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97 rows where devstage_curation_coarse = "Juvenile" and tissue_curation_coarse = "Surface Structure"

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experiment.library_selection 4

tissue_curation 3

technology 2

experiment.platform 2

experiment.library_strategy 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Surface Structure · 97 ✖

experiment.library_source 1

devstage_curation_coarse 1

  • Juvenile · 97 ✖

devstage_curation 1

Link 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
291 291 DRR224551 DRX214836 DRS236359 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin from RIKEN Wild type zebrafish at 42dpf C SAMD00222582   sample name:42dpf C                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222582 DRX214836 42dpf C 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222582       14328721000.0 71643605.0 DRR224551 0:100 1:100 A:3545040254;C:3629416092;G:3695002549;T:3459108561;N:153544 100 100     3545040254 3629416092 3695002549 3459108561 153544 DRX214836 DRS236359 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.9671 0.95979 0.04174 0.04058 0.71867 0.72143 0.44818 0.46122 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Juvenile Juvenile Fin Surface Structure
292 292 DRR224550 DRX214835 DRS236358 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin from RIKEN Wild type zebrafish at 42dpf B SAMD00222581   sample name:42dpf B                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222581 DRX214835 42dpf B 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222581       14782437000.0 73912185.0 DRR224550 0:100 1:100 A:3652595601;C:3746189790;G:3788229051;T:3595263949;N:158609 100 100     3652595601 3746189790 3788229051 3595263949 158609 DRX214835 DRS236358 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.96502 0.95776 0.0417 0.0399 0.71311 0.71423 0.46064 0.44469 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Juvenile Juvenile Fin Surface Structure
293 293 DRR224549 DRX214834 DRS236357 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin from RIKEN Wild type zebrafish at 42dpf A SAMD00222580   sample name:42dpf A                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222580 DRX214834 42dpf A 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222580       17895751600.0 89478758.0 DRR224549 0:100 1:100 A:4428562207;C:4525140210;G:4573827895;T:4368029340;N:191948 100 100     4428562207 4525140210 4573827895 4368029340 191948 DRX214834 DRS236357 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.96506 0.96043 0.04654 0.0446 0.70956 0.71153 0.49143 0.48957 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Juvenile Juvenile Fin Surface Structure
39616 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… 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
67576 67576 SRR17224787 SRX13404154 SRS11307153 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafishskin   breed:AB|age:30days|sex:pooled male and female|tissue:skin|BioSampleModel:Model organism or animal                 RNAseq of zebrafish skin mut 3 30dpf skin mut 3 30dpf RNAseq of skin     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     skin-mut_3_30dpf.R1.fq.gz skin-mut_3_30dpf.R2.fq.gz fastq fastq 8025414600.0 26751382.0 skin mut 3 30dpf.R1.fq.gz 0:150 1:150 A:1973620738;C:1947874868;G:2125741877;T:1978157854;N:19263 150 150     1973620738 1947874868 2125741877 1978157854 19263 SRX13404154 SRS11307153 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.92241 0.9178 0.03287 0.03164 0.74951 0.75258 0.53912 0.5384 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Skin Surface Structure
67577 67577 SRR17224788 SRX13404153 SRS11307153 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafishskin   breed:AB|age:30days|sex:pooled male and female|tissue:skin|BioSampleModel:Model organism or animal                 RNAseq of zebrafish skin mut 2 30dpf skin mut 2 30dpf RNAseq of skin     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     skin-mut_2_30dpf.R1.fq.gz skin-mut_2_30dpf.R2.fq.gz fastq fastq 6098938800.0 20329796.0 skin mut 2 30dpf.R1.fq.gz 0:150 1:150 A:1520021563;C:1474526796;G:1582813467;T:1521562690;N:14284 150 150     1520021563 1474526796 1582813467 1521562690 14284 SRX13404153 SRS11307153 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.92872 0.92431 0.0312 0.02974 0.75426 0.7567 0.50003 0.50362 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Skin Surface Structure
67578 67578 SRR17224789 SRX13404152 SRS11307153 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafishskin   breed:AB|age:30days|sex:pooled male and female|tissue:skin|BioSampleModel:Model organism or animal                 RNAseq of zebrafish skin mut 1 30dpf skin mut 1 30dpf RNAseq of skin     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     skin-mut_1_30dpf.R1.fq.gz skin-mut_1_30dpf.R2.fq.gz fastq fastq 5827766700.0 19425889.0 skin mut 1 30dpf.R1.fq.gz 0:150 1:150 A:1447618390;C:1412402925;G:1523986527;T:1443745018;N:13840 150 150     1447618390 1412402925 1523986527 1443745018 13840 SRX13404152 SRS11307153 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.93283 0.92736 0.02677 0.02568 0.77477 0.77731 0.45528 0.53231 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Skin Surface Structure
67579 67579 SRR17224790 SRX13404151 SRS11307153 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafishskin   breed:AB|age:30days|sex:pooled male and female|tissue:skin|BioSampleModel:Model organism or animal                 RNAseq of zebrafish skin wt 3 30dpf skin wt 3 30dpf RNAseq of skin     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     skin-wt_3_30dpf.R1.fq.gz skin-wt_3_30dpf.R2.fq.gz fastq fastq 7180880434.0 25043295.0 skin wt 3 30dpf.R1.fq.gz 0:143.99 1:142.74 A:1774318367;C:1783613777;G:1819466761;T:1803467054;N:14475 143 142     1774318367 1783613777 1819466761 1803467054 14475 SRX13404151 SRS11307153 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.95299 0.94655 0.0347 0.03421 0.74426 0.74649 0.55044 0.54733 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Skin Surface Structure
67582 67582 SRR17224793 SRX13404148 SRS11307153 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafishskin   breed:AB|age:30days|sex:pooled male and female|tissue:skin|BioSampleModel:Model organism or animal                 RNAseq of zebrafish skin wt 2 30dpf skin wt 2 30dpf RNAseq of skin     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     skin-wt_2_30dpf.R1.fq.gz skin-wt_2_30dpf.R2.fq.gz fastq fastq 5568886770.0 19196789.0 skin wt 2 30dpf.R1.fq.gz 0:145.60 1:144.50 A:1392028598;C:1367410036;G:1394084093;T:1415353000;N:11043 145 144     1392028598 1367410036 1394084093 1415353000 11043 SRX13404148 SRS11307153 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.95518 0.94706 0.03299 0.0324 0.75124 0.75294 0.50897 0.50693 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Skin Surface Structure
67583 67583 SRR17224794 SRX13404147 SRS11307153 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafishskin   breed:AB|age:30days|sex:pooled male and female|tissue:skin|BioSampleModel:Model organism or animal                 RNAseq of zebrafish skin wt 1 30dpf skin wt 1 30dpf RNAseq of skin     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     skin-wt_1_30dpf.R1.fq.gz skin-wt_1_30dpf.R2.fq.gz fastq fastq 5296036598.0 18327020.0 skin wt 1 30dpf.R1.fq.gz 0:145.04 1:143.94 A:1317620766;C:1308908827;G:1332788335;T:1336708189;N:10481 145 143     1317620766 1308908827 1332788335 1336708189 10481 SRX13404147 SRS11307153 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.95731 0.94905 0.02784 0.02784 0.77222 0.7738 0.52941 0.58327 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Skin Surface Structure
67674 67674 SRR17247007 SRX13426044 SRS11327036 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         C3   isolate:not collected|age:41dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate C3|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S340 S340 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     c3_R1.fq.gz c3_R2.fq.gz fastq fastq 4841497500.0 16138325.0 c3 R1.fq.gz 0:150 1:150 A:1386818341;C:1017922211;G:1041712160;T:1394940280;N:104508 150 150     1386818341 1017922211 1041712160 1394940280 104508 SRX13426044 SRS11327036 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.90078 0.9042 0.12147 0.12291 0.73184 0.73497 0.57479 0.5555 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67675 67675 SRR17247008 SRX13426043 SRS11327037 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         C2   isolate:not collected|age:41dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate C2|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S339 S339 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     c2_R1.fq.gz c2_R2.fq.gz fastq fastq 7688124900.0 25627083.0 c2 R1.fq.gz 0:150 1:150 A:2102172030;C:1722525598;G:1752732030;T:2110524143;N:171099 150 150     2102172030 1722525598 1752732030 2110524143 171099 SRX13426043 SRS11327037 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.8669 0.86816 0.08761 0.08688 0.70725 0.71145 0.49101 0.48619 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67676 67676 SRR17247009 SRX13426042 SRS11327035 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         C1   isolate:not collected|age:41dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate C1|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S338 S338 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     c1_R1.fq.gz c1_R2.fq.gz fastq fastq 7456776900.0 24855923.0 c1 R1.fq.gz 0:150 1:150 A:2051878608;C:1656315578;G:1687161312;T:2061254398;N:167004 150 150     2051878608 1656315578 1687161312 2061254398 167004 SRX13426042 SRS11327035 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.82556 0.82709 0.09055 0.08946 0.70471 0.70857 0.48138 0.4916 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67677 67677 SRR17247010 SRX13426041 SRS11327033 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         B3   isolate:not collected|age:33dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate B3|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S337 S337 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     b3_R1.fq.gz b3_R2.fq.gz fastq fastq 9228717900.0 30762393.0 b3 R1.fq.gz 0:150 1:150 A:2487982964;C:2099691030;G:2134638107;T:2506202131;N:203668 150 150     2487982964 2099691030 2134638107 2506202131 203668 SRX13426041 SRS11327033 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.66624 0.66885 0.06853 0.06779 0.71887 0.72066 0.4895 0.49681 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67678 67678 SRR17247011 SRX13426040 SRS11327034 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         B2   isolate:not collected|age:33dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate B2|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S336 S336 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     b2_R1.fq.gz b2_R2.fq.gz fastq fastq 6040557600.0 20135192.0 b2 R1.fq.gz 0:150 1:150 A:1664821294;C:1338719408;G:1359251973;T:1677628310;N:136615 150 150     1664821294 1338719408 1359251973 1677628310 136615 SRX13426040 SRS11327034 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.93426 0.93571 0.10066 0.10055 0.69631 0.69897 0.47588 0.46263 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure
67679 67679 SRR17247012 SRX13426039 SRS11327032 SRP351072 PRJNA789095 Danio rerio Raw sequence reads PRJNA789095 Whole Genome Sequencing normal of RNA seq of danio rerio         B1   isolate:not collected|age:33dpf|sex:pooled male and female|tissue:scaly skin|replicate:replicate=biological replicate B1|BioSampleModel:Model organism or animal                 RNAseq of danio rerio S335 S335 normal RNA seq of danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP351072     b1_R1.fq.gz b1_R2.fq.gz fastq fastq 6368555100.0 21228517.0 b1 R1.fq.gz 0:150 1:150 A:1748027301;C:1419234076;G:1440533749;T:1760617536;N:142438 150 150     1748027301 1419234076 1440533749 1760617536 142438 SRX13426039 SRS11327032 SRA1344321 shanghai ocean university|college of marine sciences shanghai ocean university 2 0.93385 0.93455 0.09654 0.09586 0.70031 0.70274 0.4679 0.47428 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-16 Juvenile Juvenile Skin Surface Structure

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;