|treatment:EM10μg/L|age:32d|library type:fr firststrand dUTP,GSM4226244,GSM4226244: Zebrafish larva EM 32 rep3; Danio rerio; RNA Seq,GSM4226244,,1,RNA samples from each individual were exacted using Trizol Invitrogen according to the manufacturer's protocol. We assessed the overall quality of extracted RNA by GEL RNA purity was checked using the NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the sequencing libraries were prepared at Annoroud Beijing Chinausing VAHTS Stranded mRNA seq Library Prep Kit Vazyme Biotech following the official protocol.,GEO Accession:GSM4226244,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP238455,,,83_R2.fq 83_R1.fq,fastq fastq,4435488900.0,14784963.0,GSM4226244 r1,0:150 1:150,A:1186018762;C:1020745541;G:1027377398;T:1201231860;N:115339,150,150,,,1186018762,1020745541,1027377398,1201231860,115339,SRX7416889,SRS5863683,SRA1014473,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.94305,0.93636,0.06449,0.06344,0.66373,0.67016,0.52576,0.52015,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-12-19,Juvenile,Juvenile,Trunk,Surface Structure 55730,SRR10741404,SRX7416888,SRS5863682,SRP238455,PRJNA596870,Transcriptome of juvenile zebrafish treated with the aromatase inhibitor exemestane and solvent control,GSE142353,Transcriptome Analysis,To reveal the transcriptomic changes during the sex differetiation in larval zebrafish we treated the lavarl fish with aromatase inhibitors EM CAS: 107868 30 4 100 µg/L as well as solvent as a control and sampled them post the exposure. Overall design: PolyA+ RNA seq were performed on 6 samples each of which was a mixture of 25 juvenile zebrafish. There are twor groups of larval zebrafish were exposed for two exposure treatments. Each group contained 3 replicates with 25 fish per replicate. The exposure treatments included 1 DMSO 10 µL/L 2 EM + DMSO. The exposure periods were 32 days for zebrafish.,parent bioproject:PRJNA596764,pubmed:31910818,,Zebrafish larva EM 32 rep2,GSM4226243,,source name:EM 32d replicates2|tissue:Whole body|strain:AB|treatment:EM10μg/L|age:32d|library type:fr firststrand dUTP,Zebrafish larva EM 32 rep2,High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 to evaluate the raw read quality statistics. Reads were mapped to the zebrafish genome Ensembl v95 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v95. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,EM 32d replicates2,The AI EM 6 methylenandrosta 1 4 diene 3 17 dione ≥ 98% purity Bervita used for juvenile zebrafish was dissolved in 10 μg/L DMSO. Two groups of juvenile zebrafish were also raised in continuous exposure to 10 μg/L EM or the solvent control for 32 days.,RNA samples from each individual were exacted using Trizol Invitrogen according to the manufacturer's protocol. We assessed the overall quality of extracted RNA by GEL RNA purity was checked using the NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the sequencing libraries were prepared at Annoroud Beijing Chinausing VAHTS Stranded mRNA seq Library Prep Kit Vazyme Biotech following the official protocol.,Zebrafish AB strain were obtained from China Zebrafish Resource Center and maintained at 28.5 oC with a light/dark cycle of 14/10 h. For each juvenile sample fifty embryos of zebrafish were maintained in a petri dish from 0 dpf and transferred to a three litter tank in the recirculation systems at 5 dpf. They were fed with paramecium at 5 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf twice a day.,tissue:Whole body|strain:AB|treatment:EM10μg/L|age:32d|library type:fr firststrand dUTP,GSM4226243,GSM4226243: Zebrafish larva EM 32 rep2; Danio rerio; RNA Seq,GSM4226243,,1,RNA samples from each individual were exacted using Trizol Invitrogen according to the manufacturer's protocol. We assessed the overall quality of extracted RNA by GEL RNA purity was checked using the NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the sequencing libraries were prepared at Annoroud Beijing Chinausing VAHTS Stranded mRNA seq Library Prep Kit Vazyme Biotech following the official protocol.,GEO Accession:GSM4226243,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP238455,,,71_R1.fq 71_R2.fq,fastq fastq,4700869500.0,15669565.0,GSM4226243 r1,0:150 1:150,A:1259665516;C:1078177861;G:1088412868;T:1274486581;N:126674,150,150,,,1259665516,1078177861,1088412868,1274486581,126674,SRX7416888,SRS5863682,SRA1014473,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93849,0.93427,0.07458,0.07421,0.66214,0.66699,0.51101,0.51068,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-12-19,Juvenile,Juvenile,Trunk,Surface Structure 55731,SRR10741403,SRX7416887,SRS5863681,SRP238455,PRJNA596870,Transcriptome of juvenile zebrafish treated with the aromatase inhibitor exemestane and solvent control,GSE142353,Transcriptome Analysis,To reveal the transcriptomic changes during the sex differetiation in larval zebrafish we treated the lavarl fish with aromatase inhibitors EM CAS: 107868 30 4 100 µg/L as well as solvent as a control and sampled them post the exposure. Overall design: PolyA+ RNA seq were performed on 6 samples each of which was a mixture of 25 juvenile zebrafish. There are twor groups of larval zebrafish were exposed for two exposure treatments. Each group contained 3 replicates with 25 fish per replicate. The exposure treatments included 1 DMSO 10 µL/L 2 EM + DMSO. The exposure periods were 32 days for zebrafish.,parent bioproject:PRJNA596764,pubmed:31910818,,Zebrafish larva EM 32 rep1,GSM4226242,,source name:EM 32d replicates1|tissue:Whole body|strain:AB|treatment:EM10μg/L|age:32d|library type:fr firststrand dUTP,Zebrafish larva EM 32 rep1,High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 to evaluate the raw read quality statistics. Reads were mapped to the zebrafish genome Ensembl v95 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v95. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,EM 32d replicates1,The AI EM 6 methylenandrosta 1 4 diene 3 17 dione ≥ 98% purity Bervita used for juvenile zebrafish was dissolved in 10 μg/L DMSO. Two groups of juvenile zebrafish were also raised in continuous exposure to 10 μg/L EM or the solvent control for 32 days.,RNA samples from each individual were exacted using Trizol Invitrogen according to the manufacturer's protocol. We assessed the overall quality of extracted RNA by GEL RNA purity was checked using the NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the sequencing libraries were prepared at Annoroud Beijing Chinausing VAHTS Stranded mRNA seq Library Prep Kit Vazyme Biotech following the official protocol.,Zebrafish AB strain were obtained from China Zebrafish Resource Center and maintained at 28.5 oC with a light/dark cycle of 14/10 h. For each juvenile sample fifty embryos of zebrafish were maintained in a petri dish from 0 dpf and transferred to a three litter tank in the recirculation systems at 5 dpf. They were fed with paramecium at 5 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf twice a day.,tissue:Whole body|strain:AB|treatment:EM10μg/L|age:32d|library type:fr firststrand dUTP,GSM4226242,GSM4226242: Zebrafish larva EM 32 rep1; Danio rerio; RNA Seq,GSM4226242,,1,RNA samples from each individual were exacted using Trizol Invitrogen according to the manufacturer's protocol. We assessed the overall quality of extracted RNA by GEL RNA purity was checked using the NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the sequencing libraries were prepared at Annoroud Beijing Chinausing VAHTS Stranded mRNA seq Library Prep Kit Vazyme Biotech following the official protocol.,GEO Accession:GSM4226242,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP238455,,,59_R1.fq 59_R2.fq,fastq fastq,4625748600.0,15419162.0,GSM4226242 r1,0:150 1:150,A:1244970811;C:1059169068;G:1069448326;T:1252147187;N:13208,150,150,,,1244970811,1059169068,1069448326,1252147187,13208,SRX7416887,SRS5863681,SRA1014473,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93911,0.94313,0.07744,0.07485,0.65561,0.65955,0.50235,0.5093,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-12-19,Juvenile,Juvenile,Trunk,Surface Structure 55732,SRR10741402,SRX7416886,SRS5863680,SRP238455,PRJNA596870,Transcriptome of juvenile zebrafish treated with the aromatase inhibitor exemestane and solvent control,GSE142353,Transcriptome Analysis,To reveal the transcriptomic changes during the sex differetiation in larval zebrafish we treated the lavarl fish with aromatase inhibitors EM CAS: 107868 30 4 100 µg/L as well as solvent as a control and sampled them post the exposure. Overall design: PolyA+ RNA seq were performed on 6 samples each of which was a mixture of 25 juvenile zebrafish. There are twor groups of larval zebrafish were exposed for two exposure treatments. Each group contained 3 replicates with 25 fish per replicate. The exposure treatments included 1 DMSO 10 µL/L 2 EM + DMSO. The exposure periods were 32 days for zebrafish.,parent bioproject:PRJNA596764,pubmed:31910818,,Zebrafish larva DMSO 32 rep3,GSM4226241,,source name:DMSO 32d replicates3|tissue:Whole body|strain:AB|treatment:DMSO10μl/L|age:32d|library type:fr firststrand dUTP,Zebrafish larva DMSO 32 rep3,High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 to evaluate the raw read quality statistics. Reads were mapped to the zebrafish genome Ensembl v95 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v95. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,DMSO 32d replicates3,The AI EM 6 methylenandrosta 1 4 diene 3 17 dione ≥ 98% purity Bervita used for juvenile zebrafish was dissolved in 10 μg/L DMSO. Two groups of juvenile zebrafish were also raised in continuous exposure to 10 μg/L EM or the solvent control for 32 days.,RNA samples from each individual were exacted using Trizol Invitrogen according to the manufacturer's protocol. We assessed the overall quality of extracted RNA by GEL RNA purity was checked using the NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the sequencing libraries were prepared at Annoroud Beijing Chinausing VAHTS Stranded mRNA seq Library Prep Kit Vazyme Biotech following the official protocol.,Zebrafish AB strain were obtained from China Zebrafish Resource Center and maintained at 28.5 oC with a light/dark cycle of 14/10 h. For each juvenile sample fifty embryos of zebrafish were maintained in a petri dish from 0 dpf and transferred to a three litter tank in the recirculation systems at 5 dpf. They were fed with paramecium at 5 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf twice a day.,tissue:Whole body|strain:AB|treatment:DMSO10μl/L|age:32d|library type:fr firststrand dUTP,GSM4226241,GSM4226241: Zebrafish larva DMSO 32 rep3; Danio rerio; RNA Seq,GSM4226241,,1,RNA samples from each individual were exacted using Trizol Invitrogen according to the manufacturer's protocol. We assessed the overall quality of extracted RNA by GEL RNA purity was checked using the NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the sequencing libraries were prepared at Annoroud Beijing Chinausing VAHTS Stranded mRNA seq Library Prep Kit Vazyme Biotech following the official protocol.,GEO Accession:GSM4226241,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP238455,,,35_R1.fq 35_R2.fq,fastq fastq,4478415000.0,14928050.0,GSM4226241 r1,0:150 1:150,A:1201233049;C:1028615474;G:1041186349;T:1207367964;N:12164,150,150,,,1201233049,1028615474,1041186349,1207367964,12164,SRX7416886,SRS5863680,SRA1014473,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.93586,0.93987,0.08327,0.08055,0.65571,0.66099,0.49706,0.4965,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-12-19,Juvenile,Juvenile,Trunk,Surface Structure 55733,SRR10741401,SRX7416885,SRS5863694,SRP238455,PRJNA596870,Transcriptome of juvenile zebrafish treated with the aromatase inhibitor exemestane and solvent control,GSE142353,Transcriptome Analysis,To reveal the transcriptomic changes during the sex differetiation in larval zebrafish we treated the lavarl fish with aromatase inhibitors EM CAS: 107868 30 4 100 µg/L as well as solvent as a control and sampled them post the exposure. Overall design: PolyA+ RNA seq were performed on 6 samples each of which was a mixture of 25 juvenile zebrafish. There are twor groups of larval zebrafish were exposed for two exposure treatments. Each group contained 3 replicates with 25 fish per replicate. The exposure treatments included 1 DMSO 10 µL/L 2 EM + DMSO. The exposure periods were 32 days for zebrafish.,parent bioproject:PRJNA596764,pubmed:31910818,,Zebrafish larva DMSO 32 rep2,GSM4226240,,source name:DMSO 32d replicates2|tissue:Whole body|strain:AB|treatment:DMSO10μl/L|age:32d|library type:fr firststrand dUTP,Zebrafish larva DMSO 32 rep2,High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 to evaluate the raw read quality statistics. Reads were mapped to the zebrafish genome Ensembl v95 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v95. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,DMSO 32d replicates2,The AI EM 6 methylenandrosta 1 4 diene 3 17 dione ≥ 98% purity Bervita used for juvenile zebrafish was dissolved in 10 μg/L DMSO. Two groups of juvenile zebrafish were also raised in continuous exposure to 10 μg/L EM or the solvent control for 32 days.,RNA samples from each individual were exacted using Trizol Invitrogen according to the manufacturer's protocol. We assessed the overall quality of extracted RNA by GEL RNA purity was checked using the NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the sequencing libraries were prepared at Annoroud Beijing Chinausing VAHTS Stranded mRNA seq Library Prep Kit Vazyme Biotech following the official protocol.,Zebrafish AB strain were obtained from China Zebrafish Resource Center and maintained at 28.5 oC with a light/dark cycle of 14/10 h. For each juvenile sample fifty embryos of zebrafish were maintained in a petri dish from 0 dpf and transferred to a three litter tank in the recirculation systems at 5 dpf. They were fed with paramecium at 5 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf twice a day.,tissue:Whole body|strain:AB|treatment:DMSO10μl/L|age:32d|library type:fr firststrand dUTP,GSM4226240,GSM4226240: Zebrafish larva DMSO 32 rep2; Danio rerio; RNA Seq,GSM4226240,,1,RNA samples from each individual were exacted using Trizol Invitrogen according to the manufacturer's protocol. We assessed the overall quality of extracted RNA by GEL RNA purity was checked using the NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the sequencing libraries were prepared at Annoroud Beijing Chinausing VAHTS Stranded mRNA seq Library Prep Kit Vazyme Biotech following the official protocol.,GEO Accession:GSM4226240,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP238455,,,23_R2.fq 23_R1.fq,fastq fastq,3968030700.0,13226769.0,GSM4226240 r1,0:150 1:150,A:1093313864;C:883373314;G:902351847;T:1088960460;N:31215,150,150,,,1093313864,883373314,902351847,1088960460,31215,SRX7416885,SRS5863694,SRA1014473,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.90792,0.91142,0.0788,0.07857,0.74324,0.74968,0.54628,0.55964,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-12-19,Juvenile,Juvenile,Trunk,Surface Structure 55734,SRR10741400,SRX7416884,SRS5863679,SRP238455,PRJNA596870,Transcriptome of juvenile zebrafish treated with the aromatase inhibitor exemestane and solvent control,GSE142353,Transcriptome Analysis,To reveal the transcriptomic changes during the sex differetiation in larval zebrafish we treated the lavarl fish with aromatase inhibitors EM CAS: 107868 30 4 100 µg/L as well as solvent as a control and sampled them post the exposure. Overall design: PolyA+ RNA seq were performed on 6 samples each of which was a mixture of 25 juvenile zebrafish. There are twor groups of larval zebrafish were exposed for two exposure treatments. Each group contained 3 replicates with 25 fish per replicate. The exposure treatments included 1 DMSO 10 µL/L 2 EM + DMSO. The exposure periods were 32 days for zebrafish.,parent bioproject:PRJNA596764,pubmed:31910818,,Zebrafish larva DMSO 32 rep1,GSM4226239,,source name:DMSO 32d replicates1|tissue:Whole body|strain:AB|treatment:DMSO10μl/L|age:32d|library type:fr firststrand dUTP,Zebrafish larva DMSO 32 rep1,High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 to evaluate the raw read quality statistics. Reads were mapped to the zebrafish genome Ensembl v95 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v95. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.,DMSO 32d replicates1,The AI EM 6 methylenandrosta 1 4 diene 3 17 dione ≥ 98% purity Bervita used for juvenile zebrafish was dissolved in 10 μg/L DMSO. Two groups of juvenile zebrafish were also raised in continuous exposure to 10 μg/L EM or the solvent control for 32 days.,RNA samples from each individual were exacted using Trizol Invitrogen according to the manufacturer's protocol. We assessed the overall quality of extracted RNA by GEL RNA purity was checked using the NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the sequencing libraries were prepared at Annoroud Beijing Chinausing VAHTS Stranded mRNA seq Library Prep Kit Vazyme Biotech following the official protocol.,Zebrafish AB strain were obtained from China Zebrafish Resource Center and maintained at 28.5 oC with a light/dark cycle of 14/10 h. For each juvenile sample fifty embryos of zebrafish were maintained in a petri dish from 0 dpf and transferred to a three litter tank in the recirculation systems at 5 dpf. They were fed with paramecium at 5 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf twice a day.,tissue:Whole body|strain:AB|treatment:DMSO10μl/L|age:32d|library type:fr firststrand dUTP,GSM4226239,GSM4226239: Zebrafish larva DMSO 32 rep1; Danio rerio; RNA Seq,GSM4226239,,1,RNA samples from each individual were exacted using Trizol Invitrogen according to the manufacturer's protocol. We assessed the overall quality of extracted RNA by GEL RNA purity was checked using the NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the sequencing libraries were prepared at Annoroud Beijing Chinausing VAHTS Stranded mRNA seq Library Prep Kit Vazyme Biotech following the official protocol.,GEO Accession:GSM4226239,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP238455,,,11_R2.fq 11_R1.fq,fastq fastq,4650824700.0,15502749.0,GSM4226239 r1,0:150 1:150,A:1238578411;C:1072241996;G:1095554001;T:1244415211;N:35081,150,150,,,1238578411,1072241996,1095554001,1244415211,35081,SRX7416884,SRS5863679,SRA1014473,GEO,"College of Life Science and Technology, Huazhong Agricultural University",2,0.94546,0.94927,0.06661,0.06468,0.66515,0.6677,0.529,0.52953,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2019-12-19,Juvenile,Juvenile,Trunk,Surface Structure