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542 rows where devstage_curation_coarse = "Juvenile" and technology = "unknown"

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tissue_curation >10

experiment.library_selection 7

experiment.platform 2

experiment.library_layout 2

devstage_curation 2

technology 1

  • unknown · 542 ✖

experiment.library_strategy 1

experiment.library_source 1

devstage_curation_coarse 1

  • Juvenile · 542 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
201 201 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
202 202 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
203 203 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
204 204 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
205 205 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
221 221 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
222 222 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
223 223 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
224 224 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
225 225 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
255 255 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
256 256 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
257 257 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
258 258 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
259 259 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
275 275 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
276 276 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
277 277 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
278 278 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
279 279 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
291 291 DRR224551 DRX214836 DRS236359 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin from RIKEN Wild type zebrafish at 42dpf C SAMD00222582   sample name:42dpf C                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222582 DRX214836 42dpf C 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222582       14328721000.0 71643605.0 DRR224551 0:100 1:100 A:3545040254;C:3629416092;G:3695002549;T:3459108561;N:153544 100 100     3545040254 3629416092 3695002549 3459108561 153544 DRX214836 DRS236359 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.9671 0.95979 0.04174 0.04058 0.71867 0.72143 0.44818 0.46122 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Juvenile Juvenile Fin Surface Structure
292 292 DRR224550 DRX214835 DRS236358 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin from RIKEN Wild type zebrafish at 42dpf B SAMD00222581   sample name:42dpf B                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222581 DRX214835 42dpf B 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222581       14782437000.0 73912185.0 DRR224550 0:100 1:100 A:3652595601;C:3746189790;G:3788229051;T:3595263949;N:158609 100 100     3652595601 3746189790 3788229051 3595263949 158609 DRX214835 DRS236358 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.96502 0.95776 0.0417 0.0399 0.71311 0.71423 0.46064 0.44469 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Juvenile Juvenile Fin Surface Structure
293 293 DRR224549 DRX214834 DRS236357 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin from RIKEN Wild type zebrafish at 42dpf A SAMD00222580   sample name:42dpf A                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222580 DRX214834 42dpf A 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222580       17895751600.0 89478758.0 DRR224549 0:100 1:100 A:4428562207;C:4525140210;G:4573827895;T:4368029340;N:191948 100 100     4428562207 4525140210 4573827895 4368029340 191948 DRX214834 DRS236357 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.96506 0.96043 0.04654 0.0446 0.70956 0.71153 0.49143 0.48957 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Juvenile Juvenile Fin Surface Structure
25267 25267 SRR25744342 SRX21467662 SRS18702380 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad eif4e1b 3 GSM7730282   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing Gonad eif4e1b 3 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / GSM7730282 GSM7730282: Gonad eif4e1b 3; Danio rerio; ssRNA seq GSM7730282 r1 GSM7730282 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_HOM3_1.fastq.gz Ovary_HOM3_2.fastq.gz fastq fastq 2170738056.0 10746228.0 GSM7730282 r1 0:101 1:101 A:531993767;C:520631008;G:565772072;T:552334154;N:7055 101 101     531993767 520631008 565772072 552334154 7055 SRX21467662 SRS18702380 SRA1698764 IMP IMP 2 0.77665 0.7702 0.14988 0.14284 0.66716 0.66957 0.49991 0.47425 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25268 25268 SRR25744343 SRX21467661 SRS18702379 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad eif4e1b 2 GSM7730281   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing Gonad eif4e1b 2 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / GSM7730281 GSM7730281: Gonad eif4e1b 2; Danio rerio; ssRNA seq GSM7730281 r1 GSM7730281 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_HOM2_1.fastq.gz Ovary_HOM2_2.fastq.gz fastq fastq 3459149000.0 17124500.0 GSM7730281 r1 0:101 1:101 A:876732239;C:796603142;G:882912604;T:902886783;N:14232 101 101     876732239 796603142 882912604 902886783 14232 SRX21467661 SRS18702379 SRA1698764 IMP IMP 2 0.81761 0.79589 0.26282 0.24746 0.70607 0.7039 0.50658 0.49236 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25269 25269 SRR25744344 SRX21467660 SRS18702381 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad eif4e1b 1 GSM7730280   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / |geo loc name:missing|collection date:missing Gonad eif4e1b 1 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b / GSM7730280 GSM7730280: Gonad eif4e1b 1; Danio rerio; ssRNA seq GSM7730280 r1 GSM7730280 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_HOM1_1.fastq.gz Ovary_HOM1_2.fastq.gz fastq fastq 2189781202.0 10840501.0 GSM7730280 r1 0:101 1:101 A:537591255;C:525448020;G:568979980;T:557754770;N:7177 101 101     537591255 525448020 568979980 557754770 7177 SRX21467660 SRS18702381 SRA1698764 IMP IMP 2 0.7459 0.74191 0.15778 0.15291 0.65543 0.65841 0.48578 0.48291 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25270 25270 SRR25744345 SRX21467659 SRS18702378 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad WT 3 GSM7730279   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing Gonad WT 3 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+ GSM7730279 GSM7730279: Gonad WT 3; Danio rerio; ssRNA seq GSM7730279 r1 GSM7730279 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_WT3_1.fastq.gz Ovary_WT3_2.fastq.gz fastq fastq 3674041448.0 18188324.0 GSM7730279 r1 0:101 1:101 A:910831144;C:876967044;G:953299105;T:932928913;N:15242 101 101     910831144 876967044 953299105 932928913 15242 SRX21467659 SRS18702378 SRA1698764 IMP IMP 2 0.89093 0.89038 0.09253 0.09348 0.73892 0.73858 0.47115 0.47218 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25271 25271 SRR25744346 SRX21467658 SRS18702377 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad WT 2 GSM7730278   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing Gonad WT 2 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+ GSM7730278 GSM7730278: Gonad WT 2; Danio rerio; ssRNA seq GSM7730278 r1 GSM7730278 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_WT2_1.fastq.gz Ovary_WT2_2.fastq.gz fastq fastq 3024886370.0 14974685.0 GSM7730278 r1 0:101 1:101 A:744374909;C:727299396;G:782294774;T:770904797;N:12494 101 101     744374909 727299396 782294774 770904797 12494 SRX21467658 SRS18702377 SRA1698764 IMP IMP 2 0.91806 0.91689 0.06949 0.07178 0.74458 0.74474 0.47548 0.47338 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
25272 25272 SRR25744347 SRX21467657 SRS18702376 SRP456724 PRJNA1008624 RNA seq of female gonads isolated from juvenile eif4e1b mutant and wild type zebrafish GSE241537 Transcriptome Analysis The mRNA cap binding protein eIF4E1b is critical for female germline development in zebrafish. To study the effect of eIF4E1b loss in zebrafish we isolated gonads with a high expression of ziwi:GFP female germline marker from wild type and eif4e1b mutant juveniles and performed RNA seq. Overall design: We performed differential expression gene analyses of wild type and eif4e1b mutant gonads n = 3 biological replicates containing 3 gonads each   pubmed:38177902   Gonad WT 1 GSM7730277   source name:Ovary|tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+|geo loc name:missing|collection date:missing Gonad WT 1 RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts Ovary   RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   tissue:Ovary|Sex:female|cell type:Gonad|genotype:tgziwi:GFP eif4e1b +/+ GSM7730277 GSM7730277: Gonad WT 1; Danio rerio; ssRNA seq GSM7730277 r1 GSM7730277 1 RNeasy Mini Kit Qiagen SMARTerStrandedRNA library Ribo Zero   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP456724   loader:fastq load.py Ovary_WT1_2.fastq.gz Ovary_WT1_1.fastq.gz fastq fastq 3571638356.0 17681378.0 GSM7730277 r1 0:101 1:101 A:876280472;C:856417516;G:935896746;T:903028845;N:14777 101 101     876280472 856417516 935896746 903028845 14777 SRX21467657 SRS18702376 SRA1698764 IMP IMP 2 0.89559 0.89353 0.09223 0.09423 0.73052 0.73012 0.47772 0.47408 101 101 B B biological fallback assumption illumina novaseq_era full_length rrna_depletion ribozero bulk unknown unknown   Austria 2023-08-23 Undetermined Juvenile Gonad Reproductive System
31837 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 33360 SRR30140788 SRX25609257 SRS22255959 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       DMSO 1 DMSO 1   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:DMSO 1|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S886 S886 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     DMSO_1_1.fq.gz DMSO_1_2.fq.gz fastq fastq 6848352600.0 22827842.0 DMSO 1 1.fq.gz 0:150 1:150 A:2042619042;C:1408327078;G:1392721721;T:2004605654;N:79105 150 150     2042619042 1408327078 1392721721 2004605654 79105 SRX25609257 SRS22255959 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
33361 33361 SRR30140789 SRX25609256 SRS22255958 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       DMSO 2 DMSO 2   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:DMSO 2|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S887 S887 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     DMSO_2_1.fq.gz DMSO_2_2.fq.gz fastq fastq 6722867400.0 22409558.0 DMSO 2 1.fq.gz 0:150 1:150 A:1987471480;C:1402576521;G:1384470516;T:1948276779;N:72104 150 150     1987471480 1402576521 1384470516 1948276779 72104 SRX25609256 SRS22255958 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
33362 33362 SRR30140790 SRX25609255 SRS22255957 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       DMSO 3 DMSO 3   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:DMSO 3|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S888 S888 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     DMSO_3_1.fq.gz DMSO_3_2.fq.gz fastq fastq 6385524600.0 21285082.0 DMSO 3 1.fq.gz 0:150 1:150 A:1858080423;C:1360978750;G:1348505877;T:1817909740;N:49810 150 150     1858080423 1360978750 1348505877 1817909740 49810 SRX25609255 SRS22255957 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
33363 33363 SRR30140791 SRX25609254 SRS22255956 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       BPS1 1 BPS1 1   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS1 1|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S889 S889 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     BPS1_1_1.fq.gz BPS1_1_2.fq.gz fastq fastq 6677891400.0 22259638.0 BPS1 1 1.fq.gz 0:150 1:150 A:1942755547;C:1419146767;G:1404962384;T:1910952784;N:73918 150 150     1942755547 1419146767 1404962384 1910952784 73918 SRX25609254 SRS22255956 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
33364 33364 SRR30140792 SRX25609253 SRS22255955 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       BPS1 2 BPS1 2   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS1 2|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S890 S890 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     BPS1_2_1.fq.gz BPS1_2_2.fq.gz fastq fastq 6521417700.0 21738059.0 BPS1 2 1.fq.gz 0:150 1:150 A:1909300221;C:1371099464;G:1358671002;T:1882282904;N:64109 150 150     1909300221 1371099464 1358671002 1882282904 64109 SRX25609253 SRS22255955 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
33365 33365 SRR30140793 SRX25609252 SRS22255954 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       BPS1 3 BPS1 3   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS1 3|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S891 S891 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     BPS1_3_1.fq.gz BPS1_3_2.fq.gz fastq fastq 6821300100.0 22737667.0 BPS1 3 1.fq.gz 0:150 1:150 A:1996014045;C:1437758871;G:1429644156;T:1957815359;N:67669 150 150     1996014045 1437758871 1429644156 1957815359 67669 SRX25609252 SRS22255954 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
33366 33366 SRR30140794 SRX25609251 SRS22255953 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       BPS100 1 BPS100 1   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS100 1|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S892 S892 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     BPS100_1_1.fq.gz BPS100_1_2.fq.gz fastq fastq 6420793800.0 21402646.0 BPS100 1 1.fq.gz 0:150 1:150 A:1856129124;C:1374411655;G:1366071243;T:1824132054;N:49724 150 150     1856129124 1374411655 1366071243 1824132054 49724 SRX25609251 SRS22255953 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
33367 33367 SRR30140795 SRX25609250 SRS22255952 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       BPS100 2 BPS100 2   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS100 2|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S893 S893 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     BPS100_2_1.fq.gz BPS100_2_2.fq.gz fastq fastq 6639336600.0 22131122.0 BPS100 2 1.fq.gz 0:150 1:150 A:1901484110;C:1438361866;G:1430361119;T:1869078551;N:50954 150 150     1901484110 1438361866 1430361119 1869078551 50954 SRX25609250 SRS22255952 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
33368 33368 SRR30140796 SRX25609249 SRS22255951 SRP524310 PRJNA1144219 Danio rerio Raw sequence reads PRJNA1144219 Whole Genome Sequencing post exposure to bisphenol S for 50 days zebrafish brain tissue was performed by RNA seq       BPS100 3 BPS100 3   strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:50 days|dev stage:BPS100 3|collection date:not collected|geo loc name:China: Qingdao|sex:intersex|tissue:Brain|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Danio rerio S894 S894 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP524310     BPS100_3_1.fq.gz BPS100_3_2.fq.gz fastq fastq 6586231800.0 21954106.0 BPS100 3 1.fq.gz 0:150 1:150 A:1875041634;C:1438699475;G:1425868891;T:1846570793;N:51007 150 150     1875041634 1438699475 1425868891 1846570793 51007 SRX25609249 SRS22255951 SRA1940694 Ocean University of China|College of Marine Life Sciences Ocean University of China                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-08-06 Juvenile Juvenile Brain Nervous System
34128 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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