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
201,DRR162540,DRX153159,DRS083220,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,muscle sample from 2 mpf zebrafish replicate5,SAMD00152488,,sample name:m02 5|age:2 month|biological replicate:5|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152488,DRX153159,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152488,,,,1063436200.0,5317181.0,DRR162540,0:100 1:100,A:275438061;C:255805442;G:257091950;T:273487067;N:1613680,100,100,,,275438061,255805442,257091950,273487067,1613680,DRX153159,DRS083220,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96295,0.92896,0.04409,0.0427,0.75355,0.76499,0.49339,0.50418,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Muscle,Muscular System
202,DRR162539,DRX153158,DRS083219,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,muscle sample from 2 mpf zebrafish replicate4,SAMD00152487,,sample name:m02 4|age:2 month|biological replicate:4|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152487,DRX153158,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152487,,,,1233640200.0,6168201.0,DRR162539,0:100 1:100,A:318959646;C:297211942;G:300002324;T:315647570;N:1818718,100,100,,,318959646,297211942,300002324,315647570,1818718,DRX153158,DRS083219,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96511,0.92512,0.04175,0.04058,0.77607,0.78835,0.48689,0.50535,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Muscle,Muscular System
203,DRR162538,DRX153157,DRS083218,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,muscle sample from 2 mpf zebrafish replicate3,SAMD00152486,,sample name:m02 3|age:2 month|biological replicate:3|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152486,DRX153157,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152486,,,,675957200.0,3379786.0,DRR162538,0:100 1:100,A:173033870;C:164578076;G:165481544;T:171780353;N:1083357,100,100,,,173033870,164578076,165481544,171780353,1083357,DRX153157,DRS083218,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.97251,0.94405,0.03347,0.03256,0.82432,0.83159,0.55228,0.47905,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Muscle,Muscular System
204,DRR162537,DRX153156,DRS083217,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,muscle sample from 2 mpf zebrafish replicate2,SAMD00152485,,sample name:m02 2|age:2 month|biological replicate:2|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152485,DRX153156,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152485,,,,1260768000.0,6303840.0,DRR162537,0:100 1:100,A:319433176;C:310903964;G:312279388;T:316219239;N:1932233,100,100,,,319433176,310903964,312279388,316219239,1932233,DRX153156,DRS083217,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.96774,0.93275,0.04099,0.04003,0.76919,0.79626,0.51687,0.50638,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Muscle,Muscular System
205,DRR162536,DRX153155,DRS083216,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,muscle sample from 2 mpf zebrafish replicate1,SAMD00152484,,sample name:m02 1|age:2 month|biological replicate:1|tissue:muscle,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152484,DRX153155,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152484,,,,1318898400.0,6594492.0,DRR162536,0:100 1:100,A:337402722;C:321381897;G:323422706;T:334658718;N:2032357,100,100,,,337402722,321381897,323422706,334658718,2032357,DRX153155,DRS083216,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.9692,0.93768,0.02944,0.02852,0.79431,0.80359,0.50636,0.51065,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Muscle,Muscular System
221,DRR162520,DRX153139,DRS083200,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,liver sample from 2 mpf zebrafish replicate5,SAMD00152468,,sample name:l02 5|age:2 month|biological replicate:5|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152468,DRX153139,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152468,,,,1264817800.0,6324089.0,DRR162520,0:100 1:100,A:351295111;C:280181229;G:281044764;T:352232836;N:63860,100,100,,,351295111,280181229,281044764,352232836,63860,DRX153139,DRS083200,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.93687,0.93419,0.07774,0.07776,0.7587,0.7609,0.56082,0.56748,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Liver,Liver and Biliary System
222,DRR162519,DRX153138,DRS083199,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,liver sample from 2 mpf zebrafish replicate4,SAMD00152467,,sample name:l02 4|age:2 month|biological replicate:4|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152467,DRX153138,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152467,,,,1762366200.0,8811831.0,DRR162519,0:100 1:100,A:481999545;C:397566169;G:399183135;T:483526493;N:90858,100,100,,,481999545,397566169,399183135,483526493,90858,DRX153138,DRS083199,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.93994,0.93528,0.06039,0.05936,0.75037,0.75394,0.52945,0.52961,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Liver,Liver and Biliary System
223,DRR162518,DRX153137,DRS083198,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,liver sample from 2 mpf zebrafish replicate3,SAMD00152466,,sample name:l02 3|age:2 month|biological replicate:3|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152466,DRX153137,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152466,,,,1464434200.0,7322171.0,DRR162518,0:100 1:100,A:400972247;C:330316514;G:329635959;T:403435022;N:74458,100,100,,,400972247,330316514,329635959,403435022,74458,DRX153137,DRS083198,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.94169,0.93517,0.075,0.07408,0.78541,0.78796,0.56483,0.56426,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Liver,Liver and Biliary System
224,DRR162517,DRX153136,DRS083197,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,liver sample from 2 mpf zebrafish replicate2,SAMD00152465,,sample name:l02 2|age:2 month|biological replicate:2|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152465,DRX153136,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152465,,,,1953667000.0,9768335.0,DRR162517,0:100 1:100,A:525411621;C:450279523;G:450410879;T:527464993;N:99984,100,100,,,525411621,450279523,450410879,527464993,99984,DRX153136,DRS083197,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.94424,0.93692,0.06451,0.06582,0.78358,0.79557,0.56036,0.57581,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Liver,Liver and Biliary System
225,DRR162516,DRX153135,DRS083196,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,liver sample from 2 mpf zebrafish replicate1,SAMD00152464,,sample name:l02 1|age:2 month|biological replicate:1|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152464,DRX153135,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152464,,,,1541676600.0,7708383.0,DRR162516,0:100 1:100,A:414776600;C:354650822;G:357258514;T:414910092;N:80572,100,100,,,414776600,354650822,357258514,414910092,80572,DRX153135,DRS083196,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.94346,0.93048,0.06888,0.06759,0.79086,0.79452,0.56037,0.55727,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Liver,Liver and Biliary System
255,DRR162486,DRX153105,DRS083166,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,gill sample from 2 mpf zebrafish replicate5,SAMD00152434,,sample name:g02 5|age:2 month|biological replicate:5|tissue:gill,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152434,DRX153105,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152434,,,,1270126600.0,6350633.0,DRR162486,0:100 1:100,A:342076596;C:293249973;G:295429735;T:339306175;N:64121,100,100,,,342076596,293249973,295429735,339306175,64121,DRX153105,DRS083166,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.9321,0.91652,0.09414,0.09195,0.70084,0.70412,0.52077,0.51571,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Gill,Respiratory System
256,DRR162485,DRX153104,DRS083165,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,gill sample from 2 mpf zebrafish replicate4,SAMD00152433,,sample name:g02 4|age:2 month|biological replicate:4|tissue:gill,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152433,DRX153104,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152433,,,,835205000.0,4176025.0,DRR162485,0:100 1:100,A:224993396;C:192858928;G:193779680;T:223531224;N:41772,100,100,,,224993396,192858928,193779680,223531224,41772,DRX153104,DRS083165,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.9392,0.92364,0.08708,0.08554,0.70579,0.71017,0.53067,0.52045,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Gill,Respiratory System
257,DRR162484,DRX153103,DRS083164,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,gill sample from 2 mpf zebrafish replicate3,SAMD00152432,,sample name:g02 3|age:2 month|biological replicate:3|tissue:gill,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152432,DRX153103,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152432,,,,1038999000.0,5194995.0,DRR162484,0:100 1:100,A:278673674;C:241111198;G:242737620;T:276422623;N:53885,100,100,,,278673674,241111198,242737620,276422623,53885,DRX153103,DRS083164,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.92129,0.9116,0.08334,0.0814,0.71707,0.71821,0.5407,0.53611,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Gill,Respiratory System
258,DRR162483,DRX153102,DRS083163,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,gill sample from 2 mpf zebrafish replicate2,SAMD00152431,,sample name:g02 2|age:2 month|biological replicate:2|tissue:gill,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152431,DRX153102,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152431,,,,632886400.0,3164432.0,DRR162483,0:100 1:100,A:169214113;C:147628963;G:147454557;T:168556741;N:32026,100,100,,,169214113,147628963,147454557,168556741,32026,DRX153102,DRS083163,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.93019,0.91653,0.08504,0.08547,0.69367,0.70707,0.50674,0.50918,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Gill,Respiratory System
259,DRR162482,DRX153101,DRS083162,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,gill sample from 2 mpf zebrafish replicate1,SAMD00152430,,sample name:g02 1|age:2 month|biological replicate:1|tissue:gill,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152430,DRX153101,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152430,,,,1323105600.0,6615528.0,DRR162482,0:100 1:100,A:355611103;C:306237205;G:307478272;T:353712733;N:66287,100,100,,,355611103,306237205,307478272,353712733,66287,DRX153101,DRS083162,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.93808,0.92302,0.08542,0.08367,0.69477,0.69897,0.52278,0.50546,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Gill,Respiratory System
275,DRR162466,DRX153085,DRS083146,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,brain sample from 2 mpf zebrafish replicate5,SAMD00152414,,sample name:b02 5|age:2 month|biological replicate:5|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152414,DRX153085,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152414,,,,1184455800.0,5922279.0,DRR162466,0:100 1:100,A:357035323;C:233685447;G:235595745;T:356085837;N:2053448,100,100,,,357035323,233685447,235595745,356085837,2053448,DRX153085,DRS083146,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.90819,0.87146,0.20659,0.19751,0.71246,0.72251,0.52523,0.52531,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Brain,Nervous System
276,DRR162465,DRX153084,DRS083145,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,brain sample from 2 mpf zebrafish replicate4,SAMD00152413,,sample name:b02 4|age:2 month|biological replicate:4|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152413,DRX153084,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152413,,,,1389141000.0,6945705.0,DRR162465,0:100 1:100,A:423029010;C:270113394;G:270981952;T:422602360;N:2414284,100,100,,,423029010,270113394,270981952,422602360,2414284,DRX153084,DRS083145,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.90961,0.87739,0.21147,0.20152,0.71492,0.72563,0.53639,0.53779,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Brain,Nervous System
277,DRR162464,DRX153083,DRS083144,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,brain sample from 2 mpf zebrafish replicate3,SAMD00152412,,sample name:b02 3|age:2 month|biological replicate:3|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152412,DRX153083,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152412,,,,2322459000.0,11612295.0,DRR162464,0:100 1:100,A:701085106;C:457451297;G:460424165;T:699185460;N:4312972,100,100,,,701085106,457451297,460424165,699185460,4312972,DRX153083,DRS083144,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.92479,0.89382,0.16108,0.1547,0.73312,0.74121,0.55089,0.55507,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Brain,Nervous System
278,DRR162463,DRX153082,DRS083143,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,brain sample from 2 mpf zebrafish replicate2,SAMD00152411,,sample name:b02 2|age:2 month|biological replicate:2|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152411,DRX153082,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152411,,,,1188406400.0,5942032.0,DRR162463,0:100 1:100,A:354575190;C:238508166;G:239587004;T:353623510;N:2112530,100,100,,,354575190,238508166,239587004,353623510,2112530,DRX153082,DRS083143,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.90922,0.8787,0.20709,0.2009,0.71614,0.7362,0.52768,0.53049,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Brain,Nervous System
279,DRR162462,DRX153081,DRS083142,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.,,,,brain sample from 2 mpf zebrafish replicate1,SAMD00152410,,sample name:b02 1|age:2 month|biological replicate:1|tissue:brain,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152410,DRX153081,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152410,,,,1033492200.0,5167461.0,DRR162462,0:100 1:100,A:310135217;C:205335529;G:207428012;T:308760225;N:1833217,100,100,,,310135217,205335529,207428012,308760225,1833217,DRX153081,DRS083142,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.9176,0.8829,0.18651,0.17848,0.72099,0.73119,0.54307,0.54697,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Brain,Nervous System
291,DRR224551,DRX214836,DRS236359,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 42dpf C,SAMD00222582,,sample name:42dpf C,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222582,DRX214836,42dpf C,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222582,,,,14328721000.0,71643605.0,DRR224551,0:100 1:100,A:3545040254;C:3629416092;G:3695002549;T:3459108561;N:153544,100,100,,,3545040254,3629416092,3695002549,3459108561,153544,DRX214836,DRS236359,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.9671,0.95979,0.04174,0.04058,0.71867,0.72143,0.44818,0.46122,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Juvenile,Juvenile,Fin,Surface Structure
292,DRR224550,DRX214835,DRS236358,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 42dpf B,SAMD00222581,,sample name:42dpf B,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222581,DRX214835,42dpf B,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222581,,,,14782437000.0,73912185.0,DRR224550,0:100 1:100,A:3652595601;C:3746189790;G:3788229051;T:3595263949;N:158609,100,100,,,3652595601,3746189790,3788229051,3595263949,158609,DRX214835,DRS236358,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96502,0.95776,0.0417,0.0399,0.71311,0.71423,0.46064,0.44469,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Juvenile,Juvenile,Fin,Surface Structure
293,DRR224549,DRX214834,DRS236357,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 42dpf A,SAMD00222580,,sample name:42dpf A,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222580,DRX214834,42dpf A,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222580,,,,17895751600.0,89478758.0,DRR224549,0:100 1:100,A:4428562207;C:4525140210;G:4573827895;T:4368029340;N:191948,100,100,,,4428562207,4525140210,4573827895,4368029340,191948,DRX214834,DRS236357,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96506,0.96043,0.04654,0.0446,0.70956,0.71153,0.49143,0.48957,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Juvenile,Juvenile,Fin,Surface Structure
24588,SRR25462256,SRX21195045,SRS18453971,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 50dpf 3,GSM7669021,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 50dpf 3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ ,GSM7669021,GSM7669021: PG HE 50dpf 3; Danio rerio; RNA Seq,GSM7669021 r1,GSM7669021,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_HE_3_S26_L003_R1_001.fastq.gz PG_HE_3_S26_L003_R2_001.fastq.gz,fastq fastq,4520051001.0,22984712.0,GSM7669021 r1,0:98.32 1:98.33,A:1134815259;C:1102592573;G:1104475707;T:1160918938;N:17248524,98,98,,,1134815259,1102592573,1104475707,1160918938,17248524,SRX21195045,SRS18453971,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.93438,0.93937,0.01237,0.01252,0.78208,0.78192,0.48454,0.49474,99,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24589,SRR25462257,SRX21195044,SRS18453970,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 50dpf 2,GSM7669020,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 50dpf 2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ ,GSM7669020,GSM7669020: PG HE 50dpf 2; Danio rerio; RNA Seq,GSM7669020 r1,GSM7669020,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_HE_2_S25_L003_R2_001.fastq.gz PG_HE_2_S25_L003_R1_001.fastq.gz,fastq fastq,3915471868.0,19847479.0,GSM7669020 r1,0:98.64 1:98.64,A:982714666;C:957212118;G:961590362;T:1003408448;N:10546274,98,98,,,982714666,957212118,961590362,1003408448,10546274,SRX21195044,SRS18453970,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.93184,0.93552,0.01275,0.01275,0.78356,0.7835,0.49472,0.48841,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24590,SRR25462258,SRX21195043,SRS18453969,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 50dpf 1,GSM7669019,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 50dpf 1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:HE cdkn1a +/ ,GSM7669019,GSM7669019: PG HE 50dpf 1; Danio rerio; RNA Seq,GSM7669019 r1,GSM7669019,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_HE_1_S24_L003_R1_001.fastq.gz PG_HE_1_S24_L003_R2_001.fastq.gz,fastq fastq,4764998144.0,24264412.0,GSM7669019 r1,0:98.18 1:98.20,A:1194676445;C:1161648051;G:1165061360;T:1221860864;N:21751424,98,98,,,1194676445,1161648051,1165061360,1221860864,21751424,SRX21195043,SRS18453969,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.91864,0.92247,0.01213,0.01245,0.7949,0.79584,0.50422,0.50318,100,98,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24591,SRR25462259,SRX21195042,SRS18453968,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 50dpf 3,GSM7669018,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 50dpf 3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+,GSM7669018,GSM7669018: PG WT 50dpf 3; Danio rerio; RNA Seq,GSM7669018 r1,GSM7669018,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_WT_3_S23_L003_R1_001.fastq.gz PG_WT_3_S23_L003_R2_001.fastq.gz,fastq fastq,6204452412.0,31480139.0,GSM7669018 r1,0:98.55 1:98.54,A:1567898375;C:1505755791;G:1512895523;T:1599284546;N:18618177,98,98,,,1567898375,1505755791,1512895523,1599284546,18618177,SRX21195042,SRS18453968,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.9312,0.93599,0.01692,0.01686,0.76426,0.76439,0.46519,0.47751,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24592,SRR25462260,SRX21195041,SRS18453967,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 50dpf 2,GSM7669017,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 50dpf 2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+,GSM7669017,GSM7669017: PG WT 50dpf 2; Danio rerio; RNA Seq,GSM7669017 r1,GSM7669017,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_WT_2_S22_L003_R1_001.fastq.gz PG_WT_2_S22_L003_R2_001.fastq.gz,fastq fastq,3907759829.0,19906505.0,GSM7669017 r1,0:98.15 1:98.15,A:991973983;C:940499355;G:946342572;T:1011476708;N:17467211,98,98,,,991973983,940499355,946342572,1011476708,17467211,SRX21195041,SRS18453967,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.91435,0.9186,0.02035,0.02032,0.764,0.76321,0.48743,0.48644,97,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
24593,SRR25462261,SRX21195040,SRS18453966,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/ zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 50dpf 1,GSM7669016,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 50dpf 1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:50dpf|genotype:WT cdkn1a +/+,GSM7669016,GSM7669016: PG WT 50dpf 1; Danio rerio; RNA Seq,GSM7669016 r1,GSM7669016,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,PG_WT_1_S21_L003_R2_001.fastq.gz PG_WT_1_S21_L003_R1_001.fastq.gz,fastq fastq,7395136401.0,37752582.0,GSM7669016 r1,0:97.94 1:97.94,A:1865709287;C:1789949400;G:1796311820;T:1908470411;N:34695483,97,97,,,1865709287,1789949400,1796311820,1908470411,34695483,SRX21195040,SRS18453966,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.9216,0.92737,0.01817,0.01802,0.76601,0.76593,0.48894,0.4975,100,99,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Juvenile,Juvenile,Gonad,Reproductive System
25267,SRR25744342,SRX21467662,SRS18702380,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad eif4e1b 3,GSM7730282,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing,Gonad eif4e1b 3,RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / ,GSM7730282,GSM7730282: Gonad eif4e1b 3; Danio rerio; ssRNA seq,GSM7730282 r1,GSM7730282,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_HOM3_1.fastq.gz Ovary_HOM3_2.fastq.gz,fastq fastq,2170738056.0,10746228.0,GSM7730282 r1,0:101 1:101,A:531993767;C:520631008;G:565772072;T:552334154;N:7055,101,101,,,531993767,520631008,565772072,552334154,7055,SRX21467662,SRS18702380,SRA1698764,IMP,IMP,2,0.77665,0.7702,0.14988,0.14284,0.66716,0.66957,0.49991,0.47425,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25268,SRR25744343,SRX21467661,SRS18702379,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad eif4e1b 2,GSM7730281,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing,Gonad eif4e1b 2,RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / ,GSM7730281,GSM7730281: Gonad eif4e1b 2; Danio rerio; ssRNA seq,GSM7730281 r1,GSM7730281,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_HOM2_1.fastq.gz Ovary_HOM2_2.fastq.gz,fastq fastq,3459149000.0,17124500.0,GSM7730281 r1,0:101 1:101,A:876732239;C:796603142;G:882912604;T:902886783;N:14232,101,101,,,876732239,796603142,882912604,902886783,14232,SRX21467661,SRS18702379,SRA1698764,IMP,IMP,2,0.81761,0.79589,0.26282,0.24746,0.70607,0.7039,0.50658,0.49236,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25269,SRR25744344,SRX21467660,SRS18702381,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad eif4e1b 1,GSM7730280,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing,Gonad eif4e1b 1,RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / ,GSM7730280,GSM7730280: Gonad eif4e1b 1; Danio rerio; ssRNA seq,GSM7730280 r1,GSM7730280,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_HOM1_1.fastq.gz Ovary_HOM1_2.fastq.gz,fastq fastq,2189781202.0,10840501.0,GSM7730280 r1,0:101 1:101,A:537591255;C:525448020;G:568979980;T:557754770;N:7177,101,101,,,537591255,525448020,568979980,557754770,7177,SRX21467660,SRS18702381,SRA1698764,IMP,IMP,2,0.7459,0.74191,0.15778,0.15291,0.65543,0.65841,0.48578,0.48291,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25270,SRR25744345,SRX21467659,SRS18702378,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad WT 3,GSM7730279,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing,Gonad WT 3,RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+,GSM7730279,GSM7730279: Gonad WT 3; Danio rerio; ssRNA seq,GSM7730279 r1,GSM7730279,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_WT3_1.fastq.gz Ovary_WT3_2.fastq.gz,fastq fastq,3674041448.0,18188324.0,GSM7730279 r1,0:101 1:101,A:910831144;C:876967044;G:953299105;T:932928913;N:15242,101,101,,,910831144,876967044,953299105,932928913,15242,SRX21467659,SRS18702378,SRA1698764,IMP,IMP,2,0.89093,0.89038,0.09253,0.09348,0.73892,0.73858,0.47115,0.47218,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25271,SRR25744346,SRX21467658,SRS18702377,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad WT 2,GSM7730278,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing,Gonad WT 2,RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+,GSM7730278,GSM7730278: Gonad WT 2; Danio rerio; ssRNA seq,GSM7730278 r1,GSM7730278,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_WT2_1.fastq.gz Ovary_WT2_2.fastq.gz,fastq fastq,3024886370.0,14974685.0,GSM7730278 r1,0:101 1:101,A:744374909;C:727299396;G:782294774;T:770904797;N:12494,101,101,,,744374909,727299396,782294774,770904797,12494,SRX21467658,SRS18702377,SRA1698764,IMP,IMP,2,0.91806,0.91689,0.06949,0.07178,0.74458,0.74474,0.47548,0.47338,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25272,SRR25744347,SRX21467657,SRS18702376,SRP456724,PRJNA1008624,RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish,GSE241537,Transcriptome Analysis,The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each,,pubmed:38177902,,Gonad WT 1,GSM7730277,,source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing,Gonad WT 1,RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Ovary,,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+,GSM7730277,GSM7730277: Gonad WT 1; Danio rerio; ssRNA seq,GSM7730277 r1,GSM7730277,1,RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP456724,,loader:fastq load.py,Ovary_WT1_2.fastq.gz Ovary_WT1_1.fastq.gz,fastq fastq,3571638356.0,17681378.0,GSM7730277 r1,0:101 1:101,A:876280472;C:856417516;G:935896746;T:903028845;N:14777,101,101,,,876280472,856417516,935896746,903028845,14777,SRX21467657,SRS18702376,SRA1698764,IMP,IMP,2,0.89559,0.89353,0.09223,0.09423,0.73052,0.73012,0.47772,0.47408,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-08-23,Undetermined,Juvenile,Gonad,Reproductive System
25326,SRR25868015,SRX21589423,SRS18766996,SRP457977,PRJNA1011833,Single cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity,GSE242133,Transcriptome Analysis,The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However knowledge about the properties of kidney hematopoietic cells and the functionality of kidney in fish immune systems remain to be elucidated. To this end our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell HSPC and immune cell types from zebrafish kidney via single cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity and displayed differential responses to viral infection indicating their diverse functional roles in antiviral immunity. Remarkably HSPCs were found to have extensive reactivities to viral infection and the trained immunity can be effectively induced in certain HSPCs. In addition the antigen stimulated adaptive immunity can be fully generated in kidney suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system and highlighted the multifaced biology of kidney in ancient vertebrates. Overall design: Kidney leukocyte PBS administered control SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.,,pubmed:38497789,,vaccinated+SVCV scRNAseq Kidney leukocyte,GSM7749529,,source name:Kidney|cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:vaccinated+SVCV|geo loc name:missing|collection date:missing,vaccinated+SVCV scRNAseq Kidney leukocyte,The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files,Kidney,,Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:vaccinated+SVCV,GSM7749529,GSM7749529: vaccinated+SVCV scRNAseq Kidney leukocyte; Danio rerio; RNA Seq,GSM7749529 r1,GSM7749529,1,Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP457977,,,vaccinated+SVCV_S1_L001_R1_001.fastq.gz vaccinated+SVCV_S1_L001_R2_001.fastq.gz,fastq fastq,48964415682.0,411465678.0,GSM7749529 r1,0:28 1:91,A:13575624351;C:10984755198;G:11582424564;T:12820058148;N:1553421,28,91,,,13575624351,10984755198,11582424564,12820058148,1553421,SRX21589423,SRS18766996,SRA1703997,"College of Life Sciences, Zhejiang University","College of Life Sciences, Zhejiang University",2,0.00754,0.93029,0.00274,0.13414,0.99168,0.81527,0.35,0.50044,28,91,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-09-01,Juvenile,Juvenile,Kidney,Renal System
25327,SRR25868016,SRX21589422,SRS18766995,SRP457977,PRJNA1011833,Single cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity,GSE242133,Transcriptome Analysis,The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However knowledge about the properties of kidney hematopoietic cells and the functionality of kidney in fish immune systems remain to be elucidated. To this end our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell HSPC and immune cell types from zebrafish kidney via single cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity and displayed differential responses to viral infection indicating their diverse functional roles in antiviral immunity. Remarkably HSPCs were found to have extensive reactivities to viral infection and the trained immunity can be effectively induced in certain HSPCs. In addition the antigen stimulated adaptive immunity can be fully generated in kidney suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system and highlighted the multifaced biology of kidney in ancient vertebrates. Overall design: Kidney leukocyte PBS administered control SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.,,pubmed:38497789,,SVCV scRNAseq Kidney leukocyte,GSM7749528,,source name:Kidney|cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:SVCV|geo loc name:missing|collection date:missing,SVCV scRNAseq Kidney leukocyte,The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files,Kidney,,Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:SVCV,GSM7749528,GSM7749528: SVCV scRNAseq Kidney leukocyte; Danio rerio; RNA Seq,GSM7749528 r1,GSM7749528,1,Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP457977,,,SVCV_S1_L001_R2_001.fastq.gz SVCV_S1_L001_R1_001.fastq.gz,fastq fastq,48037908933.0,403679907.0,GSM7749528 r1,0:28 1:91,A:13476452185;C:10712519121;G:11200837365;T:12646404590;N:1695672,28,91,,,13476452185,10712519121,11200837365,12646404590,1695672,SRX21589422,SRS18766995,SRA1703997,"College of Life Sciences, Zhejiang University","College of Life Sciences, Zhejiang University",2,0.00795,0.92383,0.00261,0.14,0.98948,0.7806,0.36862,0.54549,28,91,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-09-01,Juvenile,Juvenile,Kidney,Renal System
25328,SRR25868017,SRX21589421,SRS18766994,SRP457977,PRJNA1011833,Single cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity,GSE242133,Transcriptome Analysis,The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However knowledge about the properties of kidney hematopoietic cells and the functionality of kidney in fish immune systems remain to be elucidated. To this end our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell HSPC and immune cell types from zebrafish kidney via single cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity and displayed differential responses to viral infection indicating their diverse functional roles in antiviral immunity. Remarkably HSPCs were found to have extensive reactivities to viral infection and the trained immunity can be effectively induced in certain HSPCs. In addition the antigen stimulated adaptive immunity can be fully generated in kidney suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system and highlighted the multifaced biology of kidney in ancient vertebrates. Overall design: Kidney leukocyte PBS administered control SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.,,pubmed:38497789,,PBS scRNAseq Kidney leukocyte,GSM7749527,,source name:Kidney|cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:PBS|geo loc name:missing|collection date:missing,PBS scRNAseq Kidney leukocyte,The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files,Kidney,,Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,cell type:leukocyte|tissue:Kidney|strain:AB|age:5 wpf 7 wpf|agent:PBS,GSM7749527,GSM7749527: PBS scRNAseq Kidney leukocyte; Danio rerio; RNA Seq,GSM7749527 r1,GSM7749527,1,Leukocytes were collected from the kidney samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP457977,,,PBS_S1_L001_R1_001.fastq.gz PBS_S1_L001_R2_001.fastq.gz,fastq fastq,49559940115.0,416470085.0,GSM7749527 r1,0:28 1:91,A:13856071803;C:11114011608;G:11616674427;T:12971434952;N:1747325,28,91,,,13856071803,11114011608,11616674427,12971434952,1747325,SRX21589421,SRS18766994,SRA1703997,"College of Life Sciences, Zhejiang University","College of Life Sciences, Zhejiang University",2,0.00648,0.92681,0.00213,0.1376,0.99056,0.79866,0.40117,0.5487,28,91,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-09-01,Juvenile,Juvenile,Kidney,Renal System
26487,SRR26034371,SRX21751586,SRS18859093,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X6 tp53het tumor,GSM7774462,,source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous|geo loc name:missing|collection date:missing,19521X6 tp53het tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts.,brain,Brains were frozen at 80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous,GSM7774462,GSM7774462: 19521X6 tp53het tumor; Danio rerio; RNA Seq,GSM7774462 r1,GSM7774462,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X6_220211_A00421_0418_AHGVTMDSX3_S177_L003_R1_001.fastq.gz 19521X6_220211_A00421_0418_AHGVTMDSX3_S177_L003_R2_001.fastq.gz,fastq fastq,13856710696.0,45883148.0,GSM7774462 r1,0:151 1:151,A:3910050404;C:3019565763;G:3183961340;T:3742992264;N:140925,151,151,,,3910050404,3019565763,3183961340,3742992264,140925,SRX21751586,SRS18859093,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.8794,0.87909,0.38495,0.38479,0.69753,0.70005,0.49322,0.49442,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Juvenile,Juvenile,Brain,Nervous System
26488,SRR26034372,SRX21751585,SRS18859092,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X5 tp53het tumor,GSM7774461,,source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous|geo loc name:missing|collection date:missing,19521X5 tp53het tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts.,brain,Brains were frozen at 80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous,GSM7774461,GSM7774461: 19521X5 tp53het tumor; Danio rerio; RNA Seq,GSM7774461 r1,GSM7774461,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X5_220211_A00421_0418_AHGVTMDSX3_S176_L003_R1_001.fastq.gz 19521X5_220211_A00421_0418_AHGVTMDSX3_S176_L003_R2_001.fastq.gz,fastq fastq,18644081740.0,61735370.0,GSM7774461 r1,0:151 1:151,A:5198614433;C:4108657498;G:4307546758;T:5029072002;N:191049,151,151,,,5198614433,4108657498,4307546758,5029072002,191049,SRX21751585,SRS18859092,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.88544,0.88842,0.35896,0.35863,0.69193,0.69248,0.49682,0.50274,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Juvenile,Juvenile,Brain,Nervous System
26489,SRR26034373,SRX21751584,SRS18859091,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X4 tp53het tumor,GSM7774460,,source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous|geo loc name:missing|collection date:missing,19521X4 tp53het tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts.,brain,Brains were frozen at 80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 heterozygous,GSM7774460,GSM7774460: 19521X4 tp53het tumor; Danio rerio; RNA Seq,GSM7774460 r1,GSM7774460,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X4_220211_A00421_0418_AHGVTMDSX3_S175_L003_R1_001.fastq.gz 19521X4_220211_A00421_0418_AHGVTMDSX3_S175_L003_R2_001.fastq.gz,fastq fastq,14417628886.0,47740493.0,GSM7774460 r1,0:151 1:151,A:4016299076;C:3183962020;G:3341158152;T:3876059438;N:150200,151,151,,,4016299076,3183962020,3341158152,3876059438,150200,SRX21751584,SRS18859091,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.89118,0.89184,0.33812,0.33641,0.68947,0.68954,0.49867,0.50026,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Juvenile,Juvenile,Brain,Nervous System
26491,SRR26034375,SRX21751582,SRS18859089,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X2 tp53mut tumor,GSM7774458,,source name:brain|tissue:brain|tumor status:tumor|age:8 wpf|genotype:tp53 mutant|geo loc name:missing|collection date:missing,19521X2 tp53mut tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts.,brain,Brains were frozen at 80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:8 wpf|genotype:tp53 mutant,GSM7774458,GSM7774458: 19521X2 tp53mut tumor; Danio rerio; RNA Seq,GSM7774458 r1,GSM7774458,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X2_220211_A00421_0418_AHGVTMDSX3_S173_L003_R1_001.fastq.gz 19521X2_220211_A00421_0418_AHGVTMDSX3_S173_L003_R2_001.fastq.gz,fastq fastq,14064076580.0,46569790.0,GSM7774458 r1,0:151 1:151,A:3935649548;C:3089754695;G:3257286821;T:3781242542;N:142974,151,151,,,3935649548,3089754695,3257286821,3781242542,142974,SRX21751582,SRS18859089,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.89595,0.89655,0.35454,0.35431,0.68927,0.69077,0.47888,0.47831,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Juvenile,Juvenile,Brain,Nervous System
26492,SRR26034376,SRX21751581,SRS18859088,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X1 tp53mut tumor,GSM7774457,,source name:brain|tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 mutant|geo loc name:missing|collection date:missing,19521X1 tp53mut tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts.,brain,Brains were frozen at 80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:7 wpf|genotype:tp53 mutant,GSM7774457,GSM7774457: 19521X1 tp53mut tumor; Danio rerio; RNA Seq,GSM7774457 r1,GSM7774457,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X1_220211_A00421_0418_AHGVTMDSX3_S172_L003_R1_001.fastq.gz 19521X1_220211_A00421_0418_AHGVTMDSX3_S172_L003_R2_001.fastq.gz,fastq fastq,16911500190.0,55998345.0,GSM7774457 r1,0:151 1:151,A:4750241986;C:3698380612;G:3890633834;T:4572071732;N:172026,151,151,,,4750241986,3698380612,3890633834,4572071732,172026,SRX21751581,SRS18859088,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.89695,0.89831,0.3562,0.35542,0.68392,0.68369,0.48172,0.48641,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Juvenile,Juvenile,Brain,Nervous System
29188,SRR8176753,SRX4996870,SRS4031878,SRP480945,PRJNA1055160,Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain,PRJNA1055160,Other,We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf,,pubmed:38529407,,Nadia 30dpf ZZ Gonad Single Cell RNA Seq,Nadia 30dpf ZZ Gonad Single Cell RNA Seq,,strain:Nadia|age:30 dpf provider:John H. Postlethwait University of Oregon|genotype:ZZ|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: Nadia 30dpf ZZ gonad,Nadia 30dpf ZZ gonad,Nadia 30dpf ZZ gonad,A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP480945,,loader:fastq load.py,,,23587173438.0,167284918.0,1 I1 001.fastq.gz,0:8 1:133,A:6732844252;C:4934497997;G:5685086026;T:6219863789;N:14881374,8,133,,,6732844252,4934497997,5685086026,6219863789,14881374,SRX4996870,SRS4031878,SRA807619,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2018-11-08,Juvenile,Juvenile,Gonad,Reproductive System
29189,SRR8176754,SRX4996869,SRS4031877,SRP480945,PRJNA1055160,Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain,PRJNA1055160,Other,We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf,,pubmed:38529407,,Nadia 30dpf ZW Gonad Single Cell RNA Seq,Nadia 30dpf ZW Gonad Single Cell RNA Seq,,strain:Nadia|age:30 dpf provider:John H. Postlethwait University of Oregon|genotype:ZW|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: Nadia 30dpf ZW gonad,Nadia 30dpf ZW gonad,Nadia 30dpf ZW gonad,A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP480945,,loader:fastq load.py,,,43358808480.0,307509280.0,2 I1 001.fastq.gz,0:8 1:133,A:12290612367;C:8880655083;G:10261318751;T:11898771792;N:27450487,8,133,,,12290612367,8880655083,10261318751,11898771792,27450487,SRX4996869,SRS4031877,SRA807619,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2018-11-08,Juvenile,Juvenile,Gonad,Reproductive System
30738,SRR28346485,SRX23952998,SRS20753493,SRP495277,PRJNA1088100,Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo,GSE261604,Transcriptome Analysis,To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,AVC IWR1 scRNAseq,GSM8147318,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1|geo loc name:missing|collection date:missing,AVC IWR1 scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1,GSM8147318,GSM8147318: AVC IWR1 scRNAseq; Danio rerio; RNA Seq,GSM8147318 r1,GSM8147318,1,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495277,,loader:fastq load.py,AVC_IWR1_S1_L001_I1_001.fastq.gz AVC_IWR1_S1_L001_I2_001.fastq.gz AVC_IWR1_S1_L001_R1_001.fastq.gz AVC_IWR1_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,8596842480.0,62295960.0,GSM8147318 r1,0:10 1:10 2:28 3:90,A:1570400090;C:1308581548;G:1326249813;T:1399966642;N:1438307,10,10,28,90,1570400090,1308581548,1326249813,1399966642,1438307,SRX23952998,SRS20753493,SRA1824323,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2024-03-14,Juvenile,Juvenile,Heart,Cardiovascular System
30739,SRR28346486,SRX23952998,SRS20753493,SRP495277,PRJNA1088100,Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo,GSE261604,Transcriptome Analysis,To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,AVC IWR1 scRNAseq,GSM8147318,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1|geo loc name:missing|collection date:missing,AVC IWR1 scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1,GSM8147318,GSM8147318: AVC IWR1 scRNAseq; Danio rerio; RNA Seq,GSM8147318 r1,GSM8147318,1,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495277,,loader:fastq load.py,AVC_IWR1_S1_L002_I1_001.fastq.gz AVC_IWR1_S1_L002_I2_001.fastq.gz AVC_IWR1_S1_L002_R1_001.fastq.gz AVC_IWR1_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,8505185502.0,61631779.0,GSM8147318 r2,0:10 1:10 2:28 3:90,A:1553616390;C:1294687778;G:1312612882;T:1384504011;N:1439049,10,10,28,90,1553616390,1294687778,1312612882,1384504011,1439049,SRX23952998,SRS20753493,SRA1824323,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2024-03-14,Juvenile,Juvenile,Heart,Cardiovascular System
30740,SRR28346487,SRX23952998,SRS20753493,SRP495277,PRJNA1088100,Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo,GSE261604,Transcriptome Analysis,To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,AVC IWR1 scRNAseq,GSM8147318,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1|geo loc name:missing|collection date:missing,AVC IWR1 scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1,GSM8147318,GSM8147318: AVC IWR1 scRNAseq; Danio rerio; RNA Seq,GSM8147318 r1,GSM8147318,1,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495277,,loader:fastq load.py,AVC_IWR1_S1_L003_I1_001.fastq.gz AVC_IWR1_S1_L003_I2_001.fastq.gz AVC_IWR1_S1_L003_R1_001.fastq.gz AVC_IWR1_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,8699205498.0,63037721.0,GSM8147318 r3,0:10 1:10 2:28 3:90,A:1588465122;C:1324147204;G:1343996634;T:1415623074;N:1162856,10,10,28,90,1588465122,1324147204,1343996634,1415623074,1162856,SRX23952998,SRS20753493,SRA1824323,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2024-03-14,Juvenile,Juvenile,Heart,Cardiovascular System
30741,SRR28346488,SRX23952998,SRS20753493,SRP495277,PRJNA1088100,Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo,GSE261604,Transcriptome Analysis,To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,AVC IWR1 scRNAseq,GSM8147318,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1|geo loc name:missing|collection date:missing,AVC IWR1 scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:IWR1,GSM8147318,GSM8147318: AVC IWR1 scRNAseq; Danio rerio; RNA Seq,GSM8147318 r1,GSM8147318,1,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495277,,loader:fastq load.py,AVC_IWR1_S1_L004_I1_001.fastq.gz AVC_IWR1_S1_L004_I2_001.fastq.gz AVC_IWR1_S1_L004_R1_001.fastq.gz AVC_IWR1_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,8627728812.0,62519774.0,GSM8147318 r4,0:10 1:10 2:28 3:90,A:1576009383;C:1313466786;G:1332114241;T:1404392019;N:797231,10,10,28,90,1576009383,1313466786,1332114241,1404392019,797231,SRX23952998,SRS20753493,SRA1824323,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2024-03-14,Juvenile,Juvenile,Heart,Cardiovascular System
30742,SRR28346489,SRX23952997,SRS20753492,SRP495277,PRJNA1088100,Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo,GSE261604,Transcriptome Analysis,To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,AVC DMSO scRNAseq,GSM8147317,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO|geo loc name:missing|collection date:missing,AVC DMSO scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO,GSM8147317,GSM8147317: AVC DMSO scRNAseq; Danio rerio; RNA Seq,GSM8147317 r1,GSM8147317,1,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495277,,loader:fastq load.py,AVC_Ctrl_S1_L001_I1_001.fastq.gz AVC_Ctrl_S1_L001_I2_001.fastq.gz AVC_Ctrl_S1_L001_R1_001.fastq.gz AVC_Ctrl_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,7385103810.0,53515245.0,GSM8147317 r1,0:10 1:10 2:28 3:90,A:1329371520;C:1135299252;G:1143250549;T:1207226310;N:1224419,10,10,28,90,1329371520,1135299252,1143250549,1207226310,1224419,SRX23952997,SRS20753492,SRA1824323,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2024-03-14,Juvenile,Juvenile,Heart,Cardiovascular System
30743,SRR28346490,SRX23952997,SRS20753492,SRP495277,PRJNA1088100,Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo,GSE261604,Transcriptome Analysis,To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,AVC DMSO scRNAseq,GSM8147317,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO|geo loc name:missing|collection date:missing,AVC DMSO scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO,GSM8147317,GSM8147317: AVC DMSO scRNAseq; Danio rerio; RNA Seq,GSM8147317 r1,GSM8147317,1,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495277,,loader:fastq load.py,AVC_Ctrl_S1_L002_I1_001.fastq.gz AVC_Ctrl_S1_L002_I2_001.fastq.gz AVC_Ctrl_S1_L002_R1_001.fastq.gz AVC_Ctrl_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,7313299098.0,52994921.0,GSM8147317 r2,0:10 1:10 2:28 3:90,A:1316101332;C:1124200896;G:1133146934;T:1194866024;N:1227704,10,10,28,90,1316101332,1124200896,1133146934,1194866024,1227704,SRX23952997,SRS20753492,SRA1824323,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2024-03-14,Juvenile,Juvenile,Heart,Cardiovascular System
30744,SRR28346491,SRX23952997,SRS20753492,SRP495277,PRJNA1088100,Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo,GSE261604,Transcriptome Analysis,To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,AVC DMSO scRNAseq,GSM8147317,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO|geo loc name:missing|collection date:missing,AVC DMSO scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO,GSM8147317,GSM8147317: AVC DMSO scRNAseq; Danio rerio; RNA Seq,GSM8147317 r1,GSM8147317,1,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495277,,loader:fastq load.py,AVC_Ctrl_S1_L003_I1_001.fastq.gz AVC_Ctrl_S1_L003_I2_001.fastq.gz AVC_Ctrl_S1_L003_R1_001.fastq.gz AVC_Ctrl_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,7457857272.0,54042444.0,GSM8147317 r3,0:10 1:10 2:28 3:90,A:1341763332;C:1146520201;G:1156131488;T:1218395804;N:1009135,10,10,28,90,1341763332,1146520201,1156131488,1218395804,1009135,SRX23952997,SRS20753492,SRA1824323,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2024-03-14,Juvenile,Juvenile,Heart,Cardiovascular System
30745,SRR28346492,SRX23952997,SRS20753492,SRP495277,PRJNA1088100,Single cell transcriptional profiles of the atrioventricular canal of 1 mpf zebrafish treated with DMSO or IWR 1 endo,GSE261604,Transcriptome Analysis,To identify the crosstalk between Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs and coronary endothelial cells coECs we performed single cell RNA sequencing on all the cells of the atrioventricular canal AVC at 1 month which contains newly formed coronary vessels. To identify the extracellular ligands regulated by Wnt/ß catenin signaling we also collected AVC from fish treated with DMSO or IWR1 endo an inhibitor of Wnt/ß catenin signaling. Our analyses indicated that Fgf and/or Sema signaling are potential candidates for mediating the crosstalk between ß cat ON CMs and coECs. Overall design: We treated 1 mpf Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish with DMSO or 10 µM IWR1 endo for 48 hours. Hearts were resected from the fish treated with MTZ or DMSO respectively. We isolated AVCs from hearts and dissociated them into single cells. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,AVC DMSO scRNAseq,GSM8147317,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO|geo loc name:missing|collection date:missing,AVC DMSO scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCFdeltaC;5xUAS:NTR mCherry|treatment:DMSO,GSM8147317,GSM8147317: AVC DMSO scRNAseq; Danio rerio; RNA Seq,GSM8147317 r1,GSM8147317,1,Hearts were resected from 1 mpf Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35 mm dishes containing HBSS without xxx and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12 well plate. The AVCs were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected in low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter Thermofisher Scientific. The resulting cell suspension was loaded onto a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP495277,,loader:fastq load.py,AVC_Ctrl_S1_L004_I1_001.fastq.gz AVC_Ctrl_S1_L004_I2_001.fastq.gz AVC_Ctrl_S1_L004_R1_001.fastq.gz AVC_Ctrl_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,7430049030.0,53840935.0,GSM8147317 r4,0:10 1:10 2:28 3:90,A:1337094348;C:1142353903;G:1151539276;T:1214006711;N:689912,10,10,28,90,1337094348,1142353903,1151539276,1214006711,689912,SRX23952997,SRS20753492,SRA1824323,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2024-03-14,Juvenile,Juvenile,Heart,Cardiovascular System
31837,SRR28709001,SRX24276192,SRS21041156,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf61 Ov mt 3,GSM8212808,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing,dpf61 Ov mt 3,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 61|genotype:mutant,GSM8212808,GSM8212808: dpf61 Ov mt 3; Danio rerio; RNA Seq,GSM8212808 r1,GSM8212808,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.M43_20230510_103430.L001.1.fastq.gz NS51397.M43_20230510_103430.L001.2.fastq.gz,fastq fastq,9024444634.0,29882267.0,GSM8212808 r1,0:151 1:151,A:2471288260;C:1931225512;G:2256742565;T:2363378475;N:1809822,151,151,,,2471288260,1931225512,2256742565,2363378475,1809822,SRX24276192,SRS21041156,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31838,SRR28709002,SRX24276191,SRS21041154,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf61 Ov mt 2,GSM8212807,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing,dpf61 Ov mt 2,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 61|genotype:mutant,GSM8212807,GSM8212807: dpf61 Ov mt 2; Danio rerio; RNA Seq,GSM8212807 r1,GSM8212807,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.M41_20230510_103430.L001.1.fastq.gz NS51397.M41_20230510_103430.L001.2.fastq.gz,fastq fastq,13553131538.0,44877919.0,GSM8212807 r1,0:151 1:151,A:3707129145;C:2878818514;G:3433054125;T:3531357698;N:2772056,151,151,,,3707129145,2878818514,3433054125,3531357698,2772056,SRX24276191,SRS21041154,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31839,SRR28709003,SRX24276190,SRS21041155,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf61 Ov mt 1,GSM8212806,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:mutant|geo loc name:missing|collection date:missing,dpf61 Ov mt 1,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 61|genotype:mutant,GSM8212806,GSM8212806: dpf61 Ov mt 1; Danio rerio; RNA Seq,GSM8212806 r1,GSM8212806,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.M32_20230510_103430.L001.1.fastq.gz NS51397.M32_20230510_103430.L001.2.fastq.gz,fastq fastq,11752803234.0,38916567.0,GSM8212806 r1,0:151 1:151,A:3199511211;C:2525248103;G:2947698766;T:3077964367;N:2380787,151,151,,,3199511211,2525248103,2947698766,3077964367,2380787,SRX24276190,SRS21041155,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31840,SRR28709004,SRX24276189,SRS21041153,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf61 Ov wt 3,GSM8212805,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:wildtype|geo loc name:missing|collection date:missing,dpf61 Ov wt 3,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 61|genotype:wildtype,GSM8212805,GSM8212805: dpf61 Ov wt 3; Danio rerio; RNA Seq,GSM8212805 r1,GSM8212805,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.M17_20230510_103430.L001.1.fastq.gz NS51397.M17_20230510_103430.L001.2.fastq.gz,fastq fastq,16726684646.0,55386373.0,GSM8212805 r1,0:151 1:151,A:4912874254;C:2935821083;G:3844206542;T:5030341800;N:3440967,151,151,,,4912874254,2935821083,3844206542,5030341800,3440967,SRX24276189,SRS21041153,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31841,SRR28709005,SRX24276188,SRS21041152,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf61 Ov wt 2,GSM8212804,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:wildtype|geo loc name:missing|collection date:missing,dpf61 Ov wt 2,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 61|genotype:wildtype,GSM8212804,GSM8212804: dpf61 Ov wt 2; Danio rerio; RNA Seq,GSM8212804 r1,GSM8212804,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.M14_20230510_103430.L001.1.fastq.gz NS51397.M14_20230510_103430.L001.2.fastq.gz,fastq fastq,11600612146.0,38412623.0,GSM8212804 r1,0:151 1:151,A:3087038432;C:2559546168;G:3029729871;T:2921939557;N:2358118,151,151,,,3087038432,2559546168,3029729871,2921939557,2358118,SRX24276188,SRS21041152,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31842,SRR28709006,SRX24276187,SRS21041151,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf61 Ov wt 1,GSM8212803,,source name:Ovary|tissue:Ovary|age:dpf 61|genotype:wildtype|geo loc name:missing|collection date:missing,dpf61 Ov wt 1,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 61|genotype:wildtype,GSM8212803,GSM8212803: dpf61 Ov wt 1; Danio rerio; RNA Seq,GSM8212803 r1,GSM8212803,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.M9_20230510_103430.L001.1.fastq.gz NS51397.M9_20230510_103430.L001.2.fastq.gz,fastq fastq,19081987478.0,63185389.0,GSM8212803 r1,0:151 1:151,A:5188307750;C:4048527738;G:4868706940;T:4972575432;N:3869618,151,151,,,5188307750,4048527738,4868706940,4972575432,3869618,SRX24276187,SRS21041151,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31843,SRR28709007,SRX24276186,SRS21041150,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf47 Ov mt 3,GSM8212802,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:mutant|geo loc name:missing|collection date:missing,dpf47 Ov mt 3,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 47|genotype:mutant,GSM8212802,GSM8212802: dpf47 Ov mt 3; Danio rerio; RNA Seq,GSM8212802 r1,GSM8212802,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.C33_20230510_103430.L001.1.fastq.gz NS51397.C33_20230510_103430.L001.2.fastq.gz,fastq fastq,8256087174.0,27338037.0,GSM8212802 r1,0:151 1:151,A:2217123657;C:1857924925;G:2109544983;T:2069850323;N:1643286,151,151,,,2217123657,1857924925,2109544983,2069850323,1643286,SRX24276186,SRS21041150,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31844,SRR28709008,SRX24276185,SRS21041149,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf47 Ov mt 2,GSM8212801,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:mutant|geo loc name:missing|collection date:missing,dpf47 Ov mt 2,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 47|genotype:mutant,GSM8212801,GSM8212801: dpf47 Ov mt 2; Danio rerio; RNA Seq,GSM8212801 r1,GSM8212801,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.C32_20230510_103430.L001.1.fastq.gz NS51397.C32_20230510_103430.L001.2.fastq.gz,fastq fastq,14985320634.0,49620267.0,GSM8212801 r1,0:151 1:151,A:4058920258;C:3245799385;G:3815485722;T:3862070151;N:3045118,151,151,,,4058920258,3245799385,3815485722,3862070151,3045118,SRX24276185,SRS21041149,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31845,SRR28709009,SRX24276184,SRS21041147,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf47 Ov mt 1,GSM8212800,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:mutant|geo loc name:missing|collection date:missing,dpf47 Ov mt 1,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 47|genotype:mutant,GSM8212800,GSM8212800: dpf47 Ov mt 1; Danio rerio; RNA Seq,GSM8212800 r1,GSM8212800,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.C29_20230510_103430.L001.1.fastq.gz NS51397.C29_20230510_103430.L001.2.fastq.gz,fastq fastq,11177741176.0,37012388.0,GSM8212800 r1,0:151 1:151,A:3060199842;C:2374800912;G:2799391711;T:2941063533;N:2285178,151,151,,,3060199842,2374800912,2799391711,2941063533,2285178,SRX24276184,SRS21041147,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31846,SRR28709010,SRX24276183,SRS21041146,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf47 Ov wt 3,GSM8212799,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:wildtype|geo loc name:missing|collection date:missing,dpf47 Ov wt 3,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 47|genotype:wildtype,GSM8212799,GSM8212799: dpf47 Ov wt 3; Danio rerio; RNA Seq,GSM8212799 r1,GSM8212799,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.C21_20230510_103430.L001.1.fastq.gz NS51397.C21_20230510_103430.L001.2.fastq.gz,fastq fastq,13599817718.0,45032509.0,GSM8212799 r1,0:151 1:151,A:3724782410;C:2835413438;G:3575258078;T:3461647906;N:2715886,151,151,,,3724782410,2835413438,3575258078,3461647906,2715886,SRX24276183,SRS21041146,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31847,SRR28709011,SRX24276182,SRS21041148,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf47 Ov wt 2,GSM8212798,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:wildtype|geo loc name:missing|collection date:missing,dpf47 Ov wt 2,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 47|genotype:wildtype,GSM8212798,GSM8212798: dpf47 Ov wt 2; Danio rerio; RNA Seq,GSM8212798 r1,GSM8212798,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.C20_20230510_103430.L001.1.fastq.gz NS51397.C20_20230510_103430.L001.2.fastq.gz,fastq fastq,13632935642.0,45142171.0,GSM8212798 r1,0:151 1:151,A:3708965267;C:2903664830;G:3492295019;T:3525245989;N:2764537,151,151,,,3708965267,2903664830,3492295019,3525245989,2764537,SRX24276182,SRS21041148,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31848,SRR28709012,SRX24276181,SRS21041145,SRP502090,PRJNA1101048,Adamts9 Is Required for Development of Primary Ovarian Follicles and Maintenance of Female Sex in Zebrafish,GSE264143,Transcriptome Analysis,Previous studies have suggested that adamts9 a disintegrin and metalloprotease with thrombospondin type 1 motifs member 9 an extracellular matrix ECM metalloprotease participates in primordial germ cell PGC migration and necessary for female fertility. In this study we found that adamts9 knockout KO led to reduced body size and female to male sex conversion in adult mature zebrafish prior to or post 90 dpf dpf; however primary sex determination was not affected in early juveniles of adamts9 KO at 35 dpf. Overfeeding and lowering the rearing density rescued growth defects in female adamts9 KO fish but did not rescue defects in ovarian development in adamts9 KO. Delayed PGC proliferation significantly reduced number and size of Stage IB follicles equivalent to primary follicle in early juveniles of adamts9 KO and arrested development at Stage IB follicles in mid or late juveniles of adamts9 KO are likely causes of female infertility and sex conversion. Via RNAseq we found significant enrichment of differentially expressed genes involved in ECM organization during sexual maturation in ovaries of wildtype fish; and significant dysregulation of these genes in adamts9 KO ovaries. RNAseq analysis also showed enrichment of inflammatory transcriptomic signatures in adult ovaries of these adamts9 KO. Taken together our results indicate that adamts9 is critical for development of primary ovarian follicles and maintenance of female sex in zebrafish and loss of adamts9 in zebrafish leads to ovarian follicle arrest female infertility and sex conversion in late juveniles and mature adults. Overall design: To investigate the role of adamts9 in zebrafish ovary formation and maintainence we conducted mRNA sequencing on wildtype and mutant ovaries at dpf 41 and 67.,,,,dpf47 Ov wt 1,GSM8212797,,source name:Ovary|tissue:Ovary|age:dpf 47|genotype:wildtype|geo loc name:missing|collection date:missing,dpf47 Ov wt 1,Data were pseudoaligned with Kallisto. Assembly: GRCz11 Supplementary files format and content: tab delimited file that has raw counts for each sample.,Ovary,,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer’s protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,WT AB strain and mutant zebrafish lines were housed in the zebrafish core facility with a 14 hourh light and 10h dark photoperiod lights on at 8:30am lights off at 10:30pm; at water temperature of 28.5°C pH of approximately 7.2 and salinity/conductivity ranging from 500 to 1 200µS in two automatically controlled standalone zebrafish rearing systems. Fish are fed to satiation three times daily with a commercial food.,tissue:Ovary|age:dpf 47|genotype:wildtype,GSM8212797,GSM8212797: dpf47 Ov wt 1; Danio rerio; RNA Seq,GSM8212797 r1,GSM8212797,1,Ovary tissues were homogenized immediately in RNAzol RT reagent and stored at 800C till purification. Total RNA was purified following the manufacturer's protocol cDNA was made for three replicates for each time point by genotype with the Tecan Ovation RNAseq kit for 47 and 61dpf samples. Libraries were then prepared with the Tecan Celero EZ DNA Seq library kit for 47 and 61dpf samples.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP502090,,loader:fastq load.py,NS51397.C4_20230510_103430.L001.1.fastq.gz NS51397.C4_20230510_103430.L001.2.fastq.gz,fastq fastq,12378485324.0,40988362.0,GSM8212797 r1,0:151 1:151,A:3378421522;C:2638098449;G:3108553273;T:3250895048;N:2517032,151,151,,,3378421522,2638098449,3108553273,3250895048,2517032,SRX24276181,SRS21041145,SRA1847037,"Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences","Reproductive Developmental Biology, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2024-04-16,Juvenile,Juvenile,Gonad,Reproductive System
31932,SRR28776262,SRX24341224,SRS21101374,SRP503449,PRJNA1103351,Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration,PRJNA1103351,Other,Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.,,,,Ablated 3,Ablated rep3,,strain:AB|age:2 mpf date:2015 06 11|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Tgins:flag NTR|treatment:Metronidazole|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish hepatocytes,P2276 105,P2276 105,RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP503449,,,5_150903_BC7FRTANXX_P2276_105_1.fastq.gz 5_150903_BC7FRTANXX_P2276_105_2.fastq.gz,fastq fastq,12443422824.0,49378662.0,5 150903 BC7FRTANXX P2276 105 1.fastq.gz,0:126 1:126,A:3354062616;C:2842732118;G:2899611331;T:3337717349;N:9299410,126,126,,,3354062616,2842732118,2899611331,3337717349,9299410,SRX24341224,SRS21101374,SRA1851016,Karolinska Institutet|Cell and Molecular Biology,Karolinska Institutet,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Sweden,2024-04-23,Juvenile,Juvenile,Liver,Liver and Biliary System
31933,SRR28776263,SRX24341223,SRS21101373,SRP503449,PRJNA1103351,Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration,PRJNA1103351,Other,Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.,,,,Ablated 2,Ablated rep2,,strain:AB|age:2 mpf date:2015 06 09|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Tgins:flag NTR|treatment:Metronidazole|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish hepatocytes,P2276 103,P2276 103,RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP503449,,,5_150903_BC7FRTANXX_P2276_103_1.fastq.gz 5_150903_BC7FRTANXX_P2276_103_2.fastq.gz,fastq fastq,12508569612.0,49637181.0,5 150903 BC7FRTANXX P2276 103 1.fastq.gz,0:126 1:126,A:3285561592;C:2941406523;G:2987518362;T:3285515692;N:8567443,126,126,,,3285561592,2941406523,2987518362,3285515692,8567443,SRX24341223,SRS21101373,SRA1851016,Karolinska Institutet|Cell and Molecular Biology,Karolinska Institutet,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Sweden,2024-04-23,Juvenile,Juvenile,Liver,Liver and Biliary System
31934,SRR28776264,SRX24341222,SRS21101372,SRP503449,PRJNA1103351,Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration,PRJNA1103351,Other,Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.,,,,Ablated 1,Ablated rep1,,strain:AB|age:2 mpf date:2015 06 04|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Tgins:flag NTR|treatment:Metronidazole|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish hepatocytes,P2276 101,P2276 101,RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP503449,,,5_150903_BC7FRTANXX_P2276_101_1.fastq.gz 5_150903_BC7FRTANXX_P2276_101_2.fastq.gz,fastq fastq,12536188812.0,49746781.0,5 150903 BC7FRTANXX P2276 101 1.fastq.gz,0:126 1:126,A:3281688237;C:2958476935;G:3022979051;T:3265495888;N:7548701,126,126,,,3281688237,2958476935,3022979051,3265495888,7548701,SRX24341222,SRS21101372,SRA1851016,Karolinska Institutet|Cell and Molecular Biology,Karolinska Institutet,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Sweden,2024-04-23,Juvenile,Juvenile,Liver,Liver and Biliary System
31935,SRR28776265,SRX24341221,SRS21101375,SRP503449,PRJNA1103351,Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration,PRJNA1103351,Other,Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.,,,,Control 2,Control rep2,,strain:AB|age:2 mpf date:2015 06 11|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Wild type|treatment:Metronidazole|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish hepatocytes,P2276 106,P2276 106,RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP503449,,,5_150903_BC7FRTANXX_P2276_106_1.fastq.gz 5_150903_BC7FRTANXX_P2276_106_2.fastq.gz,fastq fastq,11797087680.0,46813840.0,5 150903 BC7FRTANXX P2276 106 1.fastq.gz,0:126 1:126,A:3087253274;C:2787897503;G:2841312816;T:3072716302;N:7907785,126,126,,,3087253274,2787897503,2841312816,3072716302,7907785,SRX24341221,SRS21101375,SRA1851016,Karolinska Institutet|Cell and Molecular Biology,Karolinska Institutet,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Sweden,2024-04-23,Juvenile,Juvenile,Liver,Liver and Biliary System
31936,SRR28776266,SRX24341220,SRS21101371,SRP503449,PRJNA1103351,Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration,PRJNA1103351,Other,Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.,,,,Control 1,Control rep1,,strain:AB|age:2 mpf date:2015 06 09|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Wild type|treatment:Metronidazole|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish hepatocytes,P2276 104,P2276 104,RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP503449,,,5_150903_BC7FRTANXX_P2276_104_1.fastq.gz 5_150903_BC7FRTANXX_P2276_104_2.fastq.gz,fastq fastq,13294186416.0,52754708.0,5 150903 BC7FRTANXX P2276 104 1.fastq.gz,0:126 1:126,A:3544892164;C:3073022881;G:3106419492;T:3559768207;N:10083672,126,126,,,3544892164,3073022881,3106419492,3559768207,10083672,SRX24341220,SRS21101371,SRA1851016,Karolinska Institutet|Cell and Molecular Biology,Karolinska Institutet,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Sweden,2024-04-23,Juvenile,Juvenile,Liver,Liver and Biliary System
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,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,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,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,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,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,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,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,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
34128,SRR31371655,SRX26745254,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PC3 R1.fq,PC3 R1.fq,CuNPs and melatonin treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PC3_R1.fq.gz PC3_R2.fq.gz,fastq fastq,8050557450.0,26657475.0,PC3 R1.fq.gz,,,,,,,,,,,,SRX26745254,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34129,SRR31371656,SRX26745253,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PC2 R1.fq,PC2 R1.fq,CuNPs and melatonin treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PC2_R1.fq.gz PC2_R2.fq.gz,fastq fastq,7072903722.0,23420211.0,PC2 R1.fq.gz,0:151 1:151,A:1848366962;C:1685927772;G:1702568524;T:1835518466;N:521998,151,151,,,1848366962,1685927772,1702568524,1835518466,521998,SRX26745253,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34130,SRR31371657,SRX26745252,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PC1 R1.fq,PC1 R1.fq,CuNPs and melatonin treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PC1_R1.fq.gz PC1_R2.fq.gz,fastq fastq,9551575668.0,31627734.0,PC1 R1.fq.gz,,,,,,,,,,,,SRX26745252,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34131,SRR31371658,SRX26745251,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PB3 R1.fq,PB3 R1.fq,CuNPs treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PB3_R1.fq.gz PB3_R2.fq.gz,fastq fastq,6839092000.0,22646000.0,PB3 R1.fq.gz,,,,,,,,,,,,SRX26745251,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34132,SRR31371659,SRX26745250,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PB2 R1.fq,PB2 R1.fq,CuNPs treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PB2_R1.fq.gz PB2_R2.fq.gz,fastq fastq,7582292558.0,25106929.0,PB2 R1.fq.gz,,,,,,,,,,,,SRX26745250,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34133,SRR31371660,SRX26745249,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,PB1 R1.fq,PB1 R1.fq,CuNPs treatment,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,PB1_R1.fq.gz PB1_R2.fq.gz,fastq fastq,8122972218.0,26897259.0,PB1 R1.fq.gz,,,,,,,,,,,,SRX26745249,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34134,SRR31371661,SRX26745248,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,CA3 R1.fq,CA3 R1.fq,control,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,CA3_R1.fq.gz CA3_R2.fq.gz,fastq fastq,7638136586.0,25291843.0,CA3 R1.fq.gz,,,,,,,,,,,,SRX26745248,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34135,SRR31371662,SRX26745247,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,CA1 R1.fq,CA1 R1.fq,control,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,CA1_R1.fq.gz CA1_R2.fq.gz,fastq fastq,7499744784.0,24833592.0,CA1 R1.fq.gz,0:151 1:151,A:1951636355;C:1801626786;G:1812560367;T:1933366696;N:554580,151,151,,,1951636355,1801626786,1812560367,1933366696,554580,SRX26745247,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34136,SRR31371663,SRX26745246,SRS23234144,SRP545712,PRJNA1186363,Danio rerio Transcriptome or Gene expression,PRJNA1186363,Other,Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin,,,,Model organism or animal sample from zebrafish,zebra001,,cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq from the gonad of Zebrafish,CA2 R1.fq,CA2 R1.fq,control,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP545712,,,CA2_R1.fq.gz CA2_R2.fq.gz,fastq fastq,6253035330.0,20705415.0,CA2 R1.fq.gz,,,,,,,,,,,,SRX26745246,SRS23234144,SRA2016483,Chinese Academy of Fishery Science|Freshwater Fishery Research Center,Chinese Academy of Fishery Science,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-11-17,Juvenile,Juvenile,Gonad,Reproductive System
34397,SRR31719829,SRX27082407,SRS23541575,SRP551495,PRJNA1198392,RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD,PRJNA1198392,Other,Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.,,,hepatocyte specific gmfb overexpression normal diet for 35 days,RNAseq MASLD HepGOE ND rep2,HepGOE ND rep2,,strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 10|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptome of liver tissues in HepGOE zebrafish of normal diet.,HepGOE ND rep2,HepGOE ND rep2,Total RNA was extracted from liver tissue for RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP551495,,,RNAseq_MASLD_HepGOE_ND_rep2_1.fq.gz RNAseq_MASLD_HepGOE_ND_rep2_2.fq.gz,fastq fastq,7177536600.0,23925122.0,RNAseq MASLD HepGOE ND rep2 1.fq.gz,0:150 1:150,A:1917334205;C:1668595888;G:1703080664;T:1887679182;N:846661,150,150,,,1917334205,1668595888,1703080664,1887679182,846661,SRX27082407,SRS23541575,SRA2034386,Southern Medical University|Biomedical Research Center,Southern Medical University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-12-15,Juvenile,Juvenile,Liver,Liver and Biliary System
34398,SRR31719830,SRX27082406,SRS23541574,SRP551495,PRJNA1198392,RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD,PRJNA1198392,Other,Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.,,,hepatocyte specific gmfb overexpression normal diet for 35 days,RNAseq MASLD HepGOE ND rep1,HepGOE ND rep1,,strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 9|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptome of liver tissues in HepGOE zebrafish of normal diet.,HepGOE ND rep1,HepGOE ND rep1,Total RNA was extracted from liver tissue for RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP551495,,,RNAseq_MASLD_HepGOE_ND_rep1_1.fq.gz RNAseq_MASLD_HepGOE_ND_rep1_2.fq.gz,fastq fastq,6621268500.0,22070895.0,RNAseq MASLD HepGOE ND rep1 1.fq.gz,0:150 1:150,A:1711419517;C:1595902037;G:1611514825;T:1702282385;N:149736,150,150,,,1711419517,1595902037,1611514825,1702282385,149736,SRX27082406,SRS23541574,SRA2034386,Southern Medical University|Biomedical Research Center,Southern Medical University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-12-15,Juvenile,Juvenile,Liver,Liver and Biliary System
34399,SRR31719831,SRX27082405,SRS23541573,SRP551495,PRJNA1198392,RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD,PRJNA1198392,Other,Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.,,,hepatocyte specific gmfb knockout high fat high cholesterol diet for 35 days,RNAseq MASLD HepGKO HFC rep2,HepGKO HFC rep2,,strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 8|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptome of liver tissues in HepGKO zebrafish of high fat high cholesterol diet.,HepGKO HFC rep2,HepGKO HFC rep2,Total RNA was extracted from liver tissue for RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP551495,,,RNAseq_MASLD_HepGKO_HFC_rep2_1.fq.gz RNAseq_MASLD_HepGKO_HFC_rep2_2.fq.gz,fastq fastq,5901646500.0,19672155.0,RNAseq MASLD HepGKO HFC rep2 1.fq.gz,0:150 1:150,A:1547939419;C:1401111812;G:1425197669;T:1527300198;N:97402,150,150,,,1547939419,1401111812,1425197669,1527300198,97402,SRX27082405,SRS23541573,SRA2034386,Southern Medical University|Biomedical Research Center,Southern Medical University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-12-15,Juvenile,Juvenile,Liver,Liver and Biliary System
34400,SRR31719832,SRX27082404,SRS23541572,SRP551495,PRJNA1198392,RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD,PRJNA1198392,Other,Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.,,,hepatocyte specific gmfb knockout high fat high cholesterol diet for 35 days,RNAseq MASLD HepGKO HFC rep1,HepGKO HFC rep1,,strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 7|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptome of liver tissues in HepGKO zebrafish of high fat high cholesterol diet.,HepGKO HFC rep1,HepGKO HFC rep1,Total RNA was extracted from liver tissue for RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP551495,,,RNAseq_MASLD_HepGKO_HFC_rep1_1.fq.gz RNAseq_MASLD_HepGKO_HFC_rep1_2.fq.gz,fastq fastq,6484178700.0,21613929.0,RNAseq MASLD HepGKO HFC rep1 1.fq.gz,0:150 1:150,A:1692850957;C:1545705390;G:1573644279;T:1671871368;N:106706,150,150,,,1692850957,1545705390,1573644279,1671871368,106706,SRX27082404,SRS23541572,SRA2034386,Southern Medical University|Biomedical Research Center,Southern Medical University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-12-15,Juvenile,Juvenile,Liver,Liver and Biliary System
34401,SRR31719833,SRX27082403,SRS23541571,SRP551495,PRJNA1198392,RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD,PRJNA1198392,Other,Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.,,,hepatocyte specific gmfb knockout normal diet for 35 days,RNAseq MASLD HepGKO ND rep2,HepGKO ND rep2,,strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 6|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptome of liver tissues in HepGKO zebrafish of normal diet.,HepGKO ND rep2,HepGKO ND rep2,Total RNA was extracted from liver tissue for RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP551495,,,RNAseq_MASLD_HepGKO_ND_rep2_1.fq.gz RNAseq_MASLD_HepGKO_ND_rep2_2.fq.gz,fastq fastq,6436941000.0,21456470.0,RNAseq MASLD HepGKO ND rep2 1.fq.gz,0:150 1:150,A:1671402056;C:1543860294;G:1570976721;T:1650596456;N:105473,150,150,,,1671402056,1543860294,1570976721,1650596456,105473,SRX27082403,SRS23541571,SRA2034386,Southern Medical University|Biomedical Research Center,Southern Medical University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-12-15,Juvenile,Juvenile,Liver,Liver and Biliary System
34402,SRR31719834,SRX27082402,SRS23541570,SRP551495,PRJNA1198392,RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD,PRJNA1198392,Other,Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.,,,hepatocyte specific gmfb knockout normal diet for 35 days,RNAseq MASLD HepGKO ND rep1,HepGKO ND rep1,,strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 5|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptome of liver tissues in HepGKO zebrafish of normal diet.,HepGKO ND rep1,HepGKO ND rep1,Total RNA was extracted from liver tissue for RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP551495,,,RNAseq_MASLD_HepGKO_ND_rep1_1.fq.gz RNAseq_MASLD_HepGKO_ND_rep1_2.fq.gz,fastq fastq,6386174700.0,21287249.0,RNAseq MASLD HepGKO ND rep1 1.fq.gz,0:150 1:150,A:1662767742;C:1527603435;G:1545756971;T:1649944714;N:101838,150,150,,,1662767742,1527603435,1545756971,1649944714,101838,SRX27082402,SRS23541570,SRA2034386,Southern Medical University|Biomedical Research Center,Southern Medical University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-12-15,Juvenile,Juvenile,Liver,Liver and Biliary System
34403,SRR31719835,SRX27082401,SRS23541569,SRP551495,PRJNA1198392,RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD,PRJNA1198392,Other,Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.,,,WT zebrafish high fat high cholesterol diet for 35 days,RNAseq MASLD WT HFC rep2,WT HFC rep2,,strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptome of liver tissues in WT zebrafish of high fat high cholesterol diet.,WT HFC rep2,WT HFC rep2,Total RNA was extracted from liver tissue for RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP551495,,,RNAseq_MASLD_WT_HFC_rep2_1.fq.gz RNAseq_MASLD_WT_HFC_rep2_2.fq.gz,fastq fastq,7088163900.0,23627213.0,RNAseq MASLD WT HFC rep2 1.fq.gz,0:150 1:150,A:1904609517;C:1635475353;G:1664944747;T:1882978732;N:155551,150,150,,,1904609517,1635475353,1664944747,1882978732,155551,SRX27082401,SRS23541569,SRA2034386,Southern Medical University|Biomedical Research Center,Southern Medical University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-12-15,Juvenile,Juvenile,Liver,Liver and Biliary System
34404,SRR31719836,SRX27082400,SRS23541568,SRP551495,PRJNA1198392,RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD,PRJNA1198392,Other,Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.,,,WT zebrafish high fat high cholesterol diet for 35 days,RNAseq MASLD WT HFC rep1,WT HFC rep1,,strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptome of liver tissues in WT zebrafish of high fat high cholesterol diet.,WT HFC rep1,WT HFC rep1,Total RNA was extracted from liver tissue for RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP551495,,,RNAseq_MASLD_WT_HFC_rep1_1.fq.gz RNAseq_MASLD_WT_HFC_rep1_2.fq.gz,fastq fastq,7053396600.0,23511322.0,RNAseq MASLD WT HFC rep1 1.fq.gz,0:150 1:150,A:1862942395;C:1655266768;G:1688002812;T:1847030526;N:154099,150,150,,,1862942395,1655266768,1688002812,1847030526,154099,SRX27082400,SRS23541568,SRA2034386,Southern Medical University|Biomedical Research Center,Southern Medical University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-12-15,Juvenile,Juvenile,Liver,Liver and Biliary System
34405,SRR31719837,SRX27082399,SRS23541567,SRP551495,PRJNA1198392,RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD,PRJNA1198392,Other,Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.,,,hepatocyte specific gmfb overexpression high fat high cholesterol diet for 35 days,RNAseq MASLD HepGOE HFC rep2,HepGOE HFC rep2,,strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 12|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptome of liver tissues in HepGOE zebrafish of high fat high cholesterol diet.,HepGOE HFC rep2,HepGOE HFC rep2,Total RNA was extracted from liver tissue for RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP551495,,,RNAseq_MASLD_HepGOE_HFC_rep2_1.fq.gz RNAseq_MASLD_HepGOE_HFC_rep2_2.fq.gz,fastq fastq,7004757600.0,23349192.0,RNAseq MASLD HepGOE HFC rep2 1.fq.gz,0:150 1:150,A:1846708800;C:1647727254;G:1676955416;T:1833207397;N:158733,150,150,,,1846708800,1647727254,1676955416,1833207397,158733,SRX27082399,SRS23541567,SRA2034386,Southern Medical University|Biomedical Research Center,Southern Medical University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-12-15,Juvenile,Juvenile,Liver,Liver and Biliary System
34406,SRR31719838,SRX27082398,SRS23541566,SRP551495,PRJNA1198392,RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD,PRJNA1198392,Other,Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.,,,hepatocyte specific gmfb overexpression high fat high cholesterol diet for 35 days,RNAseq MASLD HepGOE HFC rep1,HepGOE HFC rep1,,strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 11|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptome of liver tissues in HepGOE zebrafish of high fat high cholesterol diet.,HepGOE HFC rep1,HepGOE HFC rep1,Total RNA was extracted from liver tissue for RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP551495,,,RNAseq_MASLD_HepGOE_HFC_rep1_1.fq.gz RNAseq_MASLD_HepGOE_HFC_rep1_2.fq.gz,fastq fastq,8211524400.0,27371748.0,RNAseq MASLD HepGOE HFC rep1 1.fq.gz,0:150 1:150,A:2217820195;C:1876471113;G:1906298333;T:2210753213;N:181546,150,150,,,2217820195,1876471113,1906298333,2210753213,181546,SRX27082398,SRS23541566,SRA2034386,Southern Medical University|Biomedical Research Center,Southern Medical University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-12-15,Juvenile,Juvenile,Liver,Liver and Biliary System
34407,SRR31719839,SRX27082397,SRS23541565,SRP551495,PRJNA1198392,RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD,PRJNA1198392,Other,Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.,,,WT zebrafish normal diet for 35 days,RNAseq MASLD WT ND rep2,WT ND rep2,,strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptome of liver tissues in WT zebrafish of normal diet.,WT ND rep2,WT ND rep2,Total RNA was extracted from liver tissue for RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP551495,,,RNAseq_MASLD_WT_ND_rep2_1.fq.gz RNAseq_MASLD_WT_ND_rep2_2.fq.gz,fastq fastq,6966786300.0,23222621.0,RNAseq MASLD WT ND rep2 1.fq.gz,0:150 1:150,A:1855652140;C:1619780884;G:1651213951;T:1839982276;N:157049,150,150,,,1855652140,1619780884,1651213951,1839982276,157049,SRX27082397,SRS23541565,SRA2034386,Southern Medical University|Biomedical Research Center,Southern Medical University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-12-15,Juvenile,Juvenile,Liver,Liver and Biliary System
34408,SRR31719840,SRX27082396,SRS23541564,SRP551495,PRJNA1198392,RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD,PRJNA1198392,Other,Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.,,,WT zebrafish normal diet for 35 days,RNAseq MASLD WT ND rep1,WT ND rep1,,strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptome of liver tissues in WT zebrafish of normal diet.,WT ND rep1,WT ND rep1,Total RNA was extracted from liver tissue for RNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP551495,,,RNAseq_MASLD_WT_ND_rep1_1.fq.gz RNAseq_MASLD_WT_ND_rep1_2.fq.gz,fastq fastq,7149668700.0,23832229.0,RNAseq MASLD WT ND rep1 1.fq.gz,0:150 1:150,A:1869145140;C:1695095352;G:1726444600;T:1858824841;N:158767,150,150,,,1869145140,1695095352,1726444600,1858824841,158767,SRX27082396,SRS23541564,SRA2034386,Southern Medical University|Biomedical Research Center,Southern Medical University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2024-12-15,Juvenile,Juvenile,Liver,Liver and Biliary System