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980 rows where devstage_curation = "Adult" and tissue_curation_coarse = "Liver and Biliary System"

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experiment.library_selection 10

experiment.platform 6

technology 4

experiment.library_source 3

experiment.library_strategy 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Liver and Biliary System · 980 ✖

tissue_curation 1

devstage_curation_coarse 1

devstage_curation 1

  • Adult · 980 ✖
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
206 206 DRR162535 DRX153154 DRS083215 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 39 mpf zebrafish replicate5 SAMD00152483   sample name:l39 5|age:39 month|biological replicate:5|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152483 DRX153154 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 SAMD00152483       1222686600.0 6113433.0 DRR162535 0:100 1:100 A:332248505;C:277678269;G:280475826;T:332221614;N:62386 100 100     332248505 277678269 280475826 332221614 62386 DRX153154 DRS083215 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 0.94973 0.95168 0.05815 0.0574 0.80714 0.80992 0.2996 0.29323 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Liver Liver and Biliary System
207 207 DRR162534 DRX153153 DRS083214 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 39 mpf zebrafish replicate4 SAMD00152482   sample name:l39 4|age:39 month|biological replicate:4|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152482 DRX153153 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 SAMD00152482       1640116400.0 8200582.0 DRR162534 0:100 1:100 A:453347555;C:365904202;G:366450625;T:454324883;N:89135 100 100     453347555 365904202 366450625 454324883 89135 DRX153153 DRS083214 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 0.93653 0.93054 0.09033 0.08864 0.7417 0.74341 0.47622 0.47803 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Liver Liver and Biliary System
208 208 DRR162533 DRX153152 DRS083213 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 39 mpf zebrafish replicate3 SAMD00152481   sample name:l39 3|age:39 month|biological replicate:3|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152481 DRX153152 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 SAMD00152481       1676561000.0 8382805.0 DRR162533 0:100 1:100 A:458233101;C:380058901;G:378567207;T:459616427;N:85364 100 100     458233101 380058901 378567207 459616427 85364 DRX153152 DRS083213 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 0.94088 0.93572 0.08357 0.08412 0.78516 0.79383 0.58177 0.569 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Liver Liver and Biliary System
209 209 DRR162532 DRX153151 DRS083212 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 39 mpf zebrafish replicate2 SAMD00152480   sample name:l39 2|age:39 month|biological replicate:2|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152480 DRX153151 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 SAMD00152480       1818896600.0 9094483.0 DRR162532 0:100 1:100 A:513353000;C:395752133;G:399719533;T:509976715;N:95219 100 100     513353000 395752133 399719533 509976715 95219 DRX153151 DRS083212 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 0.92557 0.90731 0.10552 0.10279 0.73655 0.73963 0.55463 0.53901 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Liver Liver and Biliary System
210 210 DRR162531 DRX153150 DRS083211 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 39 mpf zebrafish replicate1 SAMD00152479   sample name:l39 1|age:39 month|biological replicate:1|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152479 DRX153150 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 SAMD00152479       1365495000.0 6827475.0 DRR162531 0:100 1:100 A:397961331;C:285103195;G:285088182;T:397271923;N:70369 100 100     397961331 285103195 285088182 397271923 70369 DRX153150 DRS083211 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 0.91718 0.9094 0.12236 0.12108 0.74905 0.75213 0.52227 0.52956 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Liver Liver and Biliary System
211 211 DRR162530 DRX153149 DRS083210 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 16 mpf zebrafish replicate5 SAMD00152478   sample name:l16 5|age:16 month|biological replicate:5|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152478 DRX153149 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 SAMD00152478       1350377800.0 6751889.0 DRR162530 0:100 1:100 A:386028757;C:288772838;G:290958369;T:384548737;N:69099 100 100     386028757 288772838 290958369 384548737 69099 DRX153149 DRS083210 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 0.93516 0.92365 0.08362 0.08141 0.82446 0.82769 0.62055 0.62498 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Liver Liver and Biliary System
212 212 DRR162529 DRX153148 DRS083209 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 16 mpf zebrafish replicate4 SAMD00152477   sample name:l16 4|age:16 month|biological replicate:4|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152477 DRX153148 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 SAMD00152477       1336103200.0 6680516.0 DRR162529 0:100 1:100 A:382497123;C:284680985;G:285893391;T:382963813;N:67888 100 100     382497123 284680985 285893391 382963813 67888 DRX153148 DRS083209 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 0.9394 0.94216 0.0736 0.07267 0.81909 0.82063 0.34071 0.35081 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Liver Liver and Biliary System
213 213 DRR162528 DRX153147 DRS083208 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 16 mpf zebrafish replicate3 SAMD00152476   sample name:l16 3|age:16 month|biological replicate:3|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152476 DRX153147 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 SAMD00152476       1382207400.0 6911037.0 DRR162528 0:100 1:100 A:389944369;C:300605191;G:301498468;T:390090609;N:68763 100 100     389944369 300605191 301498468 390090609 68763 DRX153147 DRS083208 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 0.93205 0.92544 0.08167 0.0803 0.80164 0.80472 0.60042 0.52988 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Liver Liver and Biliary System
214 214 DRR162527 DRX153146 DRS083207 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 16 mpf zebrafish replicate2 SAMD00152475   sample name:l16 2|age:16 month|biological replicate:2|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152475 DRX153146 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 SAMD00152475       1420870200.0 7104351.0 DRR162527 0:100 1:100 A:390283357;C:318567042;G:320772328;T:391175121;N:72352 100 100     390283357 318567042 320772328 391175121 72352 DRX153146 DRS083207 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 0.95451 0.95673 0.03982 0.04064 0.83765 0.84053 0.16589 0.16881 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Liver Liver and Biliary System
215 215 DRR162526 DRX153145 DRS083206 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 16 mpf zebrafish replicate1 SAMD00152474   sample name:l16 1|age:16 month|biological replicate:1|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152474 DRX153145 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 SAMD00152474       1153415600.0 5767078.0 DRR162526 0:100 1:100 A:331352139;C:244998423;G:248301842;T:328704463;N:58733 100 100     331352139 244998423 248301842 328704463 58733 DRX153145 DRS083206 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 0.95303 0.95385 0.03203 0.03206 0.86592 0.86734 0.23054 0.23207 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Liver Liver and Biliary System
216 216 DRR162525 DRX153144 DRS083205 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 7 mpf zebrafish replicate5 SAMD00152473   sample name:l07 5|age:7 month|biological replicate:5|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152473 DRX153144 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 SAMD00152473       890770600.0 4453853.0 DRR162525 0:100 1:100 A:256905080;C:188672401;G:188524159;T:256621928;N:47032 100 100     256905080 188672401 188524159 256621928 47032 DRX153144 DRS083205 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 0.9268 0.9203 0.08741 0.08714 0.79013 0.80292 0.60305 0.60127 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Liver Liver and Biliary System
217 217 DRR162524 DRX153143 DRS083204 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 7 mpf zebrafish replicate4 SAMD00152472   sample name:l07 4|age:7 month|biological replicate:4|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152472 DRX153143 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 SAMD00152472       1483455800.0 7417279.0 DRR162524 0:100 1:100 A:436293893;C:304891230;G:308137580;T:434055810;N:77287 100 100     436293893 304891230 308137580 434055810 77287 DRX153143 DRS083204 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 0.91896 0.90192 0.0717 0.07014 0.81085 0.8132 0.58351 0.59366 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Liver Liver and Biliary System
218 218 DRR162523 DRX153142 DRS083203 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 7 mpf zebrafish replicate3 SAMD00152471   sample name:l07 3|age:7 month|biological replicate:3|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152471 DRX153142 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 SAMD00152471       1864489400.0 9322447.0 DRR162523 0:100 1:100 A:502417821;C:427210740;G:431014519;T:503749673;N:96647 100 100     502417821 427210740 431014519 503749673 96647 DRX153142 DRS083203 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 0.95976 0.96143 0.04395 0.04468 0.79448 0.79782 0.263 0.26714 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Liver Liver and Biliary System
219 219 DRR162522 DRX153141 DRS083202 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 7 mpf zebrafish replicate2 SAMD00152470   sample name:l07 2|age:7 month|biological replicate:2|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152470 DRX153141 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 SAMD00152470       2033108200.0 10165541.0 DRR162522 0:100 1:100 A:551635703;C:463271027;G:463695854;T:554401182;N:104434 100 100     551635703 463271027 463695854 554401182 104434 DRX153141 DRS083202 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 0.94795 0.94217 0.05903 0.0589 0.79131 0.79462 0.54196 0.5496 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Liver Liver and Biliary System
220 220 DRR162521 DRX153140 DRS083201 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 7 mpf zebrafish replicate1 SAMD00152469   sample name:l07 1|age:7 month|biological replicate:1|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152469 DRX153140 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 SAMD00152469       1468954400.0 7344772.0 DRR162521 0:100 1:100 A:395399684;C:336608951;G:340607200;T:396263402;N:75163 100 100     395399684 336608951 340607200 396263402 75163 DRX153140 DRS083201 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 0.95562 0.95778 0.02931 0.02966 0.86667 0.8686 0.15375 0.16038 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Adult Adult Liver Liver and Biliary System
9355 9355 ERR2983453 ERX2986069 ERS2955657 ERP112513 PRJEB30097 RNA Seq of Danionine species E-MTAB-7476 Transcriptome Analysis Tissues specific transcriptomes of Danio rerio Danio albolineatus and Danio aesculapii Brain Liver and Gonads. ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05   Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers. R3wL SAMEA5147912 University of Hamburg, Institute of Zoology, Molecular Animal Physiology ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147912|INSDC center name:University of Hamburg Institute of Zoology Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R3wL|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:3|organism part:liver|sample name:E MTAB 7476:R3wL|scientific name:Danio rerio|sex:female|strain:tu                 Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species E MTAB 7476:R3wL p R3wL p RNA Seq of Danionine species Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers. Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:liver RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112513 Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05 FCHNW2WBBXX_L6_HKZEBodsEAADRAAPEI-207_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAADRAAPEI-207_2.fq.gz fastq fastq 3900536400.0 19502682.0 E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAADRAAPEI 207 0:100 1:100 A:1018803847;C:926996866;G:925339368;T:1028563032;N:833287 100 100     1018803847 926996866 925339368 1028563032 833287 ERX2986069 ERS2955657 ERA1674470 University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive 2 0.97722 0.97727 0.02792 0.02783 0.84476 0.84664 0.17004 0.16966 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2018-12-05 Adult Adult Liver Liver and Biliary System
9358 9358 ERR2983450 ERX2986066 ERS2955654 ERP112513 PRJEB30097 RNA Seq of Danionine species E-MTAB-7476 Transcriptome Analysis Tissues specific transcriptomes of Danio rerio Danio albolineatus and Danio aesculapii Brain Liver and Gonads. ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05   Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers. R1wL SAMEA5147909 University of Hamburg, Institute of Zoology, Molecular Animal Physiology ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147909|INSDC center name:University of Hamburg Institute of Zoology Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R1wL|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:1|organism part:liver|sample name:E MTAB 7476:R1wL|scientific name:Danio rerio|sex:female|strain:tu                 Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species E MTAB 7476:R1wL p R1wL p RNA Seq of Danionine species Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers. Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:liver RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112513 Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05 FCHNW2WBBXX_L6_HKZEBodsEAACRAAPEI-206_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAACRAAPEI-206_2.fq.gz fastq fastq 3542921400.0 17714607.0 E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAACRAAPEI 206 0:100 1:100 A:927287253;C:840581371;G:838113814;T:936174847;N:764115 100 100     927287253 840581371 838113814 936174847 764115 ERX2986066 ERS2955654 ERA1674470 University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive 2 0.9748 0.9739 0.02815 0.02746 0.84248 0.84439 0.17403 0.17668 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2018-12-05 Adult Adult Liver Liver and Biliary System
9833 9833 ERR4029234 ERX4030550 ERS4513988 ERP121186 PRJEB37848 RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E-MTAB-8959 Transcriptome Analysis The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss. Tissue types included liver skin muscle heart gut gill eye brain for all three species with additionally pyloric caeca kidney head kidney and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts FPKM or TPM were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation. ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16   Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. ZF L 1 SAMEA6786308 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786308|INSDC center name:CIGENE Faculty of Biosciences The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF L 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:liver|sample name:E MTAB 8959:ZF L 1|scientific name:Danio rerio|sex:male                 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E MTAB 8959:ZF L 1 p ZF L 1 p RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. Experimental Factor: organism part:liver|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP121186 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16 ZF-L-1_ATTACTCG-TATAGCCT_R1_001.fastq.gz ZF-L-1_ATTACTCG-TATAGCCT_R2_001.fastq.gz fastq fastq 6531942312.0 25920406.0 E MTAB 8959:ZF L 1 ATTACTCG TATAGCCT R 0:126 1:126 A:1742074981;C:1508007466;G:1507640617;T:1773534883;N:684365 126 126     1742074981 1508007466 1507640617 1773534883 684365 ERX4030550 ERS4513988 ERA2508028 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive 2 0.95365 0.94664 0.057 0.05639 0.78334 0.78451 0.57079 0.57336 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Norway 2020-04-16 Adult Adult Liver Liver and Biliary System
9836 9836 ERR4029231 ERX4030547 ERS4513985 ERP121186 PRJEB37848 RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E-MTAB-8959 Transcriptome Analysis The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss. Tissue types included liver skin muscle heart gut gill eye brain for all three species with additionally pyloric caeca kidney head kidney and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts FPKM or TPM were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation. ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16   Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. ZF G 1 SAMEA6786305 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786305|INSDC center name:CIGENE Faculty of Biosciences The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF G 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:gut|sample name:E MTAB 8959:ZF G 1|scientific name:Danio rerio|sex:male                 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E MTAB 8959:ZF G 1 p ZF G 1 p RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. Experimental Factor: organism part:gut|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP121186 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16 ZF-G-1_ATTACTCG-GTACTGAC_R1_001.fastq.gz ZF-G-1_ATTACTCG-GTACTGAC_R2_001.fastq.gz fastq fastq 4704841764.0 18670007.0 E MTAB 8959:ZF G 1 ATTACTCG GTACTGAC R 0:126 1:126 A:1201875466;C:1104244497;G:1149324323;T:1248857914;N:539564 126 126     1201875466 1104244497 1149324323 1248857914 539564 ERX4030547 ERS4513985 ERA2508028 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive 2 0.95324 0.95304 0.0643 0.06517 0.67588 0.68239 0.55928 0.55357 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Norway 2020-04-16 Adult Adult Liver Liver and Biliary System
9839 9839 ERR4029220 ERX4030536 ERS4513974 ERP121186 PRJEB37848 RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E-MTAB-8959 Transcriptome Analysis The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss. Tissue types included liver skin muscle heart gut gill eye brain for all three species with additionally pyloric caeca kidney head kidney and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts FPKM or TPM were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation. ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16   Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. ZF L 3 SAMEA6786294 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:16Z|External Id:SAMEA6786294|INSDC center name:CIGENE Faculty of Biosciences The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:16Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF L 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:liver|sample name:E MTAB 8959:ZF L 3|scientific name:Danio rerio|sex:female                 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E MTAB 8959:ZF L 3 p ZF L 3 p RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. Experimental Factor: organism part:liver|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP121186 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16 ZF-L-3_ATTACTCG-CCTATCCT_R1_001.fastq.gz ZF-L-3_ATTACTCG-CCTATCCT_R2_001.fastq.gz fastq fastq 4015386648.0 15934074.0 E MTAB 8959:ZF L 3 ATTACTCG CCTATCCT R 0:126 1:126 A:1056740845;C:942055204;G:937642096;T:1078450107;N:498396 126 126     1056740845 942055204 937642096 1078450107 498396 ERX4030536 ERS4513974 ERA2508028 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive 2 0.96926 0.97065 0.03757 0.03737 0.81592 0.81742 0.30093 0.3039 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Norway 2020-04-16 Adult Adult Liver Liver and Biliary System
9840 9840 ERR4029216 ERX4030532 ERS4513970 ERP121186 PRJEB37848 RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E-MTAB-8959 Transcriptome Analysis The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss. Tissue types included liver skin muscle heart gut gill eye brain for all three species with additionally pyloric caeca kidney head kidney and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts FPKM or TPM were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation. ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16   Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. ZF L 6 SAMEA6786290 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:15Z|External Id:SAMEA6786290|INSDC center name:CIGENE Faculty of Biosciences The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:15Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF L 6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:liver|sample name:E MTAB 8959:ZF L 6|scientific name:Danio rerio|sex:not available                 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E MTAB 8959:ZF L 6 p ZF L 6 p RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. Experimental Factor: organism part:liver|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP121186 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16 ZF-L-6_ATTACTCG-GGCTCTGA_R1_001.fastq.gz ZF-L-6_ATTACTCG-GGCTCTGA_R2_001.fastq.gz fastq fastq 4678483320.0 18565410.0 E MTAB 8959:ZF L 6 ATTACTCG GGCTCTGA R 0:126 1:126 A:1222934876;C:1105593331;G:1115480454;T:1234057377;N:417282 126 126     1222934876 1105593331 1115480454 1234057377 417282 ERX4030532 ERS4513970 ERA2508028 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive 2 0.96734 0.97048 0.03122 0.02865 0.84293 0.84482 0.2604 0.27423 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Norway 2020-04-16 Adult Adult Liver Liver and Biliary System
9841 9841 ERR4029215 ERX4030531 ERS4513969 ERP121186 PRJEB37848 RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E-MTAB-8959 Transcriptome Analysis The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss. Tissue types included liver skin muscle heart gut gill eye brain for all three species with additionally pyloric caeca kidney head kidney and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125 bp reads. Processed count tables per species as raw counts FPKM or TPM were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation. ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 04 16   Protocols: Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. ZF L 5 SAMEA6786289 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences ENA FIRST PUBLIC:2020 04 30T04:03:51Z|ENA LAST UPDATE:2020 04 16T14:24:15Z|External Id:SAMEA6786289|INSDC center name:CIGENE Faculty of Biosciences The Norwegian University of Life Sciences|INSDC first public:2020 04 30T04:03:51Z|INSDC last update:2020 04 16T14:24:15Z|INSDC status:public|Submitter Id:E MTAB 8959:ZF L 5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:liver|sample name:E MTAB 8959:ZF L 5|scientific name:Danio rerio|sex:not available                 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss E MTAB 8959:ZF L 5 p ZF L 5 p RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss Tissue samples of multiple types were collected from adult individuals of zebrafish medaka and rainbow trout. Liver tissue samples were taken in replicates of four or three in the case of rainbow trout. All fish were raised in fresh water under standard rearing conditions in aquaculture facilities rainbow trout: Aquagen broodstock tanks at NIVA solbergstranda or animal laboratory facilities zebrafish medaka: VetBio adamstuen. Total RNA was extracted from the tissue samples using the RNeasy Plus Universal Kit QIAGEN. Quality was determined on a 2100 Bioanalyzer using the RNA 6000 Nano Kit Agilent. Concentration was determined using a Nanodrop 8000 spectrophotometer Thermo Scientific. cDNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit Illumina. Library mean length was determined by running on a 2100 Bioanalyzer using the DNA 1000 Kit Agilent and library concentration was determined with the Qbit BR Kit Thermo Scientific. Experimental Factor: organism part:liver|Experimental Factor: organism:Danio rerio RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP121186 Illumina HiSeq 2500 paired end sequencing; RNA seq of tissue panel samples from zebrafish Danio rerio medaka Oryzias latipes and rainbow trout Oncorhynchus mykiss ENA FIRST PUBLIC:2020 04 30|ENA LAST UPDATE:2020 06 19 ZF-L-5_ATTACTCG-ATAGAGGC_R1_001.fastq.gz ZF-L-5_ATTACTCG-ATAGAGGC_R2_001.fastq.gz fastq fastq 4735140228.0 18790239.0 E MTAB 8959:ZF L 5 ATTACTCG ATAGAGGC R 0:126 1:126 A:1234730507;C:1119686445;G:1126456409;T:1253805646;N:461221 126 126     1234730507 1119686445 1126456409 1253805646 461221 ERX4030531 ERS4513969 ERA2508028 CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive CIGENE, Faculty of Biosciences, The Norwegian University of Life Sciences|European Nucleotide Archive 2 0.96297 0.96851 0.02196 0.02241 0.86598 0.8687 0.25119 0.2498 126 126 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Norway 2020-04-16 Adult Adult Liver Liver and Biliary System
26525 26525 SRR26078869 SRX21793734 SRS18895475 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       liver specific overexpression of Igfbp7 3 LOE replicate 3   strain:transgenic strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:LOE replicate=biological replicate3|BioSampleModel:Model organism or animal                 liver specific overexpression of Igfbp7 3 LOE3 LOE3 liver specific overexpression of Igfbp7 3     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     LOE3_1.fq.gz LOE3_2.fq.gz fastq fastq 7457209500.0 24857365.0 LOE3 1.fq.gz 0:150 1:150 A:1965670426;C:1773372970;G:1762457648;T:1955346803;N:361653 150 150     1965670426 1773372970 1762457648 1955346803 361653 SRX21793734 SRS18895475 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.89541 0.89576 0.04195 0.04177 0.82536 0.82375 0.53368 0.5374 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
26526 26526 SRR26078870 SRX21793733 SRS18895474 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       liver specific overexpression of Igfbp7 2 LOE replicate 2   strain:transgenic strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:LOE replicate=biological replicate2|BioSampleModel:Model organism or animal                 liver specific overexpression of Igfbp7 2 LOE2 LOE2 liver specific overexpression of Igfbp7 2     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     LOE2_1.fq.gz LOE2_2.fq.gz fastq fastq 7069059900.0 23563533.0 LOE2 1.fq.gz 0:150 1:150 A:1835774064;C:1704925495;G:1698942360;T:1829075424;N:342557 150 150     1835774064 1704925495 1698942360 1829075424 342557 SRX21793733 SRS18895474 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.89965 0.90019 0.0524 0.05247 0.80669 0.80525 0.53582 0.49543 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
26527 26527 SRR26078871 SRX21793732 SRS18895473 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       liver specific overexpression of Igfbp7 1 LOE replicate 1   strain:transgenic strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:LOE replicate=biological replicate1|BioSampleModel:Model organism or animal                 liver specific overexpression of Igfbp7 1 LOE1 LOE1 liver specific overexpression of Igfbp7 1     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     LOE1_1.fq.gz LOE1_2.fq.gz fastq fastq 7110174300.0 23700581.0 LOE1 1.fq.gz 0:150 1:150 A:1847016218;C:1713941614;G:1708466537;T:1840442742;N:307189 150 150     1847016218 1713941614 1708466537 1840442742 307189 SRX21793732 SRS18895473 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.8999 0.89917 0.04883 0.04874 0.80858 0.80716 0.51686 0.52442 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
26528 26528 SRR26078872 SRX21793731 SRS18895469 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       Igfbp7 Konckout 3 KO replicate 3   strain:mutant|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:KO replicate=biological replicate3|BioSampleModel:Model organism or animal                 Igfbp7 Konckout 3 KO3 KO3 Igfbp7 Konckout 3     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     KO3_1.fq.gz KO3_2.fq.gz fastq fastq 6966225300.0 23220751.0 KO3 1.fq.gz 0:150 1:150 A:1854162705;C:1635332068;G:1634647432;T:1841746656;N:336439 150 150     1854162705 1635332068 1634647432 1841746656 336439 SRX21793731 SRS18895469 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.94279 0.94294 0.0551 0.05481 0.78861 0.78739 0.54327 0.50468 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
26529 26529 SRR26078873 SRX21793730 SRS18895470 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       Igfbp7 Konckout 2 KO replicate 2   strain:mutant|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:KO replicate=biological replicate2|BioSampleModel:Model organism or animal                 Igfbp7 Konckout 2 KO2 KO2 Igfbp7 Konckout 2     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     KO2_1.fq.gz KO2_2.fq.gz fastq fastq 7465655100.0 24885517.0 KO2 1.fq.gz 0:150 1:150 A:1988715771;C:1750416778;G:1753335257;T:1972838856;N:348438 150 150     1988715771 1750416778 1753335257 1972838856 348438 SRX21793730 SRS18895470 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.94231 0.94227 0.04975 0.04965 0.802 0.80018 0.50781 0.54557 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
26530 26530 SRR26078874 SRX21793729 SRS18895472 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       Igfbp7 Konckout 1 KO replicate 1   strain:mutant|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:KO replicate=biological replicate1|BioSampleModel:Model organism or animal                 Igfbp7 Konckout 1 KO1 KO1 Igfbp7 Konckout 1     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     KO1_1.fq.gz KO1_2.fq.gz fastq fastq 7208655000.0 24028850.0 KO1 1.fq.gz 0:150 1:150 A:1937720737;C:1672178897;G:1677582029;T:1920894866;N:278471 150 150     1937720737 1672178897 1677582029 1920894866 278471 SRX21793729 SRS18895472 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.93429 0.93361 0.05126 0.05122 0.80827 0.80718 0.48739 0.49469 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
26531 26531 SRR26078875 SRX21793728 SRS18895471 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       wild type 3 WT replicate 3   strain:wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:WT replicate=biological replicate3|BioSampleModel:Model organism or animal                 wild type 3 WT3 WT3 wild type 3     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     WT3_1.fq.gz WT3_2.fq.gz fastq fastq 7267116600.0 24223722.0 WT3 1.fq.gz 0:150 1:150 A:1946606247;C:1693037772;G:1694230444;T:1932894815;N:347322 150 150     1946606247 1693037772 1694230444 1932894815 347322 SRX21793728 SRS18895471 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.94026 0.94007 0.05203 0.05132 0.79622 0.79393 0.52332 0.51051 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
26532 26532 SRR26078876 SRX21793727 SRS18895467 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       wild type 2 WT replicate 2   strain:wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:WT replicate=biological replicate2|BioSampleModel:Model organism or animal                 wild type 2 WT2 WT2 wild type 2     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     WT2_1.fq.gz WT2_2.fq.gz fastq fastq 7206849900.0 24022833.0 WT2 1.fq.gz 0:150 1:150 A:1947268148;C:1660088486;G:1665583448;T:1933561073;N:348745 150 150     1947268148 1660088486 1665583448 1933561073 348745 SRX21793727 SRS18895467 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.93368 0.93327 0.06754 0.06713 0.78681 0.7861 0.53133 0.53795 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
26533 26533 SRR26078877 SRX21793726 SRS18895468 SRP461206 PRJNA1018104 Global liver transcriptome assay of WT Igfbp7 null mutant and Igfbp7 LOE animals PRJNA1018104 Other The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients however its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 / null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique respectively. The zebrafish NAFLD models in wildtypes igfbp7 / mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.       wild type 1 WT replicate 1   strain:wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1 corresponding to 40 mg/fish/day|replicate:WT replicate=biological replicate1|BioSampleModel:Model organism or animal                 wild type 1 WT1 WT1 wild type 1     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP461206     WT1_1.fq.gz WT1_2.fq.gz fastq fastq 7170532200.0 23901774.0 WT1 1.fq.gz 0:150 1:150 A:1931584106;C:1658793663;G:1662799956;T:1917012316;N:342159 150 150     1931584106 1658793663 1662799956 1917012316 342159 SRX21793726 SRS18895468 SRA1713671 First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology First Hospital of Shanxi Medical University 2 0.93456 0.93372 0.06482 0.06467 0.77327 0.77266 0.52308 0.53023 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-09-16 Adult Adult Liver Liver and Biliary System
28496 28496 SRR26321412 SRX22029502 SRS19102283 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       3dpci 1 R27   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 3 dpci R27 R27 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R27.fastq fastq 23400.0 312.0 R27.fastq 0:75 A:7949;C:4612;G:4730;T:6100;N:9 75       7949 4612 4730 6100 9 SRX22029502 SRS19102283 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.89642   0.06772   0.99827   0.75   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28497 28497 SRR26321413 SRX22029501 SRS19102284 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       1dpci 4 R22   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 1 dpci R22 R22 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R22.fastq fastq 23400.0 312.0 R22.fastq 0:75 A:7470;C:4460;G:5063;T:6404;N:3 75       7470 4460 5063 6404 3 SRX22029501 SRS19102284 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.87073   0.12167   0.99801   0.73157   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28498 28498 SRR26321414 SRX22029500 SRS19102281 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       R21 R21   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 1 dpci R21 R21 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R21.fastq fastq 23400.0 312.0 R21.fastq 0:75 A:7540;C:4349;G:4857;T:6646;N:8 75       7540 4349 4857 6646 8 SRX22029500 SRS19102281 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.8839   0.04494   0.99768   0.72769   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28499 28499 SRR26321415 SRX22029499 SRS19102282 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       1dpci 2 R18   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 1 dpci R18 R18 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R18.fastq fastq 23400.0 312.0 R18.fastq 0:75 A:7380;C:4430;G:5069;T:6518;N:3 75       7380 4430 5069 6518 3 SRX22029499 SRS19102282 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.87259   0.11196   0.99784   0.69791   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28500 28500 SRR26321416 SRX22029498 SRS19102280 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       1dpci 1 R17   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 1 dpci R17 R17 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R17.fastq fastq 23400.0 312.0 R17.fastq 0:75 A:7322;C:4455;G:5111;T:6507;N:5 75       7322 4455 5111 6507 5 SRX22029498 SRS19102280 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.90439   0.12749   0.99813   0.71052   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28501 28501 SRR26321417 SRX22029497 SRS19102279 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       SHAM 5 R1   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver sham R1 R1 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R1.fastq fastq 23400.0 312.0 R1.fastq 0:75 A:7934;C:4560;G:4922;T:5980;N:4 75       7934 4560 4922 5980 4 SRX22029497 SRS19102279 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.87045   0.10526   0.99805   0.71978   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28502 28502 SRR26321418 SRX22029496 SRS19102277 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       SHAM 4 R64   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver sham R64 R64 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R64.fastq fastq 23400.0 312.0 R64.fastq 0:75 A:7844;C:4626;G:4804;T:6126;N:0 75       7844 4626 4804 6126 0 SRX22029496 SRS19102277 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.90119   0.07509   0.99839   0.8   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28503 28503 SRR26321419 SRX22029495 SRS19102278 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       SHAM 3 R61   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver sham R61 R61 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R61.fastq fastq 23400.0 312.0 R61.fastq 0:75 A:7454;C:4556;G:4960;T:6425;N:5 75       7454 4556 4960 6425 5 SRX22029495 SRS19102278 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.89098   0.06015   0.99813   0.77102   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28504 28504 SRR26321420 SRX22029494 SRS19102276 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       7dpci 4 30   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 7 dpci 30 30 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     30.fastq fastq 23400.0 312.0 30.fastq 0:75 A:7732;C:4528;G:5150;T:5987;N:3 75       7732 4528 5150 5987 3 SRX22029494 SRS19102276 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.88447   0.13147   0.99772   0.71584   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28505 28505 SRR26321421 SRX22029493 SRS19102275 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       R11 R11   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 7 dpci R11 R11 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R11.fastq fastq 23400.0 312.0 R11.fastq 0:75 A:7818;C:4507;G:5107;T:5956;N:12 75       7818 4507 5107 5956 12 SRX22029493 SRS19102275 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.89345   0.11475   0.99847   0.82258   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28506 28506 SRR26321422 SRX22029492 SRS19102274 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       7dpci 2 31   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 7 dpci 31 31 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     31.fastq fastq 23400.0 312.0 31.fastq 0:75 A:7470;C:4619;G:4802;T:6504;N:5 75       7470 4619 4802 6504 5 SRX22029492 SRS19102274 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.87699   0.11111   0.99829   0.78918   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28507 28507 SRR26321423 SRX22029491 SRS19102273 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       7dpci 1 R9   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 7 dpci R9 R9 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R9.fastq fastq 23400.0 312.0 R9.fastq 0:75 A:8130;C:4537;G:4809;T:5917;N:7 75       8130 4537 4809 5917 7 SRX22029491 SRS19102273 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.83588   0.05725   0.99801   0.68586   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28508 28508 SRR26321424 SRX22029490 SRS19102272 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       3dpci 4 R33   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 3 dpci R33 R33 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R33.fastq fastq 23400.0 312.0 R33.fastq 0:75 A:7745;C:4421;G:4867;T:6360;N:7 75       7745 4421 4867 6360 7 SRX22029490 SRS19102272 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.87259   0.07335   0.99805   0.71428   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28509 28509 SRR26321425 SRX22029489 SRS19102271 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       3dpci 3 R31   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 3 dpci R31 R31 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R31.fastq fastq 23400.0 312.0 R31.fastq 0:75 A:7441;C:4483;G:5163;T:6313;N:0 75       7441 4483 5163 6313 0 SRX22029489 SRS19102271 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.9   0.05925   0.9977   0.68325   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28510 28510 SRR26321426 SRX22029488 SRS19102270 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       3dpci 2 R29   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 3 dpci R29 R29 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R29.fastq fastq 23400.0 312.0 R29.fastq 0:75 A:7379;C:4698;G:5166;T:6156;N:1 75       7379 4698 5166 6156 1 SRX22029488 SRS19102270 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.91016   0.05859   0.99797   0.74528   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28511 28511 SRR26321427 SRX22029487 SRS19102269 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       SHAM 2 R62   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver sham R62 R62 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R62.fastq fastq 23400.0 312.0 R62.fastq 0:75 A:7383;C:4566;G:4713;T:6728;N:10 75       7383 4566 4713 6728 10 SRX22029487 SRS19102269 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.91571   0.05363   0.99835   0.77674   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28512 28512 SRR26321428 SRX22029486 SRS19102268 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury     Replicate 1 for SHAM SHAM 1 R63   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia: Melbourne|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver sham R63 R63 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R63.fastq fastq 23400.0 312.0 R63.fastq 0:75 A:7516;C:4606;G:4765;T:6508;N:5 75       7516 4606 4765 6508 5 SRX22029486 SRS19102268 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.90385   0.0423   0.99805   0.72429   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
29581 29581 SRR27387424 SRX23063703 SRS20023725 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Control Liver control liver 5   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control liver replicate5|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T1 5 T1 5 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A7_1.fastq.gz A7_2.fastq.gz fastq fastq 7139648700.0 23798829.0 A7 1.fastq.gz 0:150 1:150 A:1898040242;C:1678584917;G:1680422296;T:1882535161;N:66084 150 150     1898040242 1678584917 1680422296 1882535161 66084 SRX23063703 SRS20023725 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94633 0.94658 0.04866 0.0489 0.77098 0.77041 0.48393 0.49328 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29592 29592 SRR27387435 SRX23063692 SRS20023714 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Control Liver control liver 4   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control liver replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T1 4 T1 4 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A6_1.fastq.gz A6_2.fastq.gz fastq fastq 7080291000.0 23600970.0 A6 1.fastq.gz 0:150 1:150 A:1890410803;C:1656924196;G:1658022500;T:1874867839;N:65662 150 150     1890410803 1656924196 1658022500 1874867839 65662 SRX23063692 SRS20023714 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94344 0.94345 0.05044 0.05028 0.7683 0.76838 0.48933 0.49113 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29600 29600 SRR27387443 SRX23063684 SRS20023706 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Combined Liver combined liver 6   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined liver replicate6|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T4 6 T4 6 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A21_1.fastq.gz A21_2.fastq.gz fastq fastq 8613810000.0 28712700.0 A21 1.fastq.gz 0:150 1:150 A:2301535821;C:2013247658;G:2021540738;T:2277424933;N:60850 150 150     2301535821 2013247658 2021540738 2277424933 60850 SRX23063684 SRS20023706 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94372 0.94375 0.04559 0.04554 0.80397 0.80446 0.54615 0.54931 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29601 29601 SRR27387444 SRX23063683 SRS20023705 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Combined Liver combined liver 5   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined liver replicate5|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T4 5 T4 5 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A20_1.fastq.gz A20_2.fastq.gz fastq fastq 7660898400.0 25536328.0 A20 1.fastq.gz 0:150 1:150 A:2045662664;C:1793844486;G:1797425064;T:2023911614;N:54572 150 150     2045662664 1793844486 1797425064 2023911614 54572 SRX23063683 SRS20023705 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94307 0.94399 0.04996 0.04972 0.79916 0.79967 0.55321 0.55159 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29602 29602 SRR27387445 SRX23063682 SRS20023704 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Combined Liver combined liver 4   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined liver replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T4 4 T4 4 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A19_1.fastq.gz A19_2.fastq.gz fastq fastq 8492667000.0 28308890.0 A19 1.fastq.gz 0:150 1:150 A:2287240764;C:1972022212;G:1977128547;T:2256183819;N:91658 150 150     2287240764 1972022212 1977128547 2256183819 91658 SRX23063682 SRS20023704 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94222 0.94087 0.05048 0.05023 0.78847 0.7876 0.54394 0.54327 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29603 29603 SRR27387446 SRX23063681 SRS20023703 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Control Liver control liver 3   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control liver replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T1 3 T1 3 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A5_1.fastq.gz A5_2.fastq.gz fastq fastq 6365746500.0 21219155.0 A5 1.fastq.gz 0:150 1:150 A:1680943294;C:1504416528;G:1516780057;T:1663547544;N:59077 150 150     1680943294 1504416528 1516780057 1663547544 59077 SRX23063681 SRS20023703 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.96138 0.96072 0.01946 0.01949 0.84372 0.84437 0.21657 0.2162 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29604 29604 SRR27387447 SRX23063680 SRS20023702 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Combined Liver combined liver 3   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined liver replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T4 3 T4 3 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A18_1.fastq.gz A18_2.fastq.gz fastq fastq 6080801100.0 20269337.0 A18 1.fastq.gz 0:150 1:150 A:1625543543;C:1426271281;G:1432771006;T:1596174300;N:40970 150 150     1625543543 1426271281 1432771006 1596174300 40970 SRX23063680 SRS20023702 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94461 0.94384 0.04104 0.04107 0.81294 0.81369 0.55086 0.55066 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29605 29605 SRR27387448 SRX23063679 SRS20023701 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Combined Liver combined liver 2   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined liver replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T4 2 T4 2 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A17_1.fastq.gz A17_2.fastq.gz fastq fastq 8357049600.0 27856832.0 A17 1.fastq.gz 0:150 1:150 A:2228408702;C:1962845144;G:1962818306;T:2202917758;N:59690 150 150     2228408702 1962845144 1962818306 2202917758 59690 SRX23063679 SRS20023701 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94277 0.9436 0.0454 0.04526 0.76039 0.76012 0.53857 0.49252 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29606 29606 SRR27387449 SRX23063678 SRS20023700 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Combined Liver combined liver 1   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined liver replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T4 1 T4 1 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A16_1.fastq.gz A16_2.fastq.gz fastq fastq 8697886500.0 28992955.0 A16 1.fastq.gz 0:150 1:150 A:2308292580;C:2052173268;G:2056418654;T:2280941830;N:60168 150 150     2308292580 2052173268 2056418654 2280941830 60168 SRX23063678 SRS20023700 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94941 0.95075 0.03814 0.03814 0.80359 0.80511 0.45866 0.46697 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29607 29607 SRR27387450 SRX23063677 SRS20023699 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Nanoplastics Liver nps liver 6   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps liver replicate6|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T3 6 T3 6 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A14_1.fastq.gz A14_2.fastq.gz fastq fastq 6328078200.0 21093594.0 A14 1.fastq.gz 0:150 1:150 A:1651110799;C:1522543378;G:1523353407;T:1631026281;N:44335 150 150     1651110799 1522543378 1523353407 1631026281 44335 SRX23063677 SRS20023699 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.95918 0.95893 0.03288 0.03279 0.7989 0.79892 0.46602 0.44771 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29608 29608 SRR27387451 SRX23063676 SRS20023698 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Nanoplastics Liver nps liver 5   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps liver replicate5|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T3 5 T3 5 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A13_1.fastq.gz A13_2.fastq.gz fastq fastq 6682736400.0 22275788.0 A13 1.fastq.gz 0:150 1:150 A:1770006493;C:1580541555;G:1583340681;T:1748799643;N:48028 150 150     1770006493 1580541555 1583340681 1748799643 48028 SRX23063676 SRS20023698 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94674 0.94767 0.04088 0.04069 0.79362 0.79326 0.51807 0.55709 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29609 29609 SRR27387452 SRX23063675 SRS20023697 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Nanoplastics Liver nps liver 4   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps liver replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T3 4 T3 4 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A12_1.fastq.gz A12_2.fastq.gz fastq fastq 7223844300.0 24079481.0 A12 1.fastq.gz 0:150 1:150 A:1898044988;C:1723221670;G:1728581768;T:1873946251;N:49623 150 150     1898044988 1723221670 1728581768 1873946251 49623 SRX23063675 SRS20023697 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.95897 0.9583 0.03099 0.03094 0.81359 0.81414 0.36697 0.38046 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29610 29610 SRR27387453 SRX23063674 SRS20023696 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Nanoplastics Liver nps liver 3   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps liver replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T3 3 T3 3 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A11_1.fastq.gz A11_2.fastq.gz fastq fastq 7712327100.0 25707757.0 A11 1.fastq.gz 0:150 1:150 A:2078269634;C:1786227652;G:1790988947;T:2056786923;N:53944 150 150     2078269634 1786227652 1790988947 2056786923 53944 SRX23063674 SRS20023696 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.93754 0.93849 0.05229 0.05261 0.79762 0.79841 0.52961 0.55954 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29611 29611 SRR27387454 SRX23063673 SRS20023695 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Nanoplastics Liver nps liver 2   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps liver replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T3 2 T3 2 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A10_1.fastq.gz A10_2.fastq.gz fastq fastq 9006367500.0 30021225.0 A10 1.fastq.gz 0:150 1:150 A:2405095208;C:2108519804;G:2119356079;T:2373332498;N:63911 150 150     2405095208 2108519804 2119356079 2373332498 63911 SRX23063673 SRS20023695 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.93857 0.93907 0.04235 0.04254 0.74401 0.74442 0.53865 0.54012 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29612 29612 SRR27387455 SRX23063672 SRS20023694 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Nanoplastics Liver nps liver 1   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:nps liver replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T3 1 T3 1 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A8_1.fastq.gz A8_2.fastq.gz fastq fastq 9705357300.0 32351191.0 A8 1.fastq.gz 0:150 1:150 A:2549361250;C:2315598558;G:2319533236;T:2520797865;N:66391 150 150     2549361250 2315598558 2319533236 2520797865 66391 SRX23063672 SRS20023694 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.95257 0.95219 0.03953 0.03882 0.80085 0.80052 0.5024 0.50544 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29613 29613 SRR27387456 SRX23063671 SRS20023693 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       6PPDQ Liver 6ppdq liver 6   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq liver replicate6|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T2 6 T2 6 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A28_1.fastq.gz A28_2.fastq.gz fastq fastq 7312027200.0 24373424.0 A28 1.fastq.gz 0:150 1:150 A:1933027768;C:1734543239;G:1734058319;T:1910343929;N:53945 150 150     1933027768 1734543239 1734058319 1910343929 53945 SRX23063671 SRS20023693 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94984 0.95024 0.04435 0.04424 0.77804 0.77869 0.5448 0.51681 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29614 29614 SRR27387457 SRX23063670 SRS20023692 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Control Liver control liver 2   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control liver replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T1 2 T1 2 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A3_1.fastq.gz A3_2.fastq.gz fastq fastq 10383955200.0 34613184.0 A3 1.fastq.gz 0:150 1:150 A:2778093066;C:2424701453;G:2429080701;T:2751982231;N:97749 150 150     2778093066 2424701453 2429080701 2751982231 97749 SRX23063670 SRS20023692 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94514 0.94539 0.05128 0.05171 0.80697 0.80669 0.55446 0.54855 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29615 29615 SRR27387458 SRX23063669 SRS20023691 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       Control Liver control liver 1   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:control liver replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T1 1 T1 1 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A1_1.fastq.gz A1_2.fastq.gz fastq fastq 6990799500.0 23302665.0 A1 1.fastq.gz 0:150 1:150 A:1852168539;C:1650230337;G:1654609197;T:1833725714;N:65713 150 150     1852168539 1650230337 1654609197 1833725714 65713 SRX23063669 SRS20023691 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.95142 0.95049 0.03481 0.03455 0.80955 0.81089 0.42523 0.42786 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29616 29616 SRR27387459 SRX23063668 SRS20023690 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       6PPDQ Liver 6ppdq liver 5   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq liver replicate5|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T2 5 T2 5 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A27_1.fastq.gz A27_2.fastq.gz fastq fastq 8327205000.0 27757350.0 A27 1.fastq.gz 0:150 1:150 A:2188059959;C:1983666022;G:1992428805;T:2162994610;N:55604 150 150     2188059959 1983666022 1992428805 2162994610 55604 SRX23063668 SRS20023690 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.95557 0.95521 0.03496 0.035 0.81377 0.81428 0.44899 0.45358 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29617 29617 SRR27387460 SRX23063667 SRS20023689 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       6PPDQ Liver 6ppdq liver 4   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq liver replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T2 4 T2 4 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A26_1.fastq.gz A26_2.fastq.gz fastq fastq 6407337900.0 21357793.0 A26 1.fastq.gz 0:150 1:150 A:1685351213;C:1524796223;G:1531286302;T:1665857949;N:46213 150 150     1685351213 1524796223 1531286302 1665857949 46213 SRX23063667 SRS20023689 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.96413 0.96363 0.02797 0.02805 0.8505 0.85194 0.38255 0.38447 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29618 29618 SRR27387461 SRX23063666 SRS20023688 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       6PPDQ Liver 6ppdq liver 3   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq liver replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T2 3 T2 3 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A25_1.fastq.gz A25_2.fastq.gz fastq fastq 8578160400.0 28593868.0 A25 1.fastq.gz 0:150 1:150 A:2253186424;C:2047305045;G:2050974170;T:2226633669;N:61092 150 150     2253186424 2047305045 2050974170 2226633669 61092 SRX23063666 SRS20023688 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.95088 0.95107 0.04217 0.04231 0.77875 0.77922 0.5388 0.53743 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29619 29619 SRR27387462 SRX23063665 SRS20023687 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       6PPDQ Liver 6ppdq liver 2   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq liver replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T2 2 T2 2 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A23_1.fastq.gz A23_2.fastq.gz fastq fastq 7606031100.0 25353437.0 A23 1.fastq.gz 0:150 1:150 A:2040128163;C:1774614072;G:1775629532;T:2015605795;N:53538 150 150     2040128163 1774614072 1775629532 2015605795 53538 SRX23063665 SRS20023687 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.945 0.94581 0.04313 0.04324 0.81617 0.8172 0.55094 0.55944 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
29620 29620 SRR27387463 SRX23063664 SRS20023686 SRP480720 PRJNA1059246 Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish PRJNA1059246 Other Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq.       6PPDQ Liver 6ppdq liver 1   strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:liver|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:6ppdq liver replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish T2 1 T2 1 PCR enrichment of adaptor ligated DNA     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP480720     A22_1.fastq.gz A22_2.fastq.gz fastq fastq 6116767200.0 20389224.0 A22 1.fastq.gz 0:150 1:150 A:1642510559;C:1422754642;G:1431247073;T:1620185548;N:69378 150 150     1642510559 1422754642 1431247073 1620185548 69378 SRX23063664 SRS20023686 SRA1777576 Nord University|Faculty of Biosciences and Aquaculture Nord University 2 0.94746 0.9454 0.0432 0.04289 0.80748 0.80752 0.56194 0.55666 150 150 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2023-12-30 Adult Adult Liver Liver and Biliary System
31980 31980 SRR28892728 SRX24451189 SRS21204958 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         TP3   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 6|BioSampleModel:Model organism or animal                 Adult zebrafish liver TP3 TP3 mRNAseq of zebrafish liver replication 3 of TP     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     TP3_1.fq.gz TP3_2.fq.gz fastq fastq 6657069900.0 22190233.0 TP3 1.fq.gz 0:150 1:150 A:1808410149;C:1512668682;G:1536153888;T:1799837181;N:0 150 150     1808410149 1512668682 1536153888 1799837181 0 SRX24451189 SRS21204958 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
31981 31981 SRR28892729 SRX24451188 SRS21204959 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         TP2   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 5|BioSampleModel:Model organism or animal                 Adult zebrafish liver TP2 TP2 mRNAseq of zebrafish liver replication 2 of TP     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     TP2_1.fq.gz TP2_2.fq.gz fastq fastq 6617368500.0 22057895.0 TP2 1.fq.gz 0:150 1:150 A:1799646726;C:1503407966;G:1523443584;T:1790870224;N:0 150 150     1799646726 1503407966 1523443584 1790870224 0 SRX24451188 SRS21204959 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
31982 31982 SRR28892730 SRX24451187 SRS21204956 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         TP1   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 4|BioSampleModel:Model organism or animal                 Adult zebrafish liver TP1 TP1 mRNAseq of zebrafish liver replication 1 of TP     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     TP1_1.fq.gz TP1_2.fq.gz fastq fastq 6432586800.0 21441956.0 TP1 1.fq.gz 0:150 1:150 A:1743341515;C:1465440262;G:1488109144;T:1735695879;N:0 150 150     1743341515 1465440262 1488109144 1735695879 0 SRX24451187 SRS21204956 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
31983 31983 SRR28892731 SRX24451186 SRS21204957 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         CONT3   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 3|BioSampleModel:Model organism or animal                 Adult zebrafish liver CON3 CON3 mRNAseq of zebrafish liver replication 3 of CONT     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     CONT3_1.fq.gz CONT3_2.fq.gz fastq fastq 6595768200.0 21985894.0 CONT3 1.fq.gz 0:150 1:150 A:1762107185;C:1525175684;G:1547321856;T:1761163475;N:0 150 150     1762107185 1525175684 1547321856 1761163475 0 SRX24451186 SRS21204957 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
31984 31984 SRR28892732 SRX24451185 SRS21204954 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         CONT2   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 2|BioSampleModel:Model organism or animal                 Adult zebrafish liver CON2 CON2 mRNAseq of zebrafish liver replication 2 of CONT     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     CONT2_1.fq.gz CONT2_2.fq.gz fastq fastq 6175346400.0 20584488.0 CONT2 1.fq.gz 0:150 1:150 A:1656546719;C:1421990443;G:1442409824;T:1654399414;N:0 150 150     1656546719 1421990443 1442409824 1654399414 0 SRX24451185 SRS21204954 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
31985 31985 SRR28892733 SRX24451184 SRS21204955 SRP505641 PRJNA1107713 Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis PRJNA1107713 Other High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.         CONT1   strain:not applicable|isolate:not applicable|breed:not collected|cultivar:not applicable|ecotype:AB ecotype|age:5 month|collection date:2022 11 24|geo loc name:China|sex:male|tissue:liver|replicate:replicate=biological replicate 1|BioSampleModel:Model organism or animal                 Adult zebrafish liver CON1 CON1 mRNAseq of zebrafish liver replication 1 of CONT     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED DNBSEQ DNBSEQ-T7   SRP505641     CONT1_1.fq.gz CONT1_2.fq.gz fastq fastq 6342828300.0 21142761.0 CONT1 1.fq.gz 0:150 1:150 A:1698306803;C:1464261565;G:1482929449;T:1697330483;N:0 150 150     1698306803 1464261565 1482929449 1697330483 0 SRX24451184 SRS21204955 SRA1858747 Beibu Gulf University|college of Food Engineering Beibu Gulf University                       B B biological fallback assumption bgi bgi unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Adult Adult Liver Liver and Biliary System
32508 32508 SRR29290248 SRX24807391 SRS21522263 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     15 days experimental group parallel 1 liver transcriptome L4 1   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 09|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 14|experiment description:Exposure to 80 100 mesh tire wear particles for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L4 1 L4 1 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TMFA6-7L.R1.fq.gz TMFA6-7L.R2.fq.gz fastq fastq 5892231600.0 19640772.0 TMFA6 7L.R1.fq.gz 0:150 1:150 A:1471743634;C:1450664701;G:1502453832;T:1466956960;N:412473 150 150     1471743634 1450664701 1502453832 1466956960 412473 SRX24807391 SRS21522263 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32509 32509 SRR29290249 SRX24807390 SRS21522262 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     30 days experimental group parallel 3 liver transcriptome L3 3   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 23|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 13|experiment description:Exposed to tire wear particles above 120 mesh excretion for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L3 3 L3 3 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TLSC-5L.R1.fq.gz TLSC-5L.R2.fq.gz fastq fastq 6269295000.0 20897650.0 TLSC 5L.R1.fq.gz 0:150 1:150 A:1541736942;C:1578334203;G:1620160556;T:1528907120;N:156179 150 150     1541736942 1578334203 1620160556 1528907120 156179 SRX24807390 SRS21522262 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32510 32510 SRR29290250 SRX24807389 SRS21522261 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     30 days experimental group parallel 2 liver transcriptome L3 2   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 23|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 12|experiment description:Exposed to tire wear particles above 120 mesh excretion for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L3 2 L3 2 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TLSB-3L.R1.fq.gz TLSB-3L.R2.fq.gz fastq fastq 6206673000.0 20688910.0 TLSB 3L.R1.fq.gz 0:150 1:150 A:1592564670;C:1487253074;G:1531600191;T:1595004475;N:250590 150 150     1592564670 1487253074 1531600191 1595004475 250590 SRX24807389 SRS21522261 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32511 32511 SRR29290251 SRX24807388 SRS21522260 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     30 days experimental group parallel 1 liver transcriptome L3 1   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 23|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 11|experiment description:Exposed to tire wear particles above 120 mesh excretion for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L3 1 L3 1 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TLSA-1L.R1.fq.gz TLSA-1L.R2.fq.gz fastq fastq 6188928300.0 20629761.0 TLSA 1L.R1.fq.gz 0:150 1:150 A:1584479312;C:1464260894;G:1549296685;T:1590644766;N:246643 150 150     1584479312 1464260894 1549296685 1590644766 246643 SRX24807388 SRS21522260 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32512 32512 SRR29290252 SRX24807387 SRS21522259 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     15 days experimental group parallel 3 liver transcriptome L2 3   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 08|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 16|experiment description:Exposed to 120 or above tire wear particles for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L2 3 L2 3 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TLFC1-3L.R1.fq.gz TLFC1-3L.R2.fq.gz fastq fastq 6367070400.0 21223568.0 TLFC1 3L.R1.fq.gz 0:150 1:150 A:1579430230;C:1587605262;G:1613210542;T:1586578782;N:245584 150 150     1579430230 1587605262 1613210542 1586578782 245584 SRX24807387 SRS21522259 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32513 32513 SRR29290253 SRX24807386 SRS21522258 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     15 days experimental group parallel 2 liver transcriptome L2 2   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 08|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 15|experiment description:Exposed to 120 or above tire wear particles for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L2 2 L2 2 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TLFB1-3L.R1.fq.gz TLFB1-3L.R2.fq.gz fastq fastq 6996653100.0 23322177.0 TLFB1 3L.R1.fq.gz 0:150 1:150 A:1803878205;C:1678057588;G:1715367000;T:1799170285;N:180022 150 150     1803878205 1678057588 1715367000 1799170285 180022 SRX24807386 SRS21522258 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32514 32514 SRR29290254 SRX24807385 SRS21522257 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     15 days experimental group parallel 1 liver transcriptome L2 1   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 08|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 14|experiment description:Exposed to 120 or above tire wear particles for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L2 1 L2 1 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TLFA6-7L.R1.fq.gz TLFA6-7L.R2.fq.gz fastq fastq 6109509300.0 20365031.0 TLFA6 7L.R1.fq.gz 0:150 1:150 A:1525902154;C:1507317327;G:1549698641;T:1526193716;N:397462 150 150     1525902154 1507317327 1549698641 1526193716 397462 SRX24807385 SRS21522257 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32515 32515 SRR29290255 SRX24807384 SRS21522256 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     30 days experimental group parallel 3 liver transcriptome L7 3   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 25|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 13|experiment description:Exposed to tire wear particles 40 60 mesh excretion for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L7 3 L7 3 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TSSC-5L.R1.fq.gz TSSC-5L.R2.fq.gz fastq fastq 6846271200.0 22820904.0 TSSC 5L.R1.fq.gz 0:150 1:150 A:1704275603;C:1639794530;G:1792628691;T:1709317043;N:255333 150 150     1704275603 1639794530 1792628691 1709317043 255333 SRX24807384 SRS21522256 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32516 32516 SRR29290256 SRX24807383 SRS21522255 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     Control parallel 3 liver transcriptome L1 3   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 11|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 13|experiment description:Sample from control group|BioSampleModel:Model organism or animal                 Zebrafish liver L1 3 L1 3 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     FCFC1-3L.R1.fq.gz FCFC1-3L.R2.fq.gz fastq fastq 6360438000.0 21201460.0 FCFC1 3L.R1.fq.gz 0:150 1:150 A:1591177652;C:1544470038;G:1615057708;T:1609485267;N:247335 150 150     1591177652 1544470038 1615057708 1609485267 247335 SRX24807383 SRS21522255 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32517 32517 SRR29290257 SRX24807382 SRS21522254 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     30 days experimental group parallel 2 liver transcriptome L7 2   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 25|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 12|experiment description:Exposed to tire wear particles 40 60 mesh excretion for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L7 2 L7 2 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TSSB-3L.R1.fq.gz TSSB-3L.R2.fq.gz fastq fastq 6285285600.0 20950952.0 TSSB 3L.R1.fq.gz 0:150 1:150 A:1584093051;C:1516123512;G:1599998121;T:1584824364;N:246552 150 150     1584093051 1516123512 1599998121 1584824364 246552 SRX24807382 SRS21522254 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32518 32518 SRR29290258 SRX24807381 SRS21522253 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     30 days experimental group parallel 1 liver transcriptome L7 1   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 25|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 11|experiment description:Exposed to tire wear particles 40 60 mesh excretion for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L7 1 L7 1 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TSSA-1L.R1.fq.gz TSSA-1L.R2.fq.gz fastq fastq 6078740100.0 20262467.0 TSSA 1L.R1.fq.gz 0:150 1:150 A:1530149533;C:1486474895;G:1528868563;T:1533006599;N:240510 150 150     1530149533 1486474895 1528868563 1533006599 240510 SRX24807381 SRS21522253 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32519 32519 SRR29290259 SRX24807380 SRS21522252 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     15 days experimental group parallel 3 liver transcriptome L6 3   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 10|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 16|experiment description:Exposure to 40 60 mesh tire wear particles for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L6 3 L6 3 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TSFC1-3L.R1.fq.gz TSFC1-3L.R2.fq.gz fastq fastq 6857466600.0 22858222.0 TSFC1 3L.R1.fq.gz 0:150 1:150 A:1755136176;C:1642995302;G:1688825155;T:1770233592;N:276375 150 150     1755136176 1642995302 1688825155 1770233592 276375 SRX24807380 SRS21522252 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32520 32520 SRR29290260 SRX24807379 SRS21522251 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     15 days experimental group parallel 2 liver transcriptome L6 2   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 10|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 15|experiment description:Exposure to 40 60 mesh tire wear particles for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L6 2 L6 2 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TSFB1-3L.R1.fq.gz TSFB1-3L.R2.fq.gz fastq fastq 7250329800.0 24167766.0 TSFB1 3L.R1.fq.gz 0:150 1:150 A:1825803037;C:1766132142;G:1813762639;T:1844348502;N:283480 150 150     1825803037 1766132142 1813762639 1844348502 283480 SRX24807379 SRS21522251 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32521 32521 SRR29290261 SRX24807378 SRS21522250 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     15 days experimental group parallel 1 liver transcriptome L6 1   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 10|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 14|experiment description:Exposure to 40 60 mesh tire wear particles for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L6 1 L6 1 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TSFA1-3L.R1.fq.gz TSFA1-3L.R2.fq.gz fastq fastq 6257752800.0 20859176.0 TSFA1 3L.R1.fq.gz 0:150 1:150 A:1588621972;C:1490176001;G:1573465475;T:1605244426;N:244926 150 150     1588621972 1490176001 1573465475 1605244426 244926 SRX24807378 SRS21522250 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32522 32522 SRR29290262 SRX24807377 SRS21522249 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     30 days experimental group parallel 3 liver transcriptome L5 3   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 24|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 13|experiment description:Exposed to tire wear particles 80 100 mesh excretion for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L5 3 L5 3 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TMSC-5L.R1.fq.gz TMSC-5L.R2.fq.gz fastq fastq 6227549100.0 20758497.0 TMSC 5L.R1.fq.gz 0:150 1:150 A:1601663321;C:1467885504;G:1549957271;T:1607796578;N:246426 150 150     1601663321 1467885504 1549957271 1607796578 246426 SRX24807377 SRS21522249 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32523 32523 SRR29290263 SRX24807376 SRS21522248 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     30 days experimental group parallel 2 liver transcriptome L5 2   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 24|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 12|experiment description:Exposed to tire wear particles 80 100 mesh excretion for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L5 2 L5 2 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TMSB-3L.R1.fq.gz TMSB-3L.R2.fq.gz fastq fastq 5889087600.0 19630292.0 TMSB 3L.R1.fq.gz 0:150 1:150 A:1507527640;C:1395223794;G:1475557797;T:1510549619;N:228750 150 150     1507527640 1395223794 1475557797 1510549619 228750 SRX24807376 SRS21522248 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32524 32524 SRR29290264 SRX24807375 SRS21522247 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     30 days experimental group parallel 1 liver transcriptome L5 1   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 24|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 11|experiment description:Exposed to tire wear particles 80 100 mesh excretion for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L5 1 L5 1 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TMSA-1L.R1.fq.gz TMSA-1L.R2.fq.gz fastq fastq 6438780300.0 21462601.0 TMSA 1L.R1.fq.gz 0:150 1:150 A:1651115385;C:1542448300;G:1589631411;T:1655336061;N:249143 150 150     1651115385 1542448300 1589631411 1655336061 249143 SRX24807375 SRS21522247 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32525 32525 SRR29290265 SRX24807374 SRS21522246 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     15 days experimental group parallel 3 liver transcriptome L4 3   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 09|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 16|experiment description:Exposure to 80 100 mesh tire wear particles for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L4 3 L4 3 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TMFC1-3L.R1.fq.gz TMFC1-3L.R2.fq.gz fastq fastq 6083883300.0 20279611.0 TMFC1 3L.R1.fq.gz 0:150 1:150 A:1510698562;C:1511134044;G:1540128451;T:1521679717;N:242526 150 150     1510698562 1511134044 1540128451 1521679717 242526 SRX24807374 SRS21522246 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32526 32526 SRR29290266 SRX24807373 SRS21522245 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     15 days experimental group parallel 2 liver transcriptome L4 2   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 09|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 15|experiment description:Exposure to 80 100 mesh tire wear particles for 15 days|BioSampleModel:Model organism or animal                 Zebrafish liver L4 2 L4 2 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     TMFB1-3L.R1.fq.gz TMFB1-3L.R2.fq.gz fastq fastq 5908013700.0 19693379.0 TMFB1 3L.R1.fq.gz 0:150 1:150 A:1507137134;C:1415511620;G:1463261753;T:1521838130;N:265063 150 150     1507137134 1415511620 1463261753 1521838130 265063 SRX24807373 SRS21522245 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32527 32527 SRR29290267 SRX24807372 SRS21522244 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     Control parallel 2 liver transcriptome L1 2   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 11|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 12|experiment description:Sample from control group|BioSampleModel:Model organism or animal                 Zebrafish liver L1 2 L1 2 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     FCFB1-3L.R1.fq.gz FCFB1-3L.R2.fq.gz fastq fastq 6637856700.0 22126189.0 FCFB1 3L.R1.fq.gz 0:150 1:150 A:1714779556;C:1575842801;G:1628771136;T:1718209685;N:253522 150 150     1714779556 1575842801 1628771136 1718209685 253522 SRX24807372 SRS21522244 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32528 32528 SRR29290268 SRX24807371 SRS21522243 SRP511901 PRJNA1120203 Study of liver transcriptome in zebrafish May 29 '24 PRJNA1120203 Other Liver of the transcriptome data from zebrafish exposed to small car tire wear particles     Control parallel 1 liver transcriptome L1 1   strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 11|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 11|experiment description:Sample from control group|BioSampleModel:Model organism or animal                 Zebrafish liver L1 1 L1 1 Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.     OTHER METATRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP511901     FCFA1-3L.R1.fq.gz FCFA1-3L.R2.fq.gz fastq fastq 7360809900.0 24536033.0 FCFA1 3L.R1.fq.gz 0:150 1:150 A:1885247052;C:1777296186;G:1818891778;T:1879185198;N:189686 150 150     1885247052 1777296186 1818891778 1879185198 189686 SRX24807371 SRS21522243 SRA1889615 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-05 Adult Adult Liver Liver and Biliary System
32695 32695 SRR29406579 SRX24920076 SRS21625737 SRP513845 PRJNA1123436 Transcriptome analysis of liver tissue of zebrafish PRJNA1123436 Other We studied transcriptomic changes in the liver of zebrafish exposed to a certain concentration of tire wear particles.     Large particle sizes were exposed to the first parallel group for xxx days 4 1L LTFA 1L   isolate:zebrafish|breed:Wild type|age:3 months|collection date:2023 10 28|geo loc name:China:Qingdao|sex:missing|tissue:liver|isolation source:not applicable|lat lon:not collected|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNA Seq in Danio rerio: adult liver LTFA 1L LTFA 1L normal RNA Seq nodules     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513845     LTFA-1L.R1.fq.gz LTFA-1L.R2.fq.gz fastq fastq 7055070900.0 23516903.0 LTFA 1L.R1.fq.gz 0:150 1:150 A:1807337916;C:1674299371;G:1741443458;T:1831719305;N:270850 150 150     1807337916 1674299371 1741443458 1831719305 270850 SRX24920076 SRS21625737 SRA1897556 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology 2 0.91757 0.91901 0.05066 0.05102 0.77171 0.77374 0.48939 0.495 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-06-13 Adult Adult Liver Liver and Biliary System
32696 32696 SRR29406580 SRX24920075 SRS21625738 SRP513845 PRJNA1123436 Transcriptome analysis of liver tissue of zebrafish PRJNA1123436 Other We studied transcriptomic changes in the liver of zebrafish exposed to a certain concentration of tire wear particles.     A third parallel group with medium particle size was exposed for 15 days 3 5L MTFC 5L   isolate:zebrafish|breed:Wild type|age:3 months|collection date:2023 10 26|geo loc name:China:Qingdao|sex:missing|tissue:liver|isolation source:not applicable|lat lon:not collected|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 RNA Seq in Danio rerio: adult liver MTFC 5L MTFC 5L normal RNA Seq nodules     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513845     MTFC-5L.R1.fq.gz MTFC-5L.R2.fq.gz fastq fastq 5884371600.0 19614572.0 MTFC 5L.R1.fq.gz 0:150 1:150 A:1511226389;C:1383833941;G:1480444885;T:1508613837;N:252548 150 150     1511226389 1383833941 1480444885 1508613837 252548 SRX24920075 SRS21625738 SRA1897556 Qingdao University of Science and technology|College of marine science and biological engineeri Qingdao University of Science and technology 2 0.87714 0.87949 0.01411 0.0137 0.86198 0.86285 0.19648 0.19651 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-06-13 Adult Adult Liver Liver and Biliary 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");;