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82 rows where devstage_curation_coarse = "Juvenile" and experiment.library_selection = "Oligo-dT"

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tissue_curation 6

technology 3

experiment.library_layout 2

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • Oligo-dT · 82 ✖

devstage_curation_coarse 1

  • Juvenile · 82 ✖

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
33360 33360 SRR30140788 SRX25609257 SRS22255959 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       DMSO 1 DMSO 1   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:DMSO 1|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S886 S886 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     DMSO_1_1.fq.gz DMSO_1_2.fq.gz fastq fastq 6848352600.0 22827842.0 DMSO 1 1.fq.gz 0:150 1:150 A:2042619042;C:1408327078;G:1392721721;T:2004605654;N:79105 150 150     2042619042 1408327078 1392721721 2004605654 79105 SRX25609257 SRS22255959 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
33361 33361 SRR30140789 SRX25609256 SRS22255958 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       DMSO 2 DMSO 2   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:DMSO 2|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S887 S887 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     DMSO_2_1.fq.gz DMSO_2_2.fq.gz fastq fastq 6722867400.0 22409558.0 DMSO 2 1.fq.gz 0:150 1:150 A:1987471480;C:1402576521;G:1384470516;T:1948276779;N:72104 150 150     1987471480 1402576521 1384470516 1948276779 72104 SRX25609256 SRS22255958 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
33362 33362 SRR30140790 SRX25609255 SRS22255957 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       DMSO 3 DMSO 3   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:DMSO 3|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S888 S888 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     DMSO_3_1.fq.gz DMSO_3_2.fq.gz fastq fastq 6385524600.0 21285082.0 DMSO 3 1.fq.gz 0:150 1:150 A:1858080423;C:1360978750;G:1348505877;T:1817909740;N:49810 150 150     1858080423 1360978750 1348505877 1817909740 49810 SRX25609255 SRS22255957 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
33363 33363 SRR30140791 SRX25609254 SRS22255956 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       BPS1 1 BPS1 1   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS1 1|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S889 S889 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     BPS1_1_1.fq.gz BPS1_1_2.fq.gz fastq fastq 6677891400.0 22259638.0 BPS1 1 1.fq.gz 0:150 1:150 A:1942755547;C:1419146767;G:1404962384;T:1910952784;N:73918 150 150     1942755547 1419146767 1404962384 1910952784 73918 SRX25609254 SRS22255956 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
33364 33364 SRR30140792 SRX25609253 SRS22255955 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       BPS1 2 BPS1 2   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS1 2|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S890 S890 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     BPS1_2_1.fq.gz BPS1_2_2.fq.gz fastq fastq 6521417700.0 21738059.0 BPS1 2 1.fq.gz 0:150 1:150 A:1909300221;C:1371099464;G:1358671002;T:1882282904;N:64109 150 150     1909300221 1371099464 1358671002 1882282904 64109 SRX25609253 SRS22255955 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
33365 33365 SRR30140793 SRX25609252 SRS22255954 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       BPS1 3 BPS1 3   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS1 3|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S891 S891 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     BPS1_3_1.fq.gz BPS1_3_2.fq.gz fastq fastq 6821300100.0 22737667.0 BPS1 3 1.fq.gz 0:150 1:150 A:1996014045;C:1437758871;G:1429644156;T:1957815359;N:67669 150 150     1996014045 1437758871 1429644156 1957815359 67669 SRX25609252 SRS22255954 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
33366 33366 SRR30140794 SRX25609251 SRS22255953 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       BPS100 1 BPS100 1   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS100 1|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S892 S892 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     BPS100_1_1.fq.gz BPS100_1_2.fq.gz fastq fastq 6420793800.0 21402646.0 BPS100 1 1.fq.gz 0:150 1:150 A:1856129124;C:1374411655;G:1366071243;T:1824132054;N:49724 150 150     1856129124 1374411655 1366071243 1824132054 49724 SRX25609251 SRS22255953 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
33367 33367 SRR30140795 SRX25609250 SRS22255952 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       BPS100 2 BPS100 2   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS100 2|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S893 S893 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     BPS100_2_1.fq.gz BPS100_2_2.fq.gz fastq fastq 6639336600.0 22131122.0 BPS100 2 1.fq.gz 0:150 1:150 A:1901484110;C:1438361866;G:1430361119;T:1869078551;N:50954 150 150     1901484110 1438361866 1430361119 1869078551 50954 SRX25609250 SRS22255952 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
33368 33368 SRR30140796 SRX25609249 SRS22255951 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       BPS100 3 BPS100 3   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS100 3|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S894 S894 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     BPS100_3_1.fq.gz BPS100_3_2.fq.gz fastq fastq 6586231800.0 21954106.0 BPS100 3 1.fq.gz 0:150 1:150 A:1875041634;C:1438699475;G:1425868891;T:1846570793;N:51007 150 150     1875041634 1438699475 1425868891 1846570793 51007 SRX25609249 SRS22255951 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
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
54727 54727 SRR10150436 SRX6875873 SRS5411730 SRP222654 PRJNA571187 single cell RNA Seq of juvenile zebrafish PRJNA571187 Other single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit       whole organism single cell RNA seq of juvenile zebrafish SC2S3   strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal                 single cell RNA Seq of zebrafish: whole organism of juvenile I4S2 I4S2 A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP222654     S3-I4-Hiseq_S2_L001_R1_001.fastq.gz S3-I4-Hiseq_S2_L001_R2_001.fastq.gz fastq fastq 3487596300.0 11625321.0 S3 I4 Hiseq S2 L001 R1 001.fastq.gz 0:150 1:150 A:892777135;C:554604922;G:602698080;T:1437353489;N:162674 150 150     892777135 554604922 602698080 1437353489 162674 SRX6875873 SRS5411730 SRA965192 Sun Yat- sen University|Life Sicence School Sun Yat- sen University 2 0.20171 0.89797 0.05294 0.15018 0.98557 0.78865 0.5155 0.57581 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2019-09-20 Juvenile Juvenile Whole Organism All anatomical structures
54728 54728 SRR10150437 SRX6875872 SRS5411730 SRP222654 PRJNA571187 single cell RNA Seq of juvenile zebrafish PRJNA571187 Other single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit       whole organism single cell RNA seq of juvenile zebrafish SC2S3   strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal                 single cell RNA Seq of zebrafish: whole organism of juvenile I4S1 I4S1 A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP222654     S3-I4-Hiseq_S1_L001_R1_001.fastq.gz S3-I4-Hiseq_S1_L001_R2_001.fastq.gz fastq fastq 7508763300.0 25029211.0 S3 I4 Hiseq S1 L001 R1 001.fastq.gz 0:150 1:150 A:1913388616;C:1347525105;G:1432782100;T:2815014523;N:52956 150 150     1913388616 1347525105 1432782100 2815014523 52956 SRX6875872 SRS5411730 SRA965192 Sun Yat- sen University|Life Sicence School Sun Yat- sen University 2 0.07221 0.85601 0.01751 0.14578 0.98569 0.78642 0.49143 0.56028 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2019-09-20 Juvenile Juvenile Whole Organism All anatomical structures
54729 54729 SRR10150438 SRX6875871 SRS5411730 SRP222654 PRJNA571187 single cell RNA Seq of juvenile zebrafish PRJNA571187 Other single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit       whole organism single cell RNA seq of juvenile zebrafish SC2S3   strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal                 single cell RNA Seq of zebrafish: whole organism of juvenile I3S2 I3S2 A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP222654     S3-I3-Hiseq_S2_L001_R1_001.fastq.gz S3-I3-Hiseq_S2_L001_R2_001.fastq.gz fastq fastq 4273728900.0 14245763.0 S3 I3 Hiseq S2 L001 R1 001.fastq.gz 0:150 1:150 A:1093044190;C:680068409;G:740119940;T:1760292389;N:203972 150 150     1093044190 680068409 740119940 1760292389 203972 SRX6875871 SRS5411730 SRA965192 Sun Yat- sen University|Life Sicence School Sun Yat- sen University 2 0.20465 0.90036 0.05289 0.14865 0.98553 0.7877 0.49162 0.55234 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2019-09-20 Juvenile Juvenile Whole Organism All anatomical structures
54730 54730 SRR10150439 SRX6875870 SRS5411730 SRP222654 PRJNA571187 single cell RNA Seq of juvenile zebrafish PRJNA571187 Other single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit       whole organism single cell RNA seq of juvenile zebrafish SC2S3   strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal                 single cell RNA Seq of zebrafish: whole organism of juvenile I3S1 I3S1 A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP222654     S3-I3-Hiseq_S1_L001_R1_001.fastq.gz S3-I3-Hiseq_S1_L001_R2_001.fastq.gz fastq fastq 9027772200.0 30092574.0 S3 I3 Hiseq S1 L001 R1 001.fastq.gz 0:150 1:150 A:2295058606;C:1618993604;G:1725968569;T:3387689160;N:62261 150 150     2295058606 1618993604 1725968569 3387689160 62261 SRX6875870 SRS5411730 SRA965192 Sun Yat- sen University|Life Sicence School Sun Yat- sen University 2 0.07429 0.86204 0.01816 0.14367 0.98638 0.78754 0.51152 0.56418 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2019-09-20 Juvenile Juvenile Whole Organism All anatomical structures
54731 54731 SRR10150440 SRX6875869 SRS5411730 SRP222654 PRJNA571187 single cell RNA Seq of juvenile zebrafish PRJNA571187 Other single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit       whole organism single cell RNA seq of juvenile zebrafish SC2S3   strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal                 single cell RNA Seq of zebrafish: whole organism of juvenile I2S2 I2S2 A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP222654     S3-I2-Hiseq_S2_L001_R1_001.fastq.gz S3-I2-Hiseq_S2_L001_R2_001.fastq.gz fastq fastq 3198554400.0 10661848.0 S3 I2 Hiseq S2 L001 R1 001.fastq.gz 0:150 1:150 A:818748615;C:508568675;G:554517575;T:1316569216;N:150319 150 150     818748615 508568675 554517575 1316569216 150319 SRX6875869 SRS5411730 SRA965192 Sun Yat- sen University|Life Sicence School Sun Yat- sen University 2 0.2074 0.89961 0.05315 0.14953 0.98514 0.78849 0.48568 0.56678 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2019-09-20 Juvenile Juvenile Whole Organism All anatomical structures
54732 54732 SRR10150441 SRX6875868 SRS5411730 SRP222654 PRJNA571187 single cell RNA Seq of juvenile zebrafish PRJNA571187 Other single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit       whole organism single cell RNA seq of juvenile zebrafish SC2S3   strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal                 single cell RNA Seq of zebrafish: whole organism of juvenile I2S1 I2S1 A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP222654     S3-I2-Hiseq_S1_L001_R1_001.fastq.gz S3-I2-Hiseq_S1_L001_R2_001.fastq.gz fastq fastq 7025021100.0 23416737.0 S3 I2 Hiseq S1 L001 R1 001.fastq.gz 0:150 1:150 A:1791257403;C:1265471598;G:1350119282;T:2618125524;N:47293 150 150     1791257403 1265471598 1350119282 2618125524 47293 SRX6875868 SRS5411730 SRA965192 Sun Yat- sen University|Life Sicence School Sun Yat- sen University 2 0.0595 0.8397 0.01378 0.14017 0.98602 0.78618 0.49684 0.57243 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2019-09-20 Juvenile Juvenile Whole Organism All anatomical structures
54733 54733 SRR10150442 SRX6875867 SRS5411730 SRP222654 PRJNA571187 single cell RNA Seq of juvenile zebrafish PRJNA571187 Other single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit       whole organism single cell RNA seq of juvenile zebrafish SC2S3   strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal                 single cell RNA Seq of zebrafish: whole organism of juvenile I1S2 I1S2 A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP222654     S3-I1-Hiseq_S2_L001_R1_001.fastq.gz S3-I1-Hiseq_S2_L001_R2_001.fastq.gz fastq fastq 3657667800.0 12192226.0 S3 I1 Hiseq S2 L001 R1 001.fastq.gz 0:150 1:150 A:936855915;C:580324428;G:630608753;T:1509707910;N:170794 150 150     936855915 580324428 630608753 1509707910 170794 SRX6875867 SRS5411730 SRA965192 Sun Yat- sen University|Life Sicence School Sun Yat- sen University 2 0.20478 0.89817 0.05194 0.15048 0.98543 0.78817 0.49956 0.57664 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2019-09-20 Juvenile Juvenile Whole Organism All anatomical structures
54734 54734 SRR10150443 SRX6875866 SRS5411730 SRP222654 PRJNA571187 single cell RNA Seq of juvenile zebrafish PRJNA571187 Other single cell RNA Seq of juvenile zebrafish using the 10x Genomics platform with Chromium Single Cell three prime v2 Reagent Kit       whole organism single cell RNA seq of juvenile zebrafish SC2S3   strain:AB|age:30 dpf|sex:not collected|tissue:whole organism|genotype:WT|BioSampleModel:Model organism or animal                 single cell RNA Seq of zebrafish: whole organism of juvenile I1S1 I1S1 A single Juvenile fish at about 30 dpf was anesthetized in tricaine and euthanized on ice. Then it was washed three times with 200 L ice cold HBSS supplemented with 1% BSA and transferred into 200 L Dissociation buffer 1 TrypLE Thermo Fisher Scientific in 1 HBSS [Ca+/Mg+ free] GIBCO. Next the solution was incubated for 20 minutes and mixed occasionally with a pipette. 120 L HBSS and 80 L Digestion cocktail stock 5 mg/mL collagenase Sigma Aldrich 10 mg/mL pronase Sigma Aldrich 10 mg/mL proteinase K Sigma Aldrich were added and the suspension was pipetted until the larva was invisible. The cell suspension was washed with wash buffer twice and pelleted by centrifuging at 600g for 8 minutes at 4 C and resuspended in wash buffer. The cells were filtered through a 35 m strainer and processed using the 10x Genomics platform with Chromium Single Cell 3 v2 Reagent Kit.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP222654     S3-I1-Hiseq_S1_L001_R1_001.fastq.gz S3-I1-Hiseq_S1_L001_R2_001.fastq.gz fastq fastq 7809763800.0 26032546.0 S3 I1 Hiseq S1 L001 R1 001.fastq.gz 0:150 1:150 A:1991021603;C:1400155384;G:1489635110;T:2928896892;N:54811 150 150     1991021603 1400155384 1489635110 2928896892 54811 SRX6875866 SRS5411730 SRA965192 Sun Yat- sen University|Life Sicence School Sun Yat- sen University 2 0.06891 0.85095 0.01881 0.14251 0.98555 0.78772 0.49154 0.57233 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2019-09-20 Juvenile Juvenile Whole Organism All anatomical structures
67572 67572 SRR17224783 SRX13404158 SRS11307154 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafisheye   breed:AB|age:30days|sex:pooled male and female|tissue:eyes|BioSampleModel:Model organism or animal                 RNAseq of zebrafish eye mut 1 30dpf eye mut 1 30dpf RNAseq of eye     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     eye_mut_1_30dpf.R1.fastq.gz eye_mut_1_30dpf.R2.fastq.gz fastq fastq 6647236232.0 22010716.0 eye mut 1 30dpf.R1.fastq.gz 0:151 1:151 A:1828748374;C:1496039359;G:1520471614;T:1801966254;N:10631 151 151     1828748374 1496039359 1520471614 1801966254 10631 SRX13404158 SRS11307154 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.91773 0.91812 0.11227 0.11178 0.6687 0.66931 0.47877 0.47805 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Eye Sensory System
67573 67573 SRR17224784 SRX13404157 SRS11307154 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafisheye   breed:AB|age:30days|sex:pooled male and female|tissue:eyes|BioSampleModel:Model organism or animal                 RNAseq of zebrafish eye wt 3 30dpf eye wt 3 30dpf RNAseq of eye     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     eye_wt_3_30dpf.R1.fastq.gz eye_wt_3_30dpf.R2.fastq.gz fastq fastq 6665043964.0 22069682.0 eye wt 3 30dpf.R1.fastq.gz 0:151 1:151 A:1837907813;C:1496332954;G:1517206099;T:1813585697;N:11401 151 151     1837907813 1496332954 1517206099 1813585697 11401 SRX13404157 SRS11307154 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.92328 0.92376 0.11972 0.11905 0.69002 0.69039 0.48654 0.48588 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Eye Sensory System
67574 67574 SRR17224785 SRX13404156 SRS11307154 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafisheye   breed:AB|age:30days|sex:pooled male and female|tissue:eyes|BioSampleModel:Model organism or animal                 RNAseq of zebrafish eye wt 2 30dpf eye wt 2 30dpf RNAseq of eye     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     eye_wt_2_30dpf.R1.fastq.gz eye_wt_2_30dpf.R2.fastq.gz fastq fastq 7313252536.0 24216068.0 eye wt 2 30dpf.R1.fastq.gz 0:151 1:151 A:2005760880;C:1644712229;G:1691008059;T:1971759242;N:12126 151 151     2005760880 1644712229 1691008059 1971759242 12126 SRX13404156 SRS11307154 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.92458 0.92267 0.11276 0.11098 0.68834 0.6939 0.48994 0.48977 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Eye Sensory System
67575 67575 SRR17224786 SRX13404155 SRS11307154 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafisheye   breed:AB|age:30days|sex:pooled male and female|tissue:eyes|BioSampleModel:Model organism or animal                 RNAseq of zebrafish eye wt 1 30dpf eye wt 1 30dpf RNAseq of eye     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     eye_wt_1_30dpf.R1.fastq.gz eye_wt_1_30dpf.R2.fastq.gz fastq fastq 7374231470.0 24417985.0 eye wt 1 30dpf.R1.fastq.gz 0:151 1:151 A:2032283041;C:1657026689;G:1681898985;T:2003011689;N:11066 151 151     2032283041 1657026689 1681898985 2003011689 11066 SRX13404155 SRS11307154 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.92217 0.92217 0.11433 0.11344 0.69045 0.69087 0.48935 0.47534 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Eye Sensory System
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
67580 67580 SRR17224791 SRX13404150 SRS11307154 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafisheye   breed:AB|age:30days|sex:pooled male and female|tissue:eyes|BioSampleModel:Model organism or animal                 RNAseq of zebrafish eye mut 3 30dpf eye mut 3 30dpf RNAseq of eye     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     eye_mut_3_30dpf.R1.fastq.gz eye_mut_3_30dpf.R2.fastq.gz fastq fastq 7370863566.0 24406833.0 eye mut 3 30dpf.R1.fastq.gz 0:151 1:151 A:2035593457;C:1650415961;G:1678944830;T:2005897248;N:12070 151 151     2035593457 1650415961 1678944830 2005897248 12070 SRX13404150 SRS11307154 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.9169 0.91717 0.11546 0.11616 0.66249 0.66312 0.47895 0.47697 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Eye Sensory System
67581 67581 SRR17224792 SRX13404149 SRS11307154 SRP350669 PRJNA788440 Danio rerio Raw sequence reads PRJNA788440 Whole Genome Sequencing Danio rerio Raw sequence reads of eyes and skin         zebrafisheye   breed:AB|age:30days|sex:pooled male and female|tissue:eyes|BioSampleModel:Model organism or animal                 RNAseq of zebrafish eye mut 2 30dpf eye mut 2 30dpf RNAseq of eye     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP350669     eye_mut_2_30dpf.R1.fastq.gz eye_mut_2_30dpf.R2.fastq.gz fastq fastq 6025971496.0 19953548.0 eye mut 2 30dpf.R1.fastq.gz 0:151 1:151 A:1659612510;C:1355527081;G:1377376165;T:1633446020;N:9720 151 151     1659612510 1355527081 1377376165 1633446020 9720 SRX13404149 SRS11307154 SRA1343194 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University 2 0.91909 0.92042 0.11187 0.11181 0.66884 0.66985 0.48856 0.49166 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-14 Juvenile Juvenile Eye Sensory System
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
70056 70056 SRR19392694 SRX15447454 SRS13169844 SRP376956 PRJNA842165 Danio rerio Raw sequence reads PRJNA842165 Whole Genome Sequencing the RNA seq of 45dpf whole fish         whole zebrafish   breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal                 RNAseq of zebrafish mut 3 45dpf mut 3 45dpf RNAseq of whole fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP376956     6Hmut_3_R1.fastq.gz 6Hmut_3_R2.fastq.gz fastq fastq 6560549850.0 21723675.0 6Hmut 3 R1.fastq.gz 0:151 1:151 A:1737437159;C:1534810355;G:1561501860;T:1726789854;N:10622 151 151     1737437159 1534810355 1561501860 1726789854 10622 SRX15447454 SRS13169844 SRA1426081 Huazhong Agricultural university|Huazhong Agricultural university Huazhong Agricultural university 2 0.93435 0.93393 0.06267 0.06345 0.65776 0.65871 0.49762 0.49344 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-05-25 Juvenile Juvenile Whole Organism All anatomical structures
70057 70057 SRR19392695 SRX15447453 SRS13169844 SRP376956 PRJNA842165 Danio rerio Raw sequence reads PRJNA842165 Whole Genome Sequencing the RNA seq of 45dpf whole fish         whole zebrafish   breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal                 RNAseq of zebrafish mut 2 45dpf mut 2 45dpf RNAseq of whole fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP376956     6Hmut_2_R1.fastq.gz 6Hmut_2_R2.fastq.gz fastq fastq 6478614532.0 21452366.0 6Hmut 2 R1.fastq.gz 0:151 1:151 A:1722746415;C:1511301958;G:1537581513;T:1706974238;N:10408 151 151     1722746415 1511301958 1537581513 1706974238 10408 SRX15447453 SRS13169844 SRA1426081 Huazhong Agricultural university|Huazhong Agricultural university Huazhong Agricultural university 2 0.94033 0.93884 0.0793 0.07897 0.66979 0.67063 0.51091 0.50721 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-05-25 Juvenile Juvenile Whole Organism All anatomical structures
70058 70058 SRR19392696 SRX15447452 SRS13169844 SRP376956 PRJNA842165 Danio rerio Raw sequence reads PRJNA842165 Whole Genome Sequencing the RNA seq of 45dpf whole fish         whole zebrafish   breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal                 RNAseq of zebrafish mut 1 45dpf mut 1 45dpf RNAseq of whole fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP376956     6Hmut_1_R1.fastq.gz 6Hmut_1_R2.fastq.gz fastq fastq 7131696780.0 23614890.0 6Hmut 1 R1.fastq.gz 0:151 1:151 A:1896556650;C:1662708805;G:1692110221;T:1880309012;N:12092 151 151     1896556650 1662708805 1692110221 1880309012 12092 SRX15447452 SRS13169844 SRA1426081 Huazhong Agricultural university|Huazhong Agricultural university Huazhong Agricultural university 2 0.93784 0.93841 0.07685 0.07715 0.65969 0.65999 0.50615 0.51174 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-05-25 Juvenile Juvenile Whole Organism All anatomical structures
70059 70059 SRR19392697 SRX15447451 SRS13169844 SRP376956 PRJNA842165 Danio rerio Raw sequence reads PRJNA842165 Whole Genome Sequencing the RNA seq of 45dpf whole fish         whole zebrafish   breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal                 RNAseq of zebrafish wt 3 45dpf wt 3 45dpf RNAseq of whole fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP376956     wt_3_R1.fastq.gz wt_3_R2.fastq.gz fastq fastq 6772530000.0 22575100.0 wt 3 R1.fastq.gz 0:150 1:150 A:1761127291;C:1612285256;G:1643602723;T:1755489964;N:24766 150 150     1761127291 1612285256 1643602723 1755489964 24766 SRX15447451 SRS13169844 SRA1426081 Huazhong Agricultural university|Huazhong Agricultural university Huazhong Agricultural university 2 0.94155 0.94016 0.04781 0.04747 0.67054 0.67227 0.49488 0.49322 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-05-25 Juvenile Juvenile Whole Organism All anatomical structures
70060 70060 SRR19392698 SRX15447450 SRS13169844 SRP376956 PRJNA842165 Danio rerio Raw sequence reads PRJNA842165 Whole Genome Sequencing the RNA seq of 45dpf whole fish         whole zebrafish   breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal                 RNAseq of zebrafish wt 2 45dpf wt 2 45dpf RNAseq of whole fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP376956     wt_2_R1.fastq.gz wt_2_R2.fastq.gz fastq fastq 7643857500.0 25479525.0 wt 2 R1.fastq.gz 0:150 1:150 A:1983773833;C:1824285264;G:1856615811;T:1979155020;N:27572 150 150     1983773833 1824285264 1856615811 1979155020 27572 SRX15447450 SRS13169844 SRA1426081 Huazhong Agricultural university|Huazhong Agricultural university Huazhong Agricultural university 2 0.93966 0.93936 0.04464 0.04509 0.66947 0.67006 0.47294 0.48847 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-05-25 Juvenile Juvenile Whole Organism All anatomical structures
70061 70061 SRR19392699 SRX15447449 SRS13169844 SRP376956 PRJNA842165 Danio rerio Raw sequence reads PRJNA842165 Whole Genome Sequencing the RNA seq of 45dpf whole fish         whole zebrafish   breed:AB|age:45days|sex:pooled male and female|tissue:whole fish|BioSampleModel:Model organism or animal                 RNAseq of zebrafish wt 1 45dpf wt 1 45dpf RNAseq of whole fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP376956     wt_1_R1.fastq.gz wt_1_R2.fastq.gz fastq fastq 7810923300.0 26036411.0 wt 1 R1.fastq.gz 0:150 1:150 A:2023252187;C:1867703140;G:1901935578;T:2018003438;N:28957 150 150     2023252187 1867703140 1901935578 2018003438 28957 SRX15447449 SRS13169844 SRA1426081 Huazhong Agricultural university|Huazhong Agricultural university Huazhong Agricultural university 2 0.94254 0.94222 0.04298 0.04298 0.66884 0.67073 0.47763 0.48746 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-05-25 Juvenile Juvenile Whole Organism All anatomical structures
72671 72671 SRR23060055 SRX19013379 SRS16433016 SRP417129 PRJNA922890 Danio rerio Raw sequence reads PRJNA922890 Whole Genome Sequencing normal reference transcriptome of zebrafish         BPA225 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 9|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio Z908 Z908 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP417129     BPA225_3_Clean_Data1.fq.gz BPA225_3_Clean_Data2.fq.gz fastq fastq 5922430705.0 21094865.0 BPA225 3 Clean Data1.fq.gz                       SRX19013379 SRS16433016 SRA1573339 yangzhou university|College of Animal Science and Technology yangzhou university 2 0.94064 0.94209 0.10366 0.10189 0.70092 0.6997 0.46735 0.4612 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-01-12 Juvenile Juvenile Whole Organism All anatomical structures
72672 72672 SRR23060056 SRX19013378 SRS16433015 SRP417129 PRJNA922890 Danio rerio Raw sequence reads PRJNA922890 Whole Genome Sequencing normal reference transcriptome of zebrafish         BPA225 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 8|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio Z907 Z907 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP417129     BPA225_2_Clean_Data1.fq.gz BPA225_2_Clean_Data2.fq.gz fastq fastq 5509331897.0 19639714.0 BPA225 2 Clean Data1.fq.gz                       SRX19013378 SRS16433015 SRA1573339 yangzhou university|College of Animal Science and Technology yangzhou university 2 0.9374 0.93862 0.11618 0.11425 0.69972 0.69952 0.46205 0.46585 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-01-12 Juvenile Juvenile Whole Organism All anatomical structures
72673 72673 SRR23060057 SRX19013377 SRS16433014 SRP417129 PRJNA922890 Danio rerio Raw sequence reads PRJNA922890 Whole Genome Sequencing normal reference transcriptome of zebrafish         BPA225 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 7|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio Z906 Z906 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP417129     BPA225_1_Clean_Data1.fq.gz BPA225_1_Clean_Data2.fq.gz fastq fastq 6015141019.0 21413611.0 BPA225 1 Clean Data1.fq.gz 0:140.46 1:140.44 A:1623319583;C:1384519528;G:1394796849;T:1612405771;N:99288 140 140     1623319583 1384519528 1394796849 1612405771 99288 SRX19013377 SRS16433014 SRA1573339 yangzhou university|College of Animal Science and Technology yangzhou university 2 0.9392 0.94002 0.10822 0.10578 0.69146 0.69063 0.46651 0.4618 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-01-12 Juvenile Juvenile Whole Organism All anatomical structures
72674 72674 SRR23060058 SRX19013376 SRS16433013 SRP417129 PRJNA922890 Danio rerio Raw sequence reads PRJNA922890 Whole Genome Sequencing normal reference transcriptome of zebrafish         BPA15 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 6|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio Z905 Z905 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP417129     BPA15_3_Clean_Data1.fq.gz BPA15_3_Clean_Data2.fq.gz fastq fastq 5412693513.0 19255194.0 BPA15 3 Clean Data1.fq.gz                       SRX19013376 SRS16433013 SRA1573339 yangzhou university|College of Animal Science and Technology yangzhou university 2 0.939 0.93943 0.11111 0.10838 0.69798 0.69777 0.46519 0.46877 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-01-12 Juvenile Juvenile Whole Organism All anatomical structures
72675 72675 SRR23060059 SRX19013375 SRS16433012 SRP417129 PRJNA922890 Danio rerio Raw sequence reads PRJNA922890 Whole Genome Sequencing normal reference transcriptome of zebrafish         BPA15 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 5|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio Z904 Z904 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP417129     BPA15_2_Clean_Data1.fq.gz BPA15_2_Clean_Data2.fq.gz fastq fastq 5836868617.0 20778949.0 BPA15 2 Clean Data1.fq.gz 0:140.46 1:140.45 A:1603966024;C:1315242512;G:1325577058;T:1591978988;N:104035 140 140     1603966024 1315242512 1325577058 1591978988 104035 SRX19013375 SRS16433012 SRA1573339 yangzhou university|College of Animal Science and Technology yangzhou university 2 0.93522 0.93486 0.12945 0.12692 0.69735 0.69702 0.47307 0.47198 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-01-12 Juvenile Juvenile Whole Organism All anatomical structures
72676 72676 SRR23060060 SRX19013374 SRS16433010 SRP417129 PRJNA922890 Danio rerio Raw sequence reads PRJNA922890 Whole Genome Sequencing normal reference transcriptome of zebrafish         BPA15 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio Z903 Z903 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP417129     BPA15_1_Clean_Data1.fq.gz BPA15_1_Clean_Data2.fq.gz fastq fastq 5565976271.0 19806071.0 BPA15 1 Clean Data1.fq.gz 0:140.52 1:140.51 A:1513411045;C:1269789679;G:1278952098;T:1503723540;N:99909 140 140     1513411045 1269789679 1278952098 1503723540 99909 SRX19013374 SRS16433010 SRA1573339 yangzhou university|College of Animal Science and Technology yangzhou university 2 0.93415 0.93473 0.12035 0.11811 0.69315 0.69254 0.47054 0.47231 105 105 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-01-12 Juvenile Juvenile Whole Organism All anatomical structures
72677 72677 SRR23060061 SRX19013373 SRS16433009 SRP417129 PRJNA922890 Danio rerio Raw sequence reads PRJNA922890 Whole Genome Sequencing normal reference transcriptome of zebrafish         Control 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio Z902 Z902 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP417129     Control_3_Clean_Data1.fq.gz Control_3_Clean_Data2.fq.gz fastq fastq 4866202369.0 17323282.0 Control 3 Clean Data1.fq.gz                       SRX19013373 SRS16433009 SRA1573339 yangzhou university|College of Animal Science and Technology yangzhou university 2 0.91765 0.91705 0.17214 0.16747 0.69765 0.69739 0.48756 0.49157 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-01-12 Juvenile Juvenile Whole Organism All anatomical structures
72678 72678 SRR23060062 SRX19013372 SRS16433011 SRP417129 PRJNA922890 Danio rerio Raw sequence reads PRJNA922890 Whole Genome Sequencing normal reference transcriptome of zebrafish         Control 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio Z901 Z901 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP417129     Control_2_Clean_Data1.fq.gz Control_2_Clean_Data2.fq.gz fastq fastq 5265679291.0 18766450.0 Control 2 Clean Data1.fq.gz                       SRX19013372 SRS16433011 SRA1573339 yangzhou university|College of Animal Science and Technology yangzhou university 2 0.92738 0.92679 0.17397 0.17035 0.69948 0.69891 0.48006 0.48572 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-01-12 Juvenile Juvenile Whole Organism All anatomical structures
72679 72679 SRR23060063 SRX19013371 SRS16433008 SRP417129 PRJNA922890 Danio rerio Raw sequence reads PRJNA922890 Whole Genome Sequencing normal reference transcriptome of zebrafish         Control 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not collected|tissue:Juvenile whole fish|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio Z900 Z900 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP417129     Control_1_Clean_Data1.fq.gz Control_1_Clean_Data2.fq.gz fastq fastq 5769401401.0 20486114.0 Control 1 Clean Data1.fq.gz 0:140.82 1:140.80 A:1567930643;C:1316937376;G:1327529593;T:1556929210;N:74579 140 140     1567930643 1316937376 1327529593 1556929210 74579 SRX19013371 SRS16433008 SRA1573339 yangzhou university|College of Animal Science and Technology yangzhou university 2 0.94089 0.94089 0.11671 0.11386 0.69923 0.6994 0.46151 0.46472 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-01-12 Juvenile Juvenile Whole Organism All anatomical structures
76356 76356 SRR24844103 SRX20608301 SRS17908187 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       LB023 mutant B LB023 Mut B   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense MutantB|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 missense mutant: male testes LB023 Mut B LB023 Mut B Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     LB023-Mut-B_R1_001.fastq.gz LB023-Mut-B_R2_001.fastq.gz fastq fastq 5532352200.0 18441174.0 LB023 Mut B R1 001.fastq.gz 0:150 1:150 A:1408144772;C:1348146392;G:1440174663;T:1335799503;N:86870 150 150     1408144772 1348146392 1440174663 1335799503 86870 SRX20608301 SRS17908187 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.93072 0.9289 0.0921 0.09129 0.73129 0.73143 0.55139 0.54723 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76357 76357 SRR24844100 SRX20608300 SRS17908192 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       LB023 mutant C LB023 Mut C   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense MutantC|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 missense mutant: male testes LB023 Mut C LB023 Mut C Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     LB023-Mut-C_R2_001.fastq.gz LB023-Mut-C_R1_001.fastq.gz fastq fastq 6159317100.0 20531057.0 LB023 Mut C R1 001.fastq.gz 0:150 1:150 A:1639865405;C:1424690953;G:1522945570;T:1571725037;N:90135 150 150     1639865405 1424690953 1522945570 1571725037 90135 SRX20608300 SRS17908192 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.92565 0.92502 0.07339 0.0724 0.70832 0.70924 0.50224 0.49923 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76358 76358 SRR24844101 SRX20608299 SRS17908193 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       LB023 wildtype sibling control D LB023 WT D   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense WildtypeD|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 missense wildtype sibling: male testes LB023 WT D LB023 WT D Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     LB023-WT-D_R2_001.fastq.gz LB023-WT-D_R1_001.fastq.gz fastq fastq 5436242700.0 18120809.0 LB023 WT D R1 001.fastq.gz 0:150 1:150 A:1448689171;C:1252673824;G:1358298822;T:1376497051;N:83832 150 150     1448689171 1252673824 1358298822 1376497051 83832 SRX20608299 SRS17908193 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.91802 0.91762 0.09407 0.09394 0.70916 0.7108 0.54977 0.55217 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76359 76359 SRR24844102 SRX20608298 SRS17908191 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       adad1 mutant E adad1 Mut E   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:MutantE|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 mutant: male testes adad1 Mut E adad1 Mut E Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     adad1-Mut-E_R2_001.fastq.gz adad1-Mut-E_R1_001.fastq.gz fastq fastq 4958837100.0 16529457.0 adad1 Mut E R1 001.fastq.gz 0:150 1:150 A:1311870356;C:1151609197;G:1254712533;T:1240567756;N:77258 150 150     1311870356 1151609197 1254712533 1240567756 77258 SRX20608298 SRS17908191 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.901 0.90124 0.11096 0.11139 0.71851 0.71967 0.5526 0.57121 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76360 76360 SRR24844104 SRX20608297 SRS17908190 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       adad1 mutant F adad1 Mut F   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:MutantF|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 mutant: male testes adad1 Mut F adad1 Mut F Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     adad1-Mut-F_R1_001.fastq.gz adad1-Mut-F_R2_001.fastq.gz fastq fastq 5780694600.0 19268982.0 adad1 Mut F R1 001.fastq.gz 0:150 1:150 A:1502665613;C:1371103253;G:1490414769;T:1416422204;N:88761 150 150     1502665613 1371103253 1490414769 1416422204 88761 SRX20608297 SRS17908190 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.89657 0.89588 0.10966 0.10896 0.72671 0.72728 0.57267 0.55033 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76361 76361 SRR24844105 SRX20608296 SRS17908189 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       adad1 wildtype sibling control A adad1 WT A   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:WildtypeA|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 wildtype sibling: male testes adad1 WT A adad1 WT A Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     adad1-WT-A_R1_001.fastq.gz adad1-WT-A_R2_001.fastq.gz fastq fastq 8011954200.0 26706514.0 adad1 WT A R1 001.fastq.gz 0:150 1:150 A:2090202005;C:1898897650;G:2026356221;T:1996371474;N:126850 150 150     2090202005 1898897650 2026356221 1996371474 126850 SRX20608296 SRS17908189 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.91189 0.91021 0.06102 0.06139 0.68525 0.68718 0.50676 0.50889 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76362 76362 SRR24844106 SRX20608295 SRS17908186 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       adad1 wildtype sibling control B adad1 WT B   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:WildtypeB|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 wildtype sibling: male testes adad1 WT B adad1 WT B Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     adad1-WT-B_R1_001.fastq.gz adad1-WT-B_R2_001.fastq.gz fastq fastq 7492292100.0 24974307.0 adad1 WT B R1 001.fastq.gz 0:150 1:150 A:1943185783;C:1771813934;G:1904551325;T:1872624369;N:116689 150 150     1943185783 1771813934 1904551325 1872624369 116689 SRX20608295 SRS17908186 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.90916 0.90763 0.11162 0.11123 0.67399 0.6743 0.52068 0.52927 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76363 76363 SRR24844107 SRX20608294 SRS17908185 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       adad1 wildtype sibling control C adad1 WT C   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:WildtypeC|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 wildtype sibling: male testes adad1 WT C adad1 WT C Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     adad1-WT-C_R2_001.fastq.gz adad1-WT-C_R1_001.fastq.gz fastq fastq 7521501900.0 25071673.0 adad1 WT C R1 001.fastq.gz 0:150 1:150 A:1804312038;C:1905161135;G:2076680572;T:1735230886;N:117269 150 150     1804312038 1905161135 2076680572 1735230886 117269 SRX20608294 SRS17908185 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.91415 0.91424 0.1126 0.11157 0.72861 0.72924 0.60581 0.59123 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76364 76364 SRR24844111 SRX20608293 SRS17908188 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       adad1 wildtype sibling control D adad1 WT D   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:WildtypeD|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 wildtype sibling: male testes adad1 WT D adad1 WT D Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     adad1-WT-D_R2_001.fastq.gz adad1-WT-D_R1_001.fastq.gz fastq fastq 6723661500.0 22412205.0 adad1 WT D R1 001.fastq.gz 0:150 1:150 A:1762783841;C:1577461245;G:1700257202;T:1683053935;N:105277 150 150     1762783841 1577461245 1700257202 1683053935 105277 SRX20608293 SRS17908188 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.90669 0.90515 0.1057 0.1054 0.7055 0.70648 0.53378 0.53859 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76365 76365 SRR24844108 SRX20608292 SRS17908183 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       LB023 wildtype sibling control C LB023 WT C   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense WildtypeC|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 missense wildtype sibling: male testes LB023 WT C LB023 WT C Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     LB023-WT-C_R1_001.fastq.gz LB023-WT-C_R2_001.fastq.gz fastq fastq 6931350600.0 23104502.0 LB023 WT C R1 001.fastq.gz 0:150 1:150 A:1738105921;C:1615563430;G:1915220365;T:1662351851;N:109033 150 150     1738105921 1615563430 1915220365 1662351851 109033 SRX20608292 SRS17908183 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.85918 0.86008 0.0973 0.0972 0.75621 0.75617 0.51414 0.52127 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76366 76366 SRR24844109 SRX20608291 SRS17908182 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       LB023 wildtype sibling control B LB023 WT B   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense WildtypeB|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 missense wildtype sibling: male testes LB023 WT B LB023 WT B Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     LB023-WT-B_R1_001.fastq.gz LB023-WT-B_R2_001.fastq.gz fastq fastq 6486567300.0 21621891.0 LB023 WT B R1 001.fastq.gz 0:150 1:150 A:1659315544;C:1565803285;G:1669608945;T:1591739895;N:99631 150 150     1659315544 1565803285 1669608945 1591739895 99631 SRX20608291 SRS17908182 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.92214 0.92196 0.09064 0.09079 0.70092 0.70207 0.54638 0.55145 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76367 76367 SRR24844110 SRX20608290 SRS17908184 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       LB023 wildtype sibling control A LB023 WT A   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense WildtypeA|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 missense wildtype sibling: male testes LB023 WT A LB023 WT A Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     LB023-WT-A_R1_001.fastq.gz LB023-WT-A_R2_001.fastq.gz fastq fastq 7085531700.0 23618439.0 LB023 WT A R1 001.fastq.gz 0:150 1:150 A:1870324648;C:1666204540;G:1769576825;T:1779314498;N:111189 150 150     1870324648 1666204540 1769576825 1779314498 111189 SRX20608290 SRS17908184 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.91831 0.91753 0.06037 0.06044 0.70307 0.70368 0.51531 0.51099 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76368 76368 SRR24844112 SRX20608289 SRS17908179 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       LB023 mutant F LB023 Mut F   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense MutantF|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 missense mutant: male testes LB023 Mut F LB023 Mut F Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     LB023-Mut-F_R1_001.fastq.gz LB023-Mut-F_R2_001.fastq.gz fastq fastq 7753356600.0 25844522.0 LB023 Mut F R1 001.fastq.gz 0:150 1:150 A:2031483621;C:1809017944;G:1970064517;T:1942669709;N:120809 150 150     2031483621 1809017944 1970064517 1942669709 120809 SRX20608289 SRS17908179 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.87475 0.87314 0.09092 0.09089 0.75373 0.75434 0.5602 0.56521 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76369 76369 SRR24844113 SRX20608288 SRS17908178 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       LB023 mutant E LB023 Mut E   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense MutantE|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 missense mutant: male testes LB023 Mut E LB023 Mut E Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     LB023-Mut-E_R1_001.fastq.gz LB023-Mut-E_R2_001.fastq.gz fastq fastq 4532652000.0 15108840.0 LB023 Mut E R1 001.fastq.gz 0:150 1:150 A:1199854650;C:1037858889;G:1150707006;T:1144159494;N:71961 150 150     1199854650 1037858889 1150707006 1144159494 71961 SRX20608288 SRS17908178 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.87501 0.87504 0.08393 0.08384 0.76021 0.76055 0.54045 0.54351 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76370 76370 SRR24844114 SRX20608287 SRS17908181 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       adad1 mutant C adad1 Mut C   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:MutantC|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 mutant: male testes adad1 Mut C adad1 Mut C Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     adad1-Mut-C_R1_001.fastq.gz adad1-Mut-C_R2_001.fastq.gz fastq fastq 7938136500.0 26460455.0 adad1 Mut C R1 001.fastq.gz 0:150 1:150 A:2011717685;C:1935444799;G:2053481206;T:1937375239;N:117571 150 150     2011717685 1935444799 2053481206 1937375239 117571 SRX20608287 SRS17908181 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.92456 0.92396 0.08714 0.08738 0.70575 0.70826 0.5441 0.52561 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76371 76371 SRR24844115 SRX20608286 SRS17908180 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       adad1 mutant A adad1 Mut A   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:MutantA|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 mutant: male testes adad1 Mut A adad1 Mut A Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     adad1-Mut-A_R1_001.fastq.gz adad1-Mut-A_R2_001.fastq.gz fastq fastq 7254148200.0 24180494.0 adad1 Mut A R1 001.fastq.gz 0:150 1:150 A:1849587944;C:1771248935;G:1861148471;T:1772049096;N:113754 150 150     1849587944 1771248935 1861148471 1772049096 113754 SRX20608286 SRS17908180 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.93069 0.93108 0.10454 0.10422 0.69899 0.70088 0.53698 0.55029 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System

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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");;