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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,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,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222582,,,,14328721000.0,71643605.0,DRR224551,0:100 1:100,A:3545040254;C:3629416092;G:3695002549;T:3459108561;N:153544,100,100,,,3545040254,3629416092,3695002549,3459108561,153544,DRX214836,DRS236359,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.9671,0.95979,0.04174,0.04058,0.71867,0.72143,0.44818,0.46122,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Juvenile,Juvenile,Fin,Surface Structure
292,DRR224550,DRX214835,DRS236358,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 42dpf B,SAMD00222581,,sample name:42dpf B,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222581,DRX214835,42dpf B,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222581,,,,14782437000.0,73912185.0,DRR224550,0:100 1:100,A:3652595601;C:3746189790;G:3788229051;T:3595263949;N:158609,100,100,,,3652595601,3746189790,3788229051,3595263949,158609,DRX214835,DRS236358,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96502,0.95776,0.0417,0.0399,0.71311,0.71423,0.46064,0.44469,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Juvenile,Juvenile,Fin,Surface Structure
293,DRR224549,DRX214834,DRS236357,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 42dpf A,SAMD00222580,,sample name:42dpf A,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222580,DRX214834,42dpf A,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222580,,,,17895751600.0,89478758.0,DRR224549,0:100 1:100,A:4428562207;C:4525140210;G:4573827895;T:4368029340;N:191948,100,100,,,4428562207,4525140210,4573827895,4368029340,191948,DRX214834,DRS236357,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96506,0.96043,0.04654,0.0446,0.70956,0.71153,0.49143,0.48957,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Juvenile,Juvenile,Fin,Surface Structure
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
39859,SRR2177445,SRX1161440,SRS1042403,SRP062685,PRJNA293388,Danio rerio Transcriptome or Gene expression,PRJNA293388,Other,Differential Expression between testis and ovary in two months of fish,,,Differential Expression between testis and ovary in two months of fish,,T,,isolate:Danio rerio testis|age:2 months|sex:male|tissue:testis|biomaterial provider:Department of Biology and Biotechnology|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio transcriptome sequencing,T,1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062685,,,T_R1.fastq.gz T_R2.fastq.gz,fastq fastq,7616200600.0,38081003.0,T,0:100 1:100,A:2018574469;C:1797807061;G:1758967564;T:2040674119;N:177387,100,100,,,2018574469,1797807061,1758967564,2040674119,177387,SRX1161440,SRS1042403,SRA290385,Shanghai Ocean University|Department of Biology and Biotechnology,Shanghai Ocean University,2,0.946,0.93541,0.0936,0.09298,0.62929,0.63343,0.49102,0.48875,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2016-08-01,Juvenile,Juvenile,Gonad,Reproductive System
39860,SRR2177444,SRX1161439,SRS1042402,SRP062685,PRJNA293388,Danio rerio Transcriptome or Gene expression,PRJNA293388,Other,Differential Expression between testis and ovary in two months of fish,,,Differential Expression between testis and ovary in two months of fish,,O,,isolate:Danio rerio ovary|age:2 months|sex:female|tissue:ovary|biomaterial provider:Department of Biology and Biotechnology|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio transcriptome sequencing,O,1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP062685,,,O_R1.fastq.gz O_R2.fastq.gz,fastq fastq,6602802000.0,33014010.0,O,0:100 1:100,A:1705654028;C:1598182709;G:1559109823;T:1739704779;N:150661,100,100,,,1705654028,1598182709,1559109823,1739704779,150661,SRX1161439,SRS1042402,SRA290385,Shanghai Ocean University|Department of Biology and Biotechnology,Shanghai Ocean University,2,0.94263,0.93359,0.02018,0.02017,0.74842,0.75087,0.47643,0.47578,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2016-08-01,Juvenile,Juvenile,Gonad,Reproductive System
41248,SRR3985378,SRX1987647,SRS1591650,SRP080226,PRJNA335774,wt vs mutant zebrafish Raw sequence reads,PRJNA335774,Other,be related to IS,,,mutant,Stat3 zebrafish,Stat3,,strain:AB line|age:1 month|dev stage:juvenile fish|sex:not determined|tissue:b1|biomaterial provider:nstitute of hydrobiology|treatment:KO|BioSampleModel:Model organism or animal,,,,,,,,,stat3 mutant,stat3 mutant,1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>4000</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>2001</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP080226,,,Stat3_1.fq.gz Stat3_2.fq.gz,fastq fastq,8539658400.0,28465528.0,stat3 mutant,0:150 1:150,A:2247683479;C:2023626545;G:2038225527;T:2229672357;N:450492,150,150,,,2247683479,2023626545,2038225527,2229672357,450492,SRX1987647,SRS1591650,SRA445588,Huazhong Agricultural University,Huazhong Agricultural University,2,0.88446,0.81717,0.0523,0.04777,0.69887,0.70642,0.45266,0.49099,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2017-01-18,Juvenile,Juvenile,Undetermined,Undetermined
41249,SRR3985375,SRX1987645,SRS1591255,SRP080226,PRJNA335774,wt vs mutant zebrafish Raw sequence reads,PRJNA335774,Other,be related to IS,,,wild type,,wild type zebrafish,,strain:AB|age:1 month|dev stage:juvenile fish|sex:not determined|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,wild type zebrafish,wild type control,1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>4000</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>2001</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP080226,,,WT-1_1.fq.gz WT-1_2.fq.gz,fastq fastq,8539964400.0,28466548.0,wild type control,0:150 1:150,A:2252816933;C:2019884847;G:2037382553;T:2229414884;N:465183,150,150,,,2252816933,2019884847,2037382553,2229414884,465183,SRX1987645,SRS1591255,SRA445586,Huazhong Agricultural University,Huazhong Agricultural University,2,0.88395,0.81555,0.05189,0.04746,0.69134,0.69921,0.4902,0.49597,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2017-01-18,Juvenile,Juvenile,Undetermined,Undetermined
41509,SRR4994225,SRX2329687,SRS1591255,SRP092647,PRJNA352610,Danio rerio strain:AB Raw sequence reads,PRJNA352610,Whole Genome Sequencing,wild type,,,wild type,,wild type zebrafish,,strain:AB|age:1 month|dev stage:juvenile fish|sex:not determined|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,wild type,wild type zebrafish,1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>4000</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>2001</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP092647,,,,,8539964400.0,28466548.0,wild type zebrafish,0:150 1:150,A:2252816933;C:2019884847;G:2037382553;T:2229414884;N:465183,150,150,,,2252816933,2019884847,2037382553,2229414884,465183,SRX2329687,SRS1591255,SRA490795,Huazhong Agricultural University,Huazhong Agricultural University,2,0.88393,0.81554,0.05185,0.04727,0.69138,0.69905,0.49044,0.49588,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2016-11-07,Juvenile,Juvenile,Undetermined,Undetermined
41510,SRR4994317,SRX2329715,SRS1591650,SRP092650,PRJNA352611,Danio rerio strain:AB Raw sequence reads,PRJNA352611,Whole Genome Sequencing,provide a clue for studying congenital scoliosis desease,,,mutant,Stat3 zebrafish,Stat3,,strain:AB line|age:1 month|dev stage:juvenile fish|sex:not determined|tissue:b1|biomaterial provider:nstitute of hydrobiology|treatment:KO|BioSampleModel:Model organism or animal,,,,,,,,,stat3 mutant,stat3,1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>4000</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>2001</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP092650,,,,,8539658400.0,28465528.0,stat3,0:150 1:150,A:2247683479;C:2023626545;G:2038225527;T:2229672357;N:450492,150,150,,,2247683479,2023626545,2038225527,2229672357,450492,SRX2329715,SRS1591650,SRA490799,Huazhong Agricultural University,Huazhong Agricultural University,2,0.88451,0.81718,0.05225,0.0476,0.69885,0.7065,0.48442,0.49075,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2016-11-07,Juvenile,Juvenile,Undetermined,Undetermined
41971,SRR5378568,SRX2673830,SRS2073025,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,40CT1,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:40 dpf control testis Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated testis,40CT1,40CT1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_40SCMT1_GCCAAT_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMT1_GCCAAT_L005_R2_001.fastq.gz,fastq fastq,3383566200.0,16917831.0,C1PF2ACXX NZGL00075 40SCMT1 GCCAAT L005 R1 001.fastq.gz,0:100 1:100,A:907427604;C:788874979;G:779558006;T:904812741;N:2892870,100,100,,,907427604,788874979,779558006,904812741,2892870,SRX2673830,SRS2073025,SRA549173,University of Otago|Anatomy,University of Otago,2,0.9435,0.94416,0.077,0.07807,0.62992,0.63291,0.49572,0.49386,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41972,SRR5378567,SRX2673829,SRS2073024,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,40CT2,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:40 dpf control testis Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated testis,40CT2,40CT2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_40SCMT2_CAGATC_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMT2_CAGATC_L005_R2_001.fastq.gz,fastq fastq,4228737000.0,21143685.0,C1PF2ACXX NZGL00075 40SCMT2 CAGATC L005 R2 001.fastq.gz,0:100 1:100,A:1127980638;C:991852227;G:979335663;T:1125913673;N:3654799,100,100,,,1127980638,991852227,979335663,1125913673,3654799,SRX2673829,SRS2073024,SRA549173,University of Otago|Anatomy,University of Otago,2,0.92133,0.92088,0.07288,0.07187,0.63589,0.63569,0.49565,0.49652,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41973,SRR5378566,SRX2673828,SRS2073023,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,40CT3,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:40 dpf control testis Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated testis,40CT3,40CT3,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_40SCMT3_CTTGTA_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCMT3_CTTGTA_L005_R2_001.fastq.gz,fastq fastq,3573385600.0,17866928.0,C1PF2ACXX NZGL00075 40SCMT3 CTTGTA L005 R1 001.fastq.gz,0:100 1:100,A:959171053;C:833305488;G:821071871;T:956752401;N:3084787,100,100,,,959171053,833305488,821071871,956752401,3084787,SRX2673828,SRS2073023,SRA549173,University of Otago|Anatomy,University of Otago,2,0.94254,0.94306,0.0824,0.08326,0.63035,0.63073,0.48663,0.48853,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41974,SRR5378565,SRX2673827,SRS2073022,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,40MT1,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:methyltestoster1 treated|replicate:40 dpf MT treated testis Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf methyltestoster1 treated testis,40MT1,40MT1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_40MTMT2_CCGTCC_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40MTMT2_CCGTCC_L005_R2_001.fastq.gz,fastq fastq,3390203000.0,16951015.0,C1PF2ACXX NZGL00075 40MTMT2 CCGTCC L005 R1 001.fastq.gz,0:100 1:100,A:913160038;C:786792863;G:776512460;T:910747347;N:2990292,100,100,,,913160038,786792863,776512460,910747347,2990292,SRX2673827,SRS2073022,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93965,0.93936,0.09767,0.09857,0.62775,0.62842,0.49596,0.49531,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41975,SRR5378564,SRX2673826,SRS2073021,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,40MT2,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:methyltestoster1 treated|replicate:40 dpf MT treated testis Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf methyltestoster1 treated testis,40MT2,40MT2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_40MTMT3_GTCCGC_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40MTMT3_GTCCGC_L005_R2_001.fastq.gz,fastq fastq,3004824200.0,15024121.0,C1PF2ACXX NZGL00075 40MTMT3 GTCCGC L005 R2 001.fastq.gz,0:100 1:100,A:807437097;C:699588436;G:689637394;T:805597982;N:2563291,100,100,,,807437097,699588436,689637394,805597982,2563291,SRX2673826,SRS2073021,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93696,0.93654,0.09597,0.09569,0.63335,0.63128,0.48899,0.49336,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41976,SRR5378563,SRX2673825,SRS2073020,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,40CO1,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:female|tissue:ovary|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:40 dpf control ovary Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated ovary,40CO1,40CO1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_40SCFO1_CGATGT_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFO1_CGATGT_L005_R2_001.fastq.gz,fastq fastq,2794786000.0,13973930.0,C1PF2ACXX NZGL00075 40SCFO1 CGATGT L005 R2 001.fastq.gz,0:100 1:100,A:733793512;C:667693170;G:653892765;T:737072945;N:2333608,100,100,,,733793512,667693170,653892765,737072945,2333608,SRX2673825,SRS2073020,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93457,0.93414,0.03501,0.03513,0.74416,0.74306,0.45464,0.46296,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41977,SRR5378562,SRX2673824,SRS2073019,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,40CO2,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:female|tissue:ovary|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:40 dpf control ovary Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated ovary,40CO2,40CO2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_40SCFO2_TGACCA_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFO2_TGACCA_L005_R2_001.fastq.gz,fastq fastq,3496834600.0,17484173.0,C1PF2ACXX NZGL00075 40SCFO2 TGACCA L005 R2 001.fastq.gz,0:100 1:100,A:915245192;C:837105900;G:822612411;T:918931328;N:2939769,100,100,,,915245192,837105900,822612411,918931328,2939769,SRX2673824,SRS2073019,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93222,0.9318,0.03321,0.03282,0.75077,0.74882,0.46269,0.46292,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41978,SRR5378561,SRX2673823,SRS2073018,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,40CO3,,strain:Tgvas:egfp|age:40 dpf|dev stage:juvenile|sex:female|tissue:ovary|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:40 dpf control ovary Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 40 dpf untreated ovary,40CO3,40CO3,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_40SCFO3_ACAGTG_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_40SCFO3_ACAGTG_L005_R2_001.fastq.gz,fastq fastq,4130973400.0,20654867.0,C1PF2ACXX NZGL00075 40SCFO3 ACAGTG L005 R2 001.fastq.gz,0:100 1:100,A:1088505082;C:983093552;G:963601484;T:1092305451;N:3467831,100,100,,,1088505082,983093552,963601484,1092305451,3467831,SRX2673823,SRS2073018,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93407,0.93321,0.03906,0.03894,0.74509,0.74393,0.46191,0.45469,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41979,SRR5378560,SRX2673822,SRS2073017,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60CO1,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:female|tissue:ovary|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:60 dpf control ovary Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated ovary,60CO1,60CO1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_60SCFO1_GTGGCC_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO1_GTGGCC_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO1_GTGGCC_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO1_GTGGCC_L004_R2_001.fastq.gz,fastq fastq fastq fastq,3581758800.0,17908794.0,C1PF2ACXX NZGL00075 60SCFO1 GTGGCC L003 R2 001.fastq.gz,0:100 1:100,A:935420703;C:859741152;G:842371309;T:940446466;N:3779170,100,100,,,935420703,859741152,842371309,940446466,3779170,SRX2673822,SRS2073017,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93554,0.93458,0.02697,0.0264,0.75548,0.75398,0.46163,0.45871,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41980,SRR5378559,SRX2673821,SRS2073016,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60CO2,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:female|tissue:ovary|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:60 dpf control ovary Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated ovary,60CO2,60CO2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_60SCFO2_GTTTCG_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO2_GTTTCG_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO2_GTTTCG_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO2_GTTTCG_L004_R2_001.fastq.gz,fastq fastq fastq fastq,3004585400.0,15022927.0,C1PF2ACXX NZGL00075 60SCFO2 GTTTCG L003 R1 001.fastq.gz,0:100 1:100,A:785595086;C:720322210;G:706179659;T:789383440;N:3105005,100,100,,,785595086,720322210,706179659,789383440,3105005,SRX2673821,SRS2073016,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93549,0.93572,0.02626,0.02653,0.75217,0.75463,0.45521,0.457,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41981,SRR5378558,SRX2673820,SRS2073015,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60CO3,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:female|tissue:ovary|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:60 dpf control ovary Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated ovary,60CO3,60CO3,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP102493,,,C1PF2ACXX_NZGL00075_60SCFO3_CGTACG_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO3_CGTACG_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO3_CGTACG_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCFO3_CGTACG_L004_R2_001.fastq.gz,fastq fastq fastq fastq,3953476600.0,19767383.0,C1PF2ACXX NZGL00075 60SCFO3 CGTACG L004 R1 001.fastq.gz,0:100 1:100,A:1032933744;C:948238902;G:931243897;T:1036980742;N:4079315,100,100,,,1032933744,948238902,931243897,1036980742,4079315,SRX2673820,SRS2073015,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93441,0.93421,0.02746,0.02731,0.75659,0.75641,0.45685,0.457,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41982,SRR5378557,SRX2673819,SRS2073014,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60CT1,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:60 dpf control testis Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated testis,60CT1,60CT1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP102493,,,BC1JJDACXX_NZGL00075_60SCMT1_GAGTGG_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_60SCMT1_GAGTGG_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT1_GAGTGG_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT1_GAGTGG_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT1_GAGTGG_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT1_GAGTGG_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,4182954400.0,20914772.0,BC1JJDACXX NZGL00075 60SCMT1 GAGTGG L005 R1 001.fastq.gz,0:100 1:100,A:1126126575;C:969544687;G:954207474;T:1123657066;N:9418598,100,100,,,1126126575,969544687,954207474,1123657066,9418598,SRX2673819,SRS2073014,SRA549173,University of Otago|Anatomy,University of Otago,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41983,SRR5378556,SRX2673818,SRS2073013,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60CT2,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:60 dpf control testis Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated testis,60CT2,60CT2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP102493,,,BC1JJDACXX_NZGL00075_60SCMT2_ACTGAT_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_60SCMT2_ACTGAT_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT2_ACTGAT_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT2_ACTGAT_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT2_ACTGAT_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT2_ACTGAT_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,4555876800.0,22779384.0,BC1JJDACXX NZGL00075 60SCMT2 ACTGAT L005 R1 001.fastq.gz,0:100 1:100,A:1226376468;C:1056355551;G:1039067674;T:1223922466;N:10154641,100,100,,,1226376468,1056355551,1039067674,1223922466,10154641,SRX2673818,SRS2073013,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93701,0.939,0.09793,0.09845,0.6168,0.61682,0.49149,0.49108,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41984,SRR5378555,SRX2673817,SRS2073012,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60CT3,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:untreated|replicate:60 dpf control testis Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf untreated testis,60CT3,60CT3,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP102493,,,BC1JJDACXX_NZGL00075_60SCMT3_ATTCCT_L005_R1_001.fastq.gz BC1JJDACXX_NZGL00075_60SCMT3_ATTCCT_L005_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT3_ATTCCT_L003_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT3_ATTCCT_L003_R2_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT3_ATTCCT_L004_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60SCMT3_ATTCCT_L004_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,4716215400.0,23581077.0,C1PF2ACXX NZGL00075 60SCMT3 ATTCCT L004 R1 001.fastq.gz,0:100 1:100,A:1265703574;C:1096707638;G:1081376113;T:1262008670;N:10419405,100,100,,,1265703574,1096707638,1081376113,1262008670,10419405,SRX2673817,SRS2073012,SRA549173,University of Otago|Anatomy,University of Otago,2,0.94129,0.93998,0.08872,0.08824,0.62556,0.62526,0.47605,0.48069,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41985,SRR5378554,SRX2673816,SRS2073011,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60MT1,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:methyltestoster1 treated|replicate:60 dpf MT treated testis Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf methyltestoster1 treated testis,60MT1,60MT1,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP102493,,,C1PF2ACXX_NZGL00075_60MTMT1_AGTCAA_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMT1_AGTCAA_L005_R2_001.fastq.gz,fastq fastq,2983913800.0,14919569.0,C1PF2ACXX NZGL00075 60MTMT1 AGTCAA L005 R1 001.fastq.gz,0:100 1:100,A:807289133;C:689635666;G:678693228;T:805746458;N:2549315,100,100,,,807289133,689635666,678693228,805746458,2549315,SRX2673816,SRS2073011,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93656,0.93727,0.09689,0.09818,0.61637,0.61671,0.49189,0.49119,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41986,SRR5378553,SRX2673815,SRS2073010,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60MT2,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:methyltestoster1 treated|replicate:60 dpf MT treated testis Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf methyltestoster1 treated testis,60MT2,60MT2,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP102493,,,C1PF2ACXX_NZGL00075_60MTMT2_AGTTCC_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMT2_AGTTCC_L005_R2_001.fastq.gz,fastq fastq,3535698400.0,17678492.0,C1PF2ACXX NZGL00075 60MTMT2 AGTTCC L005 R1 001.fastq.gz,0:100 1:100,A:953667018;C:819969570;G:806855071;T:952124680;N:3082061,100,100,,,953667018,819969570,806855071,952124680,3082061,SRX2673815,SRS2073010,SRA549173,University of Otago|Anatomy,University of Otago,2,0.94013,0.93993,0.09566,0.09661,0.62591,0.62731,0.48997,0.488,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
41987,SRR5378552,SRX2673814,SRS2073009,SRP102493,PRJNA379493,Transcriptomic effects of 17 alpha methyltestosterone in gonads during zebrafish gonad development.,PRJNA379493,Other,Sexual differentiation in zebrafish is complex. Although zebrafish sex determination is primarily genetic  hormonal and environmental factors can influence sexual development. 17 alpha methyltestosterone MT  a synthetic androgen  induces female to male sex reversal in zebrafish. MT treatment is routinely used in aquaculture for production of all male populations. However  the molecular mechanisms underlying 17 alpha methyltestosterone induced gonad masculinisation in fish are poorly understood.In this study  we analysed gonad transcriptomes of zebrafish treated with 17 alpha methyltestosterone during gonadal development from 20 dpf to 40 dpf and 60 dpf and compared them with testis and ovary transcriptomes of untreated zebrafish. These data improve our understanding of the role of androgens in teleost sex differentiation.,,pubmed:28738802,,,60MT3,,strain:Tgvas:egfp|age:60 dpf|dev stage:juvenile|sex:male|tissue:testis|genotype:Tgvas:egfp|sample type:gonadal tissue|treatment:methyltestoster1 treated|replicate:60 dpf MT treated testis Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of danio rerio: 60 dpf methyltestoster1 treated testis,60MT3,60MT3,1 µg of total RNA was used with the Illumina TruSeq RNA sample preparation kit v2 for construction of each library. 100 bp paired end reads were generated using the HiSeq 2000 platform.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP102493,,,C1PF2ACXX_NZGL00075_60MTMT3_ATGTCA_L005_R1_001.fastq.gz C1PF2ACXX_NZGL00075_60MTMT3_ATGTCA_L005_R2_001.fastq.gz,fastq fastq,3198016000.0,15990080.0,C1PF2ACXX NZGL00075 60MTMT3 ATGTCA L005 R1 001.fastq.gz,0:100 1:100,A:864374636;C:739335019;G:728461692;T:863093537;N:2751116,100,100,,,864374636,739335019,728461692,863093537,2751116,SRX2673814,SRS2073009,SRA549173,University of Otago|Anatomy,University of Otago,2,0.93815,0.93857,0.10501,0.10578,0.61777,0.61968,0.49259,0.48964,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,New Zealand,2017-09-26,Juvenile,Juvenile,Gonad,Reproductive System
42042,SRR5382042,SRX2677135,SRS2075556,SRP102601,PRJNA380770,Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error,GSE97125,Transcriptome Analysis,We compare dissected ocular tissues from wild type and lrp2 /  mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2  a transmembrane receptor  cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia  binding many extracellular ligands  including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent  and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled  sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE  and zebrafish  we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4  inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap  and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage  cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes  sclera/choroid  RPE and retina in wild type and lrp2 /  mutant zebrafish at 1 mpf,,,,lrp2 mpf 1 mpf sclera 13,GSM2552012,,tissue:choroid/sclera|genotype:lrp2 / |age:1 mpf,lrp2 mpf 1 mpf sclera 13,"Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2  was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.",choroid/sclera,,Eyes were dissected were removed  stored overnight at 4C in RNAlater  and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.,Zebrafish Danio rerio were maintained at 28.5C on an  Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented  with Instant Ocean salts 60 mg/l on a 14 h light: 10 h  dark lighting cycle and fed a standard diet,genotype:lrp2 / |age:1 mpf,GSM2552012,GSM2552012: lrp2 mpf 1 mpf sclera 13; Danio rerio; RNA Seq,GSM2552012,,1,Eyes were dissected were removed  stored overnight at 4C in RNAlater  and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.,GEO Accession:GSM2552012,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP102601,,,150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAATRAAPEI-223_1.fq.gz,fastq,868203658.0,17718442.0,GSM2552012 r1,0:49 1:0,A:230139963;C:203530468;G:202078408;T:232447490;N:7329,49,0,,,230139963,203530468,202078408,232447490,7329,SRX2677135,SRS2075556,SRA549807,GEO,Medical College of Wisconsin,1,0.89611,,0.10145,,0.69449,,0.46437,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-28,Juvenile,Juvenile,Eye,Sensory System
42043,SRR5382043,SRX2677135,SRS2075556,SRP102601,PRJNA380770,Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error,GSE97125,Transcriptome Analysis,We compare dissected ocular tissues from wild type and lrp2 /  mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2  a transmembrane receptor  cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia  binding many extracellular ligands  including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent  and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled  sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE  and zebrafish  we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4  inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap  and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage  cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes  sclera/choroid  RPE and retina in wild type and lrp2 /  mutant zebrafish at 1 mpf,,,,lrp2 mpf 1 mpf sclera 13,GSM2552012,,tissue:choroid/sclera|genotype:lrp2 / |age:1 mpf,lrp2 mpf 1 mpf sclera 13,"Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2  was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.",choroid/sclera,,Eyes were dissected were removed  stored overnight at 4C in RNAlater  and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.,Zebrafish Danio rerio were maintained at 28.5C on an  Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented  with Instant Ocean salts 60 mg/l on a 14 h light: 10 h  dark lighting cycle and fed a standard diet,genotype:lrp2 / |age:1 mpf,GSM2552012,GSM2552012: lrp2 mpf 1 mpf sclera 13; Danio rerio; RNA Seq,GSM2552012,,1,Eyes were dissected were removed  stored overnight at 4C in RNAlater  and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.,GEO Accession:GSM2552012,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP102601,,,150627_I114_FCH2TT2BBXX_L7_HKZEBxagRAATRAAPEI-223_1.fq.gz,fastq,857269994.0,17495306.0,GSM2552012 r2,0:49 1:0,A:226970264;C:201146668;G:199712081;T:229432482;N:8499,49,0,,,226970264,201146668,199712081,229432482,8499,SRX2677135,SRS2075556,SRA549807,GEO,Medical College of Wisconsin,1,0.90314,,0.10194,,0.69443,,0.47706,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-28,Juvenile,Juvenile,Eye,Sensory System
42044,SRR5382040,SRX2677134,SRS2075555,SRP102601,PRJNA380770,Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error,GSE97125,Transcriptome Analysis,We compare dissected ocular tissues from wild type and lrp2 /  mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2  a transmembrane receptor  cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia  binding many extracellular ligands  including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent  and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled  sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE  and zebrafish  we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4  inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap  and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage  cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes  sclera/choroid  RPE and retina in wild type and lrp2 /  mutant zebrafish at 1 mpf,,,,lrp2 mpf 1 mpf sclera 12,GSM2552011,,tissue:choroid/sclera|genotype:lrp2 / |age:1 mpf,lrp2 mpf 1 mpf sclera 12,"Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2  was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.",choroid/sclera,,Eyes were dissected were removed  stored overnight at 4C in RNAlater  and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.,Zebrafish Danio rerio were maintained at 28.5C on an  Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented  with Instant Ocean salts 60 mg/l on a 14 h light: 10 h  dark lighting cycle and fed a standard diet,genotype:lrp2 / |age:1 mpf,GSM2552011,GSM2552011: lrp2 mpf 1 mpf sclera 12; Danio rerio; RNA Seq,GSM2552011,,1,Eyes were dissected were removed  stored overnight at 4C in RNAlater  and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.,GEO Accession:GSM2552011,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP102601,,,150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAASRAAPEI-222_1.fq.gz,fastq,818515502.0,16704398.0,GSM2552011 r1,0:49 1:0,A:214855166;C:193982000;G:192092006;T:217579339;N:6991,49,0,,,214855166,193982000,192092006,217579339,6991,SRX2677134,SRS2075555,SRA549807,GEO,Medical College of Wisconsin,1,0.89862,,0.09572,,0.69708,,0.47023,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-28,Juvenile,Juvenile,Eye,Sensory System
42045,SRR5382041,SRX2677134,SRS2075555,SRP102601,PRJNA380770,Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error,GSE97125,Transcriptome Analysis,We compare dissected ocular tissues from wild type and lrp2 /  mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2  a transmembrane receptor  cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia  binding many extracellular ligands  including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent  and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled  sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE  and zebrafish  we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4  inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap  and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage  cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes  sclera/choroid  RPE and retina in wild type and lrp2 /  mutant zebrafish at 1 mpf,,,,lrp2 mpf 1 mpf sclera 12,GSM2552011,,tissue:choroid/sclera|genotype:lrp2 / |age:1 mpf,lrp2 mpf 1 mpf sclera 12,"Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2  was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.",choroid/sclera,,Eyes were dissected were removed  stored overnight at 4C in RNAlater  and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.,Zebrafish Danio rerio were maintained at 28.5C on an  Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented  with Instant Ocean salts 60 mg/l on a 14 h light: 10 h  dark lighting cycle and fed a standard diet,genotype:lrp2 / |age:1 mpf,GSM2552011,GSM2552011: lrp2 mpf 1 mpf sclera 12; Danio rerio; RNA Seq,GSM2552011,,1,Eyes were dissected were removed  stored overnight at 4C in RNAlater  and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.,GEO Accession:GSM2552011,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP102601,,,150627_I114_FCH2TT2BBXX_L7_HKZEBxagRAASRAAPEI-222_1.fq.gz,fastq,810081377.0,16532273.0,GSM2552011 r2,0:49 1:0,A:212403857;C:192140662;G:190291379;T:215237408;N:8071,49,0,,,212403857,192140662,190291379,215237408,8071,SRX2677134,SRS2075555,SRA549807,GEO,Medical College of Wisconsin,1,0.9065,,0.09612,,0.69832,,0.4763,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-28,Juvenile,Juvenile,Eye,Sensory System
42046,SRR5382038,SRX2677133,SRS2075554,SRP102601,PRJNA380770,Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error,GSE97125,Transcriptome Analysis,We compare dissected ocular tissues from wild type and lrp2 /  mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2  a transmembrane receptor  cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia  binding many extracellular ligands  including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent  and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled  sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE  and zebrafish  we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4  inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap  and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage  cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes  sclera/choroid  RPE and retina in wild type and lrp2 /  mutant zebrafish at 1 mpf,,,,lrp2 mpf 1 mpf sclera 11,GSM2552010,,tissue:choroid/sclera|genotype:lrp2 / |age:1 mpf,lrp2 mpf 1 mpf sclera 11,"Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2  was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.",choroid/sclera,,Eyes were dissected were removed  stored overnight at 4C in RNAlater  and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.,Zebrafish Danio rerio were maintained at 28.5C on an  Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented  with Instant Ocean salts 60 mg/l on a 14 h light: 10 h  dark lighting cycle and fed a standard diet,genotype:lrp2 / |age:1 mpf,GSM2552010,GSM2552010: lrp2 mpf 1 mpf sclera 11; Danio rerio; RNA Seq,GSM2552010,,1,Eyes were dissected were removed  stored overnight at 4C in RNAlater  and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.,GEO Accession:GSM2552010,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP102601,,,150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAARRAAPEI-221_1.fq.gz,fastq,598444497.0,12213153.0,GSM2552010 r1,0:49 1:0,A:157564573;C:141303576;G:139633698;T:159937613;N:5037,49,0,,,157564573,141303576,139633698,159937613,5037,SRX2677133,SRS2075554,SRA549807,GEO,Medical College of Wisconsin,1,0.89676,,0.09842,,0.68653,,0.46649,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-28,Juvenile,Juvenile,Eye,Sensory System
42047,SRR5382039,SRX2677133,SRS2075554,SRP102601,PRJNA380770,Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error,GSE97125,Transcriptome Analysis,We compare dissected ocular tissues from wild type and lrp2 /  mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2  a transmembrane receptor  cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia  binding many extracellular ligands  including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent  and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled  sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE  and zebrafish  we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4  inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap  and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage  cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes  sclera/choroid  RPE and retina in wild type and lrp2 /  mutant zebrafish at 1 mpf,,,,lrp2 mpf 1 mpf sclera 11,GSM2552010,,tissue:choroid/sclera|genotype:lrp2 / |age:1 mpf,lrp2 mpf 1 mpf sclera 11,"Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2  was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.",choroid/sclera,,Eyes were dissected were removed  stored overnight at 4C in RNAlater  and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.,Zebrafish Danio rerio were maintained at 28.5C on an  Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented  with Instant Ocean salts 60 mg/l on a 14 h light: 10 h  dark lighting cycle and fed a standard diet,genotype:lrp2 / |age:1 mpf,GSM2552010,GSM2552010: lrp2 mpf 1 mpf sclera 11; Danio rerio; RNA Seq,GSM2552010,,1,Eyes were dissected were removed  stored overnight at 4C in RNAlater  and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.,GEO Accession:GSM2552010,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP102601,,,150627_I114_FCH2TT2BBXX_L7_HKZEBxagRAARRAAPEI-221_1.fq.gz,fastq,594578250.0,12134250.0,GSM2552010 r2,0:49 1:0,A:156350324;C:140490193;G:138869200;T:158862787;N:5746,49,0,,,156350324,140490193,138869200,158862787,5746,SRX2677133,SRS2075554,SRA549807,GEO,Medical College of Wisconsin,1,0.90485,,0.09982,,0.68521,,0.4691,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-28,Juvenile,Juvenile,Eye,Sensory System
42048,SRR5382036,SRX2677132,SRS2075553,SRP102601,PRJNA380770,Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error,GSE97125,Transcriptome Analysis,We compare dissected ocular tissues from wild type and lrp2 /  mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2  a transmembrane receptor  cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia  binding many extracellular ligands  including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent  and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled  sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE  and zebrafish  we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4  inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap  and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage  cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes  sclera/choroid  RPE and retina in wild type and lrp2 /  mutant zebrafish at 1 mpf,,,,lrp2 mpf 1 mpf retina 13,GSM2552009,,tissue:retina|genotype:lrp2 / |age:1 mpf,lrp2 mpf 1 mpf retina 13,"Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC  raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor  high content of unknown bases and low quality reads  and are removed before analysis. Bowtie2  was used to map clean reads to reference gene  and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM  method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.",retina,,Eyes were dissected were removed  stored overnight at 4C in RNAlater  and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.,Zebrafish Danio rerio were maintained at 28.5C on an  Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented  with Instant Ocean salts 60 mg/l on a 14 h light: 10 h  dark lighting cycle and fed a standard diet,genotype:lrp2 / |age:1 mpf,GSM2552009,GSM2552009: lrp2 mpf 1 mpf retina 13; Danio rerio; RNA Seq,GSM2552009,,1,Eyes were dissected were removed  stored overnight at 4C in RNAlater  and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.,GEO Accession:GSM2552009,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP102601,,,150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAAWRAAPEI-201_1.fq.gz,fastq,754821823.0,15404527.0,GSM2552009 r1,0:49 1:0,A:206101700;C:172880224;G:168016286;T:207817318;N:6295,49,0,,,206101700,172880224,168016286,207817318,6295,SRX2677132,SRS2075553,SRA549807,GEO,Medical College of Wisconsin,1,0.88663,,0.1569,,0.70934,,0.50146,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2017-03-28,Juvenile,Juvenile,Eye,Sensory System