RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

1,487 rows where technology = "unknown", tissue_curation = "Liver" and tissue_curation_coarse = "Liver and Biliary System"

✎ View and edit SQL

This data as json, CSV (advanced)

experiment.library_selection 10

devstage_curation 7

experiment.platform 6

devstage_curation_coarse 6

experiment.library_strategy 4

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Liver and Biliary System · 1,487 ✖

tissue_curation 1

  • Liver · 1,487 ✖

technology 1

  • unknown · 1,487 ✖
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
171 171 DRR075399 DRX069313 DRS075494 DRP004473 PRJDB5226 Effects of local gut tumor on whole organismal gene expressions in zebrafish DRP004473 Other How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.     The liver of control fish 7dpf Control liver SAMD00065413   sample name:3 control liver 150701 Hiseq3A l3 019|tissue type:Liver                 Illumina HiSeq 2500 sequencing of SAMD00065413 DRX069313 Control liver 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004473 Illumina HiSeq 2500 sequencing of SAMD00065413       951579036.0 26432751.0 DRR075399 0:36 A:231570583;C:228182815;G:227223430;T:264569214;N:32994 36       231570583 228182815 227223430 264569214 32994 DRX069313 DRS075494 DRA005199 ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International 1 0.8903   0.08667   0.7236   0.51557   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2018-09-19 Larval Larval Liver Liver and Biliary System
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
221 221 DRR162520 DRX153139 DRS083200 DRP004696 PRJDB7713 Age associated transcriptome analysis in 5 tissues of zebrafish DRP004696 Transcriptome Analysis We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.       liver sample from 2 mpf zebrafish replicate5 SAMD00152468   sample name:l02 5|age:2 month|biological replicate:5|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152468 DRX153139 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152468       1264817800.0 6324089.0 DRR162520 0:100 1:100 A:351295111;C:280181229;G:281044764;T:352232836;N:63860 100 100     351295111 280181229 281044764 352232836 63860 DRX153139 DRS083200 DRA007711 UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo 2 0.93687 0.93419 0.07774 0.07776 0.7587 0.7609 0.56082 0.56748 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Juvenile Juvenile Liver Liver and Biliary System
222 222 DRR162519 DRX153138 DRS083199 DRP004696 PRJDB7713 Age associated transcriptome analysis in 5 tissues of zebrafish DRP004696 Transcriptome Analysis We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.       liver sample from 2 mpf zebrafish replicate4 SAMD00152467   sample name:l02 4|age:2 month|biological replicate:4|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152467 DRX153138 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152467       1762366200.0 8811831.0 DRR162519 0:100 1:100 A:481999545;C:397566169;G:399183135;T:483526493;N:90858 100 100     481999545 397566169 399183135 483526493 90858 DRX153138 DRS083199 DRA007711 UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo 2 0.93994 0.93528 0.06039 0.05936 0.75037 0.75394 0.52945 0.52961 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Juvenile Juvenile Liver Liver and Biliary System
223 223 DRR162518 DRX153137 DRS083198 DRP004696 PRJDB7713 Age associated transcriptome analysis in 5 tissues of zebrafish DRP004696 Transcriptome Analysis We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.       liver sample from 2 mpf zebrafish replicate3 SAMD00152466   sample name:l02 3|age:2 month|biological replicate:3|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152466 DRX153137 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152466       1464434200.0 7322171.0 DRR162518 0:100 1:100 A:400972247;C:330316514;G:329635959;T:403435022;N:74458 100 100     400972247 330316514 329635959 403435022 74458 DRX153137 DRS083198 DRA007711 UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo 2 0.94169 0.93517 0.075 0.07408 0.78541 0.78796 0.56483 0.56426 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Juvenile Juvenile Liver Liver and Biliary System
224 224 DRR162517 DRX153136 DRS083197 DRP004696 PRJDB7713 Age associated transcriptome analysis in 5 tissues of zebrafish DRP004696 Transcriptome Analysis We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.       liver sample from 2 mpf zebrafish replicate2 SAMD00152465   sample name:l02 2|age:2 month|biological replicate:2|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152465 DRX153136 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152465       1953667000.0 9768335.0 DRR162517 0:100 1:100 A:525411621;C:450279523;G:450410879;T:527464993;N:99984 100 100     525411621 450279523 450410879 527464993 99984 DRX153136 DRS083197 DRA007711 UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo 2 0.94424 0.93692 0.06451 0.06582 0.78358 0.79557 0.56036 0.57581 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Juvenile Juvenile Liver Liver and Biliary System
225 225 DRR162516 DRX153135 DRS083196 DRP004696 PRJDB7713 Age associated transcriptome analysis in 5 tissues of zebrafish DRP004696 Transcriptome Analysis We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.       liver sample from 2 mpf zebrafish replicate1 SAMD00152464   sample name:l02 1|age:2 month|biological replicate:1|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152464 DRX153135 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152464       1541676600.0 7708383.0 DRR162516 0:100 1:100 A:414776600;C:354650822;G:357258514;T:414910092;N:80572 100 100     414776600 354650822 357258514 414910092 80572 DRX153135 DRS083196 DRA007711 UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo 2 0.94346 0.93048 0.06888 0.06759 0.79086 0.79452 0.56037 0.55727 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Juvenile Juvenile Liver Liver and Biliary System
280 280 DRR161311 DRX151936 DRS095335 DRP005084 PRJDB7735 Gene expression profile in adult zebrafish liver DRP005084 Transcriptome Analysis Increasing use of zebrafish in toxicological researches requires knowledge on gene expression profile in liver that play a major role in xenobiotic metabolism. Our research provide a basal gene expression profile in adult zebrafish liver.       Transcriptome of female Danio rerio liver SAMD00153247   sample name:transcriptome zebrafish female|sex:female|strain:RIKEN WT|tissue:liver                 NextSeq 500 paired end sequencing of SAMD00153247 DRX151936 f 1 1   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP005084 NextSeq 500 paired end sequencing of SAMD00153247       2338564937.0 15498367.0 DRR161311 0:75.45 1:75.44 A:613899755;C:541756858;G:548366901;T:633083422;N:1458001 75 75     613899755 541756858 548366901 633083422 1458001 DRX151936 DRS095335 DRA007652 OBICHIKU|Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine 2 0.95814 0.96362 0.05394 0.04517 0.77932 0.7834 0.37385 0.37264 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Japan 2019-05-20 Undetermined Adult Liver Liver and Biliary System
281 281 DRR161310 DRX151935 DRS095334 DRP005084 PRJDB7735 Gene expression profile in adult zebrafish liver DRP005084 Transcriptome Analysis Increasing use of zebrafish in toxicological researches requires knowledge on gene expression profile in liver that play a major role in xenobiotic metabolism. Our research provide a basal gene expression profile in adult zebrafish liver.       Transcriptome of male Danio rerio liver SAMD00153246   sample name:transcriptome zebrafish male|sex:male|strain:RIKEN WT|tissue:liver                 NextSeq 500 paired end sequencing of SAMD00153246 DRX151935 m 1 1   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP005084 NextSeq 500 paired end sequencing of SAMD00153246       2506978527.0 16611154.0 DRR161310 0:75.48 1:75.44 A:672321355;C:568289588;G:569411670;T:695545626;N:1410288 75 75     672321355 568289588 569411670 695545626 1410288 DRX151935 DRS095334 DRA007652 OBICHIKU|Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine 2 0.94746 0.95115 0.07899 0.06363 0.80837 0.8115 0.52008 0.58743 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Japan 2019-05-20 Undetermined Adult Liver Liver and Biliary System
8104 8104 ERR2455366 ERX2474426 ERS2327331 ERP107743 PRJEB25789 RNA seq of zebrafish larvae fed with different diets E-MTAB-6636 Transcriptome Analysis We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29   Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Sample 4 SAMEA104725948 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725948|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 4|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:overfeeding|organism part:liver|sample name:E MTAB 6636:Sample 4|scientific name:Danio rerio                 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets E MTAB 6636:Sample 4 s Sample 4 s RNA seq of zebrafish larvae fed with different diets Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Experimental Factor: diet:overfeeding RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   ERP107743 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 OF-4_H7MWNALXX_L6_1.fq.gz fastq 4961276550.0 33075177.0 E MTAB 6636:Sample 4 0:150 1:0 A:1349413168;C:1135314970;G:1137935563;T:1338034716;N:578133 150 0     1349413168 1135314970 1137935563 1338034716 578133 ERX2474426 ERS2327331 ERA1259907 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive 1 0.90787   0.11999   0.66123   0.49072   150   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2018-03-29 Larval Larval Liver Liver and Biliary System
8105 8105 ERR2455365 ERX2474425 ERS2327330 ERP107743 PRJEB25789 RNA seq of zebrafish larvae fed with different diets E-MTAB-6636 Transcriptome Analysis We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29   Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Sample 3 SAMEA104725947 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725947|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:fructose|organism part:liver|sample name:E MTAB 6636:Sample 3|scientific name:Danio rerio                 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets E MTAB 6636:Sample 3 s Sample 3 s RNA seq of zebrafish larvae fed with different diets Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Experimental Factor: diet:fructose RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   ERP107743 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 Fru-3_H7MWNALXX_L5_1.fq.gz fastq 5858273250.0 39055155.0 E MTAB 6636:Sample 3 0:150 1:0 A:1580150663;C:1353221682;G:1355865524;T:1568428138;N:607243 150 0     1580150663 1353221682 1355865524 1568428138 607243 ERX2474425 ERS2327330 ERA1259907 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive 1 0.91505   0.11036   0.65985   0.48443   150   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2018-03-29 Larval Larval Liver Liver and Biliary System
8106 8106 ERR2455364 ERX2474424 ERS2327329 ERP107743 PRJEB25789 RNA seq of zebrafish larvae fed with different diets E-MTAB-6636 Transcriptome Analysis We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29   Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Sample 2 SAMEA104725946 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725946|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:cholesterol|organism part:liver|sample name:E MTAB 6636:Sample 2|scientific name:Danio rerio                 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets E MTAB 6636:Sample 2 s Sample 2 s RNA seq of zebrafish larvae fed with different diets Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Experimental Factor: diet:cholesterol RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   ERP107743 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 Cho-2_H7MWNALXX_L5_1.fq.gz fastq 5636304900.0 37575366.0 E MTAB 6636:Sample 2 0:150 1:0 A:1526862069;C:1295343770;G:1298751994;T:1514766898;N:580169 150 0     1526862069 1295343770 1298751994 1514766898 580169 ERX2474424 ERS2327329 ERA1259907 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive 1 0.91032   0.11644   0.66649   0.47766   150   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2018-03-29 Larval Larval Liver Liver and Biliary System
8107 8107 ERR2455363 ERX2474423 ERS2327328 ERP107743 PRJEB25789 RNA seq of zebrafish larvae fed with different diets E-MTAB-6636 Transcriptome Analysis We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29   Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Sample 1 SAMEA104725945 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725945|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:control|organism part:liver|sample name:E MTAB 6636:Sample 1|scientific name:Danio rerio                 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets E MTAB 6636:Sample 1 s Sample 1 s RNA seq of zebrafish larvae fed with different diets Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Experimental Factor: diet:control RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   ERP107743 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 ND-1_H7MWNALXX_L5_1.fq.gz fastq 5197165350.0 34647769.0 E MTAB 6636:Sample 1 0:150 1:0 A:1430911816;C:1174811274;G:1175616551;T:1415284019;N:541690 150 0     1430911816 1174811274 1175616551 1415284019 541690 ERX2474423 ERS2327328 ERA1259907 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive 1 0.89838   0.13883   0.66129   0.48467   150   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2018-03-29 Larval Larval 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
19471 19471 ERR14031296 ERX13434262 ERS22545283 ERP166767 PRJEB83101 Fish tales of fatty liver A transcriptomic approach to understanding NAFLD inda-STUDY-IIITD-2024-11-18 13:55:50.21-189 Other Background: Non alcoholic fatty liver disease is a significant global health concern affecting millions and characterized by its complexity as a multifaceted disease. Despite its prevalence the underlying molecular mechanisms remain poorly understood. Methods: Here we propose a novel diet induced zebrafish model to investigate NAFLD. We validate this model through a series of histological examinations and molecular assessments allowing us to explore the intricate pathways involved in the disease. We employ transcriptomic analysis to identify novel players associated with NAFLD progression. Results: Our findings demonstrate that zebrafish subjected to a high fat diet exhibit weight gain while Oil Red O staining confirms significant fat deposition in the liver. Quantitative PCR analysis reveals increased expression of lipogenic genes such as acc fasn hmgcs1 hmgcra alongside markers of endoplasmic reticulum stress such as atf6 xbp1 gadd45a ddit3 and mitochondrial unfolded protein response genes such as hspd1 hspa9 clpp lonp1 indicating mitochondrial dysfunction which includes increased expression of genes encoding oxphos complexes uqcrc2 cox4i1 atp5f1b. Transcriptomic profiling uncovers novel markers such as inha gck ces2a id3 and dysregulated pathways related to metabolism insulin signaling and cellular stress responses. Conclusions: This study successfully establishes a zebrafish model that replicates key features of NAFLD including histopathological changes and metabolic dysregulation. The validation of our model allows for a deeper exploration of the molecular landscape of NAFLD. By revealing novel biomarkers and pathways through transcriptomic analysis our research opens new avenues for understanding the pathogenesis of NAFLD and potential therapeutic targets. ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05   RNA Seq Control Replicate 1 Control Replicate 1 SAMEA117477679 Kusuma School of Biological Sciences (KSBS),IIT-Delhi;Department of Computational Biology,IIITD;IISER-Bhopal;Centre for Integrative Genomics,Genopode, University of Lausanne, Lausanne 1015, Switzerland ENA first public:2024 12 05|INSDC center name:Kusuma School of Biological Sciences KSBS IIT Delhi;Department of Computational Biology IIITD;IISER Bhopal;Centre for Integrative Genomics Genopode University of Lausanne Lausanne 1015 Switzerland|INSDC status:public|Submitter Id:SAMIN0009305 Control Replicate 1|broker name:IBDC|collection date:2023 04 18|common name:zebrafish|geographic location country and/or sea:India|sample name:SAMIN0009305 Control Replicate 1|scientific name:Danio rerio                 Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9483 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166767 Illumina HiSeq X paired end sequencing; Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05 19069_Control_14_R1.fastq.gz 19070_Control_14_R2.fastq.gz fastq fastq 10004171894.0 33126397.0 RUN Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9483 0:151 1:151 A:2747978244;C:2173369585;G:2355012585;T:2716465615;N:11345865 151 151     2747978244 2173369585 2355012585 2716465615 11345865 ERX13434262 ERS22545283 ERA31000109 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-05 Undetermined Undetermined Liver Liver and Biliary System
19472 19472 ERR14031290 ERX13434256 ERS22545281 ERP166767 PRJEB83101 Fish tales of fatty liver A transcriptomic approach to understanding NAFLD inda-STUDY-IIITD-2024-11-18 13:55:50.21-189 Other Background: Non alcoholic fatty liver disease is a significant global health concern affecting millions and characterized by its complexity as a multifaceted disease. Despite its prevalence the underlying molecular mechanisms remain poorly understood. Methods: Here we propose a novel diet induced zebrafish model to investigate NAFLD. We validate this model through a series of histological examinations and molecular assessments allowing us to explore the intricate pathways involved in the disease. We employ transcriptomic analysis to identify novel players associated with NAFLD progression. Results: Our findings demonstrate that zebrafish subjected to a high fat diet exhibit weight gain while Oil Red O staining confirms significant fat deposition in the liver. Quantitative PCR analysis reveals increased expression of lipogenic genes such as acc fasn hmgcs1 hmgcra alongside markers of endoplasmic reticulum stress such as atf6 xbp1 gadd45a ddit3 and mitochondrial unfolded protein response genes such as hspd1 hspa9 clpp lonp1 indicating mitochondrial dysfunction which includes increased expression of genes encoding oxphos complexes uqcrc2 cox4i1 atp5f1b. Transcriptomic profiling uncovers novel markers such as inha gck ces2a id3 and dysregulated pathways related to metabolism insulin signaling and cellular stress responses. Conclusions: This study successfully establishes a zebrafish model that replicates key features of NAFLD including histopathological changes and metabolic dysregulation. The validation of our model allows for a deeper exploration of the molecular landscape of NAFLD. By revealing novel biomarkers and pathways through transcriptomic analysis our research opens new avenues for understanding the pathogenesis of NAFLD and potential therapeutic targets. ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05   RNA Seq Control Replicate 2 Control Replicate 2 SAMEA117477677 Kusuma School of Biological Sciences (KSBS),IIT-Delhi;Department of Computational Biology,IIITD;IISER-Bhopal;Centre for Integrative Genomics,Genopode, University of Lausanne, Lausanne 1015, Switzerland ENA first public:2024 12 05|INSDC center name:Kusuma School of Biological Sciences KSBS IIT Delhi;Department of Computational Biology IIITD;IISER Bhopal;Centre for Integrative Genomics Genopode University of Lausanne Lausanne 1015 Switzerland|INSDC status:public|Submitter Id:SAMIN0009306 Control Replicate 2|broker name:IBDC|collection date:2023 04 18|common name:zebrafish|geographic location country and/or sea:India|sample name:SAMIN0009306 Control Replicate 2|scientific name:Danio rerio                 Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9484 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166767 Illumina HiSeq X paired end sequencing; Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05 19071_Control_9_R1.fastq.gz 19072_Control_9_R2.fastq.gz fastq fastq 11659155450.0 38606475.0 RUN Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9484 0:151 1:151 A:3197012061;C:2522601146;G:2753110022;T:3173195478;N:13236743 151 151     3197012061 2522601146 2753110022 3173195478 13236743 ERX13434256 ERS22545281 ERA31000093 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-05 Undetermined Undetermined Liver Liver and Biliary System
19473 19473 ERR14031295 ERX13434261 ERS22545292 ERP166767 PRJEB83101 Fish tales of fatty liver A transcriptomic approach to understanding NAFLD inda-STUDY-IIITD-2024-11-18 13:55:50.21-189 Other Background: Non alcoholic fatty liver disease is a significant global health concern affecting millions and characterized by its complexity as a multifaceted disease. Despite its prevalence the underlying molecular mechanisms remain poorly understood. Methods: Here we propose a novel diet induced zebrafish model to investigate NAFLD. We validate this model through a series of histological examinations and molecular assessments allowing us to explore the intricate pathways involved in the disease. We employ transcriptomic analysis to identify novel players associated with NAFLD progression. Results: Our findings demonstrate that zebrafish subjected to a high fat diet exhibit weight gain while Oil Red O staining confirms significant fat deposition in the liver. Quantitative PCR analysis reveals increased expression of lipogenic genes such as acc fasn hmgcs1 hmgcra alongside markers of endoplasmic reticulum stress such as atf6 xbp1 gadd45a ddit3 and mitochondrial unfolded protein response genes such as hspd1 hspa9 clpp lonp1 indicating mitochondrial dysfunction which includes increased expression of genes encoding oxphos complexes uqcrc2 cox4i1 atp5f1b. Transcriptomic profiling uncovers novel markers such as inha gck ces2a id3 and dysregulated pathways related to metabolism insulin signaling and cellular stress responses. Conclusions: This study successfully establishes a zebrafish model that replicates key features of NAFLD including histopathological changes and metabolic dysregulation. The validation of our model allows for a deeper exploration of the molecular landscape of NAFLD. By revealing novel biomarkers and pathways through transcriptomic analysis our research opens new avenues for understanding the pathogenesis of NAFLD and potential therapeutic targets. ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05   RNA Seq NAFLD Replicate 2 NAFLD Replicate 2 SAMEA117477688 Kusuma School of Biological Sciences (KSBS),IIT-Delhi;Department of Computational Biology,IIITD;IISER-Bhopal;Centre for Integrative Genomics,Genopode, University of Lausanne, Lausanne 1015, Switzerland ENA first public:2024 12 05|INSDC center name:Kusuma School of Biological Sciences KSBS IIT Delhi;Department of Computational Biology IIITD;IISER Bhopal;Centre for Integrative Genomics Genopode University of Lausanne Lausanne 1015 Switzerland|INSDC status:public|Submitter Id:SAMIN0009308 NAFLD Replicate 2|broker name:IBDC|collection date:2023 04 18|common name:zebrafish|geographic location country and/or sea:India|sample name:SAMIN0009308 NAFLD Replicate 2|scientific name:Danio rerio                 Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9486 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166767 Illumina HiSeq X paired end sequencing; Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05 19075_NAFLD_8_R1.fastq.gz 19076_NAFLD_8_R2.fastq.gz fastq fastq 11001354150.0 36428325.0 RUN Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9486 0:151 1:151 A:3036945132;C:2390487588;G:2547341716;T:3014093258;N:12486456 151 151     3036945132 2390487588 2547341716 3014093258 12486456 ERX13434261 ERS22545292 ERA31000106 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-05 Undetermined Undetermined Liver Liver and Biliary System
19474 19474 ERR14031298 ERX13434264 ERS22545288 ERP166767 PRJEB83101 Fish tales of fatty liver A transcriptomic approach to understanding NAFLD inda-STUDY-IIITD-2024-11-18 13:55:50.21-189 Other Background: Non alcoholic fatty liver disease is a significant global health concern affecting millions and characterized by its complexity as a multifaceted disease. Despite its prevalence the underlying molecular mechanisms remain poorly understood. Methods: Here we propose a novel diet induced zebrafish model to investigate NAFLD. We validate this model through a series of histological examinations and molecular assessments allowing us to explore the intricate pathways involved in the disease. We employ transcriptomic analysis to identify novel players associated with NAFLD progression. Results: Our findings demonstrate that zebrafish subjected to a high fat diet exhibit weight gain while Oil Red O staining confirms significant fat deposition in the liver. Quantitative PCR analysis reveals increased expression of lipogenic genes such as acc fasn hmgcs1 hmgcra alongside markers of endoplasmic reticulum stress such as atf6 xbp1 gadd45a ddit3 and mitochondrial unfolded protein response genes such as hspd1 hspa9 clpp lonp1 indicating mitochondrial dysfunction which includes increased expression of genes encoding oxphos complexes uqcrc2 cox4i1 atp5f1b. Transcriptomic profiling uncovers novel markers such as inha gck ces2a id3 and dysregulated pathways related to metabolism insulin signaling and cellular stress responses. Conclusions: This study successfully establishes a zebrafish model that replicates key features of NAFLD including histopathological changes and metabolic dysregulation. The validation of our model allows for a deeper exploration of the molecular landscape of NAFLD. By revealing novel biomarkers and pathways through transcriptomic analysis our research opens new avenues for understanding the pathogenesis of NAFLD and potential therapeutic targets. ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05   RNA Seq NAFLD Replicate 3 NAFLD Replicate 3 SAMEA117477684 Kusuma School of Biological Sciences (KSBS),IIT-Delhi;Department of Computational Biology,IIITD;IISER-Bhopal;Centre for Integrative Genomics,Genopode, University of Lausanne, Lausanne 1015, Switzerland ENA first public:2024 12 05|INSDC center name:Kusuma School of Biological Sciences KSBS IIT Delhi;Department of Computational Biology IIITD;IISER Bhopal;Centre for Integrative Genomics Genopode University of Lausanne Lausanne 1015 Switzerland|INSDC status:public|Submitter Id:SAMIN0009309 NAFLD Replicate 3|broker name:IBDC|collection date:2023 04 18|common name:zebrafish|geographic location country and/or sea:India|sample name:SAMIN0009309 NAFLD Replicate 3|scientific name:Danio rerio                 Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9487 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166767 Illumina HiSeq X paired end sequencing; Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05 19077_NAFLD_9_R1.fastq.gz 19078_NAFLD_9_R2.fastq.gz fastq fastq 10367145694.0 34328297.0 RUN Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9487 0:151 1:151 A:2861355932;C:2257080818;G:2411788871;T:2828044975;N:8875098 151 151     2861355932 2257080818 2411788871 2828044975 8875098 ERX13434264 ERS22545288 ERA31000114 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-05 Undetermined Undetermined Liver Liver and Biliary System
19475 19475 ERR14031292 ERX13434258 ERS22545282 ERP166767 PRJEB83101 Fish tales of fatty liver A transcriptomic approach to understanding NAFLD inda-STUDY-IIITD-2024-11-18 13:55:50.21-189 Other Background: Non alcoholic fatty liver disease is a significant global health concern affecting millions and characterized by its complexity as a multifaceted disease. Despite its prevalence the underlying molecular mechanisms remain poorly understood. Methods: Here we propose a novel diet induced zebrafish model to investigate NAFLD. We validate this model through a series of histological examinations and molecular assessments allowing us to explore the intricate pathways involved in the disease. We employ transcriptomic analysis to identify novel players associated with NAFLD progression. Results: Our findings demonstrate that zebrafish subjected to a high fat diet exhibit weight gain while Oil Red O staining confirms significant fat deposition in the liver. Quantitative PCR analysis reveals increased expression of lipogenic genes such as acc fasn hmgcs1 hmgcra alongside markers of endoplasmic reticulum stress such as atf6 xbp1 gadd45a ddit3 and mitochondrial unfolded protein response genes such as hspd1 hspa9 clpp lonp1 indicating mitochondrial dysfunction which includes increased expression of genes encoding oxphos complexes uqcrc2 cox4i1 atp5f1b. Transcriptomic profiling uncovers novel markers such as inha gck ces2a id3 and dysregulated pathways related to metabolism insulin signaling and cellular stress responses. Conclusions: This study successfully establishes a zebrafish model that replicates key features of NAFLD including histopathological changes and metabolic dysregulation. The validation of our model allows for a deeper exploration of the molecular landscape of NAFLD. By revealing novel biomarkers and pathways through transcriptomic analysis our research opens new avenues for understanding the pathogenesis of NAFLD and potential therapeutic targets. ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05   RNA Seq NAFLD Replicate 1 NAFLD Replicate 1 SAMEA117477678 Kusuma School of Biological Sciences (KSBS),IIT-Delhi;Department of Computational Biology,IIITD;IISER-Bhopal;Centre for Integrative Genomics,Genopode, University of Lausanne, Lausanne 1015, Switzerland ENA first public:2024 12 05|INSDC center name:Kusuma School of Biological Sciences KSBS IIT Delhi;Department of Computational Biology IIITD;IISER Bhopal;Centre for Integrative Genomics Genopode University of Lausanne Lausanne 1015 Switzerland|INSDC status:public|Submitter Id:SAMIN0009307 NAFLD Replicate 1|broker name:IBDC|collection date:2023 04 18|common name:zebrafish|geographic location country and/or sea:India|sample name:SAMIN0009307 NAFLD Replicate 1|scientific name:Danio rerio                 Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9485 1 1 NaN   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP166767 Illumina HiSeq X paired end sequencing; Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05 19073_NAFLD_11_R1.fastq.gz 19074_NAFLD_11_R2.fastq.gz fastq fastq 11885531932.0 39356066.0 RUN Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9485 0:151 1:151 A:3208478929;C:2671086650;G:2843156238;T:3153091073;N:9719042 151 151     3208478929 2671086650 2843156238 3153091073 9719042 ERX13434258 ERS22545282 ERA31000101 Indian Biological Data Centre|European Nucleotide Archive Indian Biological Data Centre                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   India 2024-12-05 Undetermined Undetermined 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
28955 28955 SRR26862014 SRX22556964 SRS19565505 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   atf4a / ;atf4b / ;sec31anju221 7dpf liver rep3 GSM7905882   source name:liver|tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing atf4a / ;atf4b / ;sec31anju221 7dpf liver rep3 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905882 GSM7905882: atf4a / ;atf4b / ;sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq GSM7905882 r1 GSM7905882 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     atf4a_atf4b_sec31a_7dpf_liver_3_R1.fastq.gz atf4a_atf4b_sec31a_7dpf_liver_3_R2.fastq.gz fastq fastq 5909169300.0 19697231.0 GSM7905882 r1 0:150 1:150 A:1814217313;C:1062889607;G:1281434828;T:1750535462;N:92090 150 150     1814217313 1062889607 1281434828 1750535462 92090 SRX22556964 SRS19565505 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.76999 0.77426 0.42801 0.42392 0.8016 0.80275 0.54736 0.56955 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28956 28956 SRR26862015 SRX22556963 SRS19565504 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   atf4a / ;atf4b / ;sec31anju221 7dpf liver rep2 GSM7905881   source name:liver|tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing atf4a / ;atf4b / ;sec31anju221 7dpf liver rep2 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905881 GSM7905881: atf4a / ;atf4b / ;sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq GSM7905881 r1 GSM7905881 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     atf4a_atf4b_sec31a_7dpf_liver_2_R2.fastq.gz atf4a_atf4b_sec31a_7dpf_liver_2_R1.fastq.gz fastq fastq 5909169300.0 19697231.0 GSM7905881 r1 0:150 1:150 A:1814304871;C:1062851267;G:1281344920;T:1750575670;N:92572 150 150     1814304871 1062851267 1281344920 1750575670 92572 SRX22556963 SRS19565504 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.77 0.77338 0.42787 0.42319 0.80137 0.80314 0.56997 0.57195 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28957 28957 SRR26862016 SRX22556962 SRS19565503 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   atf4a / ;atf4b / ;sec31anju221 7dpf liver rep1 GSM7905880   source name:liver|tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing atf4a / ;atf4b / ;sec31anju221 7dpf liver rep1 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905880 GSM7905880: atf4a / ;atf4b / ;sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq GSM7905880 r1 GSM7905880 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     atf4a_atf4b_sec31a_7dpf_liver_1_R1.fastq.gz atf4a_atf4b_sec31a_7dpf_liver_1_R2.fastq.gz fastq fastq 5909169600.0 19697232.0 GSM7905880 r1 0:150 1:150 A:1814273460;C:1062781687;G:1281372048;T:1750650699;N:91706 150 150     1814273460 1062781687 1281372048 1750650699 91706 SRX22556962 SRS19565503 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.76973 0.77461 0.42583 0.42416 0.80154 0.80501 0.56619 0.57103 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28958 28958 SRR26862017 SRX22556961 SRS19565502 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   atf6 / ;sec31anju221 7dpf liver rep3 GSM7905879   source name:liver|tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing atf6 / ;sec31anju221 7dpf liver rep3 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905879 GSM7905879: atf6 / ;sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq GSM7905879 r1 GSM7905879 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     atf6_sec31a_7dpf_liver_3_R1.fastq.gz atf6_sec31a_7dpf_liver_3_R2.fastq.gz fastq fastq 5861267700.0 19537559.0 GSM7905879 r1 0:150 1:150 A:1784341701;C:1072473445;G:1285100764;T:1719260200;N:91590 150 150     1784341701 1072473445 1285100764 1719260200 91590 SRX22556961 SRS19565502 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.75325 0.76151 0.45725 0.45689 0.78798 0.78922 0.56218 0.56438 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28959 28959 SRR26862018 SRX22556960 SRS19565501 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   atf6 / ;sec31anju221 7dpf liver rep2 GSM7905878   source name:liver|tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing atf6 / ;sec31anju221 7dpf liver rep2 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905878 GSM7905878: atf6 / ;sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq GSM7905878 r1 GSM7905878 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     atf6_sec31a_7dpf_liver_2_R1.fastq.gz atf6_sec31a_7dpf_liver_2_R2.fastq.gz fastq fastq 5861267700.0 19537559.0 GSM7905878 r1 0:150 1:150 A:1784326758;C:1072428588;G:1285145147;T:1719275142;N:92065 150 150     1784326758 1072428588 1285145147 1719275142 92065 SRX22556960 SRS19565501 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.75399 0.76366 0.46023 0.46101 0.79153 0.79243 0.56082 0.56109 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28960 28960 SRR26862019 SRX22556959 SRS19565500 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   atf6 / ;sec31anju221 7dpf liver rep1 GSM7905877   source name:liver|tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing atf6 / ;sec31anju221 7dpf liver rep1 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905877 GSM7905877: atf6 / ;sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq GSM7905877 r1 GSM7905877 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     atf6_sec31a_7dpf_liver_1_R1.fastq.gz atf6_sec31a_7dpf_liver_1_R2.fastq.gz fastq fastq 5861267700.0 19537559.0 GSM7905877 r1 0:150 1:150 A:1784239507;C:1072424839;G:1285216751;T:1719294746;N:91857 150 150     1784239507 1072424839 1285216751 1719294746 91857 SRX22556959 SRS19565500 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.75279 0.76268 0.45792 0.46002 0.79251 0.79482 0.55778 0.55965 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28961 28961 SRR26862020 SRX22556958 SRS19565499 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   srebf2 / ;sec31anju221 7dpf liver rep3 GSM7905876   source name:liver|tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing srebf2 / ;sec31anju221 7dpf liver rep3 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905876 GSM7905876: srebf2 / ;sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq GSM7905876 r1 GSM7905876 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     srebf2_sec31a_7dpf_liver_3_R2.fastq.gz srebf2_sec31a_7dpf_liver_3_R1.fastq.gz fastq fastq 5510352000.0 18367840.0 GSM7905876 r1 0:150 1:150 A:1627756472;C:1023474678;G:1300851324;T:1558184587;N:84939 150 150     1627756472 1023474678 1300851324 1558184587 84939 SRX22556958 SRS19565499 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.80994 0.82412 0.13867 0.1397 0.84264 0.84228 0.58499 0.58509 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28962 28962 SRR26862021 SRX22556957 SRS19565498 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   srebf2 / ;sec31anju221 7dpf liver rep2 GSM7905875   source name:liver|tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing srebf2 / ;sec31anju221 7dpf liver rep2 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905875 GSM7905875: srebf2 / ;sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq GSM7905875 r1 GSM7905875 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     srebf2_sec31a_7dpf_liver_2_R1.fastq.gz srebf2_sec31a_7dpf_liver_2_R2.fastq.gz fastq fastq 5510352000.0 18367840.0 GSM7905875 r1 0:150 1:150 A:1627771682;C:1023494582;G:1300898781;T:1558101507;N:85448 150 150     1627771682 1023494582 1300898781 1558101507 85448 SRX22556957 SRS19565498 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.81036 0.82384 0.14055 0.13973 0.84151 0.84145 0.58974 0.57294 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28963 28963 SRR26862022 SRX22556956 SRS19565497 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   srebf2 / ;sec31anju221 7dpf liver rep1 GSM7905874   source name:liver|tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing srebf2 / ;sec31anju221 7dpf liver rep1 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905874 GSM7905874: srebf2 / ;sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq GSM7905874 r1 GSM7905874 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     srebf2_sec31a_7dpf_liver_1_R1.fastq.gz srebf2_sec31a_7dpf_liver_1_R2.fastq.gz fastq fastq 5510352300.0 18367841.0 GSM7905874 r1 0:150 1:150 A:1627704384;C:1023445689;G:1301022904;T:1558092507;N:86816 150 150     1627704384 1023445689 1301022904 1558092507 86816 SRX22556956 SRS19565497 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.81137 0.82447 0.13931 0.13977 0.84104 0.84129 0.58031 0.57864 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28964 28964 SRR26862023 SRX22556955 SRS19565496 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   srebf1 / ;sec31anju221 7dpf liver rep3 GSM7905873   source name:liver|tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing srebf1 / ;sec31anju221 7dpf liver rep3 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905873 GSM7905873: srebf1 / ;sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq GSM7905873 r1 GSM7905873 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     srebf1_sec31a_7dpf_liver_3_R1.fastq.gz srebf1_sec31a_7dpf_liver_3_R2.fastq.gz fastq fastq 6400097700.0 21333659.0 GSM7905873 r1 0:150 1:150 A:1899190871;C:1190525037;G:1467138729;T:1843142069;N:100994 150 150     1899190871 1190525037 1467138729 1843142069 100994 SRX22556955 SRS19565496 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.81425 0.82461 0.21108 0.21197 0.82221 0.82323 0.56957 0.594 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28965 28965 SRR26862024 SRX22556954 SRS19565495 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   srebf1 / ;sec31anju221 7dpf liver rep2 GSM7905872   source name:liver|tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing srebf1 / ;sec31anju221 7dpf liver rep2 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905872 GSM7905872: srebf1 / ;sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq GSM7905872 r1 GSM7905872 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     srebf1_sec31a_7dpf_liver_2_R1.fastq.gz srebf1_sec31a_7dpf_liver_2_R2.fastq.gz fastq fastq 6400098000.0 21333660.0 GSM7905872 r1 0:150 1:150 A:1898994954;C:1190735681;G:1467311615;T:1842955236;N:100514 150 150     1898994954 1190735681 1467311615 1842955236 100514 SRX22556954 SRS19565495 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.81439 0.82458 0.20976 0.20983 0.82252 0.82278 0.57027 0.58785 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28966 28966 SRR26862025 SRX22556953 SRS19565494 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   srebf1 / ;sec31anju221 7dpf liver rep1 GSM7905871   source name:liver|tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing srebf1 / ;sec31anju221 7dpf liver rep1 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905871 GSM7905871: srebf1 / ;sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq GSM7905871 r1 GSM7905871 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     srebf1_sec31a_7dpf_liver_1_R1.fastq.gz srebf1_sec31a_7dpf_liver_1_R2.fastq.gz fastq fastq 6400098000.0 21333660.0 GSM7905871 r1 0:150 1:150 A:1899112598;C:1190526850;G:1467278074;T:1843080128;N:100350 150 150     1899112598 1190526850 1467278074 1843080128 100350 SRX22556953 SRS19565494 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.81419 0.82464 0.20997 0.21061 0.82317 0.82296 0.57794 0.57323 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28967 28967 SRR26862026 SRX22556952 SRS19565493 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   xbp1 / ;sec31anju221 7dpf liver rep3 GSM7905870   source name:liver|tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing xbp1 / ;sec31anju221 7dpf liver rep3 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905870 GSM7905870: xbp1 / ;sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq GSM7905870 r1 GSM7905870 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     xbp1_sec31a_7dpf_liver_3_R1.fastq.gz xbp1_sec31a_7dpf_liver_3_R2.fastq.gz fastq fastq 6187152600.0 20623842.0 GSM7905870 r1 0:150 1:150 A:1877363692;C:1115080777;G:1381299595;T:1812977195;N:431341 150 150     1877363692 1115080777 1381299595 1812977195 431341 SRX22556952 SRS19565493 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.76954 0.76951 0.43867 0.43143 0.77993 0.78291 0.54133 0.5381 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28968 28968 SRR26862027 SRX22556951 SRS19565492 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   xbp1 / ;sec31anju221 7dpf liver rep2 GSM7905869   source name:liver|tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing xbp1 / ;sec31anju221 7dpf liver rep2 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905869 GSM7905869: xbp1 / ;sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq GSM7905869 r1 GSM7905869 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     xbp1_sec31a_7dpf_liver_2_R1.fastq.gz xbp1_sec31a_7dpf_liver_2_R2.fastq.gz fastq fastq 6187152600.0 20623842.0 GSM7905869 r1 0:150 1:150 A:1877413505;C:1115113811;G:1381185230;T:1813009192;N:430862 150 150     1877413505 1115113811 1381185230 1813009192 430862 SRX22556951 SRS19565492 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.77052 0.77186 0.4375 0.43158 0.77857 0.78376 0.54778 0.54495 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28969 28969 SRR26862028 SRX22556950 SRS19565491 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   xbp1 / ;sec31anju221 7dpf liver rep1 GSM7905868   source name:liver|tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing xbp1 / ;sec31anju221 7dpf liver rep1 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905868 GSM7905868: xbp1 / ;sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq GSM7905868 r1 GSM7905868 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     xbp1_sec31a_7dpf_liver_1_R1.fastq.gz xbp1_sec31a_7dpf_liver_1_R2.fastq.gz fastq fastq 6187152900.0 20623843.0 GSM7905868 r1 0:150 1:150 A:1877304250;C:1115136591;G:1381366555;T:1812912124;N:433380 150 150     1877304250 1115136591 1381366555 1812912124 433380 SRX22556950 SRS19565491 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.77014 0.76961 0.43869 0.43265 0.77863 0.78293 0.54465 0.54127 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28970 28970 SRR26862029 SRX22556949 SRS19565490 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   sec31anju221 7dpf liver rep3 GSM7905867   source name:liver|tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing sec31anju221 7dpf liver rep3 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905867 GSM7905867: sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq GSM7905867 r1 GSM7905867 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     sec31a_7dpf_liver_3_R1.fastq.gz sec31a_7dpf_liver_3_R2.fastq.gz fastq fastq 7290483000.0 24301610.0 GSM7905867 r1 0:150 1:150 A:2201443580;C:1310250352;G:1667114316;T:2111120776;N:553976 150 150     2201443580 1310250352 1667114316 2111120776 553976 SRX22556949 SRS19565490 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.80458 0.80677 0.27528 0.27217 0.8228 0.82507 0.58018 0.57745 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28971 28971 SRR26862030 SRX22556948 SRS19565489 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   sec31anju221 7dpf liver rep2 GSM7905866   source name:liver|tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing sec31anju221 7dpf liver rep2 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905866 GSM7905866: sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq GSM7905866 r1 GSM7905866 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     sec31a_7dpf_liver_2_R1.fastq.gz sec31a_7dpf_liver_2_R2.fastq.gz fastq fastq 7290483300.0 24301611.0 GSM7905866 r1 0:150 1:150 A:2201546187;C:1310316929;G:1666786006;T:2111279666;N:554512 150 150     2201546187 1310316929 1666786006 2111279666 554512 SRX22556948 SRS19565489 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.80528 0.80845 0.27376 0.27196 0.82286 0.82451 0.58075 0.57876 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28972 28972 SRR26862031 SRX22556947 SRS19565488 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   sec31anju221 7dpf liver rep1 GSM7905865   source name:liver|tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing sec31anju221 7dpf liver rep1 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin GSM7905865 GSM7905865: sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq GSM7905865 r1 GSM7905865 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     sec31a_7dpf_liver_1_R2.fastq.gz sec31a_7dpf_liver_1_R1.fastq.gz fastq fastq 7290483300.0 24301611.0 GSM7905865 r1 0:150 1:150 A:2201492232;C:1310255361;G:1666931918;T:2111261791;N:541998 150 150     2201492232 1310255361 1666931918 2111261791 541998 SRX22556947 SRS19565488 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.80672 0.80946 0.27449 0.27121 0.82026 0.82238 0.58542 0.58114 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28973 28973 SRR26862032 SRX22556946 SRS19565487 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   WT 7dpf liver rep3 GSM7905864   source name:liver|tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing WT 7dpf liver rep3 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin GSM7905864 GSM7905864: WT 7dpf liver rep3; Danio rerio; RNA Seq GSM7905864 r1 GSM7905864 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     ctrl_7dpf_liver_3_R1.fastq.gz ctrl_7dpf_liver_3_R2.fastq.gz fastq fastq 6492651600.0 21642172.0 GSM7905864 r1 0:150 1:150 A:1911454132;C:1210565181;G:1559325152;T:1810846037;N:461098 150 150     1911454132 1210565181 1559325152 1810846037 461098 SRX22556946 SRS19565487 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.83482 0.84576 0.18949 0.18912 0.84853 0.84914 0.67518 0.67721 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28974 28974 SRR26862033 SRX22556945 SRS19565486 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   WT 7dpf liver rep2 GSM7905863   source name:liver|tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing WT 7dpf liver rep2 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin GSM7905863 GSM7905863: WT 7dpf liver rep2; Danio rerio; RNA Seq GSM7905863 r1 GSM7905863 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     ctrl_7dpf_liver_2_R1.fastq.gz ctrl_7dpf_liver_2_R2.fastq.gz fastq fastq 6492651600.0 21642172.0 GSM7905863 r1 0:150 1:150 A:1911298884;C:1210698281;G:1559339763;T:1810859879;N:454793 150 150     1911298884 1210698281 1559339763 1810859879 454793 SRX22556945 SRS19565486 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.83478 0.84217 0.19106 0.18909 0.84642 0.84717 0.67888 0.67654 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval Liver Liver and Biliary System
28975 28975 SRR26862034 SRX22556944 SRS19565485 SRP472550 PRJNA1041773 Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing GSE248098 Transcriptome Analysis We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.   pubmed:39139065   WT 7dpf liver rep1 GSM7905862   source name:liver|tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing WT 7dpf liver rep1 Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample liver   At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin GSM7905862 GSM7905862: WT 7dpf liver rep1; Danio rerio; RNA Seq GSM7905862 r1 GSM7905862 1 At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP472550     ctrl_7dpf_liver_1_R1.fastq.gz ctrl_7dpf_liver_1_R2.fastq.gz fastq fastq 6492651600.0 21642172.0 GSM7905862 r1 0:150 1:150 A:1911338464;C:1210670533;G:1559401753;T:1810786876;N:453974 150 150     1911338464 1210670533 1559401753 1810786876 453974 SRX22556944 SRS19565485 SRA1753371 Xin Lou Lab, Medical School, Nanjing University Xin Lou Lab, Medical School, Nanjing University 2 0.83368 0.84388 0.18806 0.18877 0.84713 0.84932 0.67925 0.67975 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-11-17 Larval Larval 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
29816 29816 SRR27496346 SRX23167489 SRS20117077 SRP483191 PRJNA1063616 Protection from starvation induced liver atrophy. GSE252997 Transcriptome Analysis Starvation causes the accumulation of lipid droplets in the liver a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover cavefish are resistant to liver atrophy during starvation providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish surface fish and cavefish we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall our study identifies a conserved druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment no exogenous food was added. At 6 dpf the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.   pubmed:38467419   Liver 6dpf DMSO rep1 GSM8012203   source name:Liver|tissue:Liver|genotype:AB|treatment:DMSO|geo loc name:missing|collection date:missing Liver 6dpf DMSO rep1 Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome and counted using FeatureCounts. For normalization differential gene expression analysis and GO analysis iDEP version 0.951 was utilized with default parameters. For differential gene expression a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples. Liver Lipofermata or DMSO treatment for 48 hours For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture’s instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode. Zebrafish larvae at 6 dpf. tissue:Liver|genotype:AB|treatment:DMSO GSM8012203 GSM8012203: Liver 6dpf DMSO rep1; Danio rerio; RNA Seq GSM8012203 r1 GSM8012203 1 For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483191   loader:fastq load.py DMSO_1_R1.fastq.gz DMSO_1_R2.fastq.gz fastq fastq 3947938488.0 13072644.0 GSM8012203 r1 0:151 1:151 A:1068152483;C:899059502;G:921482728;T:1059209932;N:33843 151 151     1068152483 899059502 921482728 1059209932 33843 SRX23167489 SRS20117077 SRA1784007 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   Belgium 2024-01-11 Larval Larval Liver Liver and Biliary System
29817 29817 SRR27496347 SRX23167488 SRS20117076 SRP483191 PRJNA1063616 Protection from starvation induced liver atrophy. GSE252997 Transcriptome Analysis Starvation causes the accumulation of lipid droplets in the liver a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover cavefish are resistant to liver atrophy during starvation providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish surface fish and cavefish we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall our study identifies a conserved druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment no exogenous food was added. At 6 dpf the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.   pubmed:38467419   Liver 6dpf Lipofermata rep2 GSM8012206   source name:Liver|tissue:Liver|genotype:AB|treatment:Lipofermata|geo loc name:missing|collection date:missing Liver 6dpf Lipofermata rep2 Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome and counted using FeatureCounts. For normalization differential gene expression analysis and GO analysis iDEP version 0.951 was utilized with default parameters. For differential gene expression a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples. Liver Lipofermata or DMSO treatment for 48 hours For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture’s instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode. Zebrafish larvae at 6 dpf. tissue:Liver|genotype:AB|treatment:Lipofermata GSM8012206 GSM8012206: Liver 6dpf Lipofermata rep2; Danio rerio; RNA Seq GSM8012206 r1 GSM8012206 1 For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483191   loader:fastq load.py Lipofermata_2_R1.fastq.gz Lipofermata_2_R2.fastq.gz fastq fastq 3365739868.0 11144834.0 GSM8012206 r1 0:151 1:151 A:904693218;C:775639535;G:792394997;T:892981123;N:30995 151 151     904693218 775639535 792394997 892981123 30995 SRX23167488 SRS20117076 SRA1784007 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   Belgium 2024-01-11 Larval Larval Liver Liver and Biliary System
29818 29818 SRR27496348 SRX23167487 SRS20117075 SRP483191 PRJNA1063616 Protection from starvation induced liver atrophy. GSE252997 Transcriptome Analysis Starvation causes the accumulation of lipid droplets in the liver a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover cavefish are resistant to liver atrophy during starvation providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish surface fish and cavefish we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall our study identifies a conserved druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment no exogenous food was added. At 6 dpf the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.   pubmed:38467419   Liver 6dpf Lipofermata rep1 GSM8012205   source name:Liver|tissue:Liver|genotype:AB|treatment:Lipofermata|geo loc name:missing|collection date:missing Liver 6dpf Lipofermata rep1 Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome and counted using FeatureCounts. For normalization differential gene expression analysis and GO analysis iDEP version 0.951 was utilized with default parameters. For differential gene expression a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples. Liver Lipofermata or DMSO treatment for 48 hours For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture’s instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode. Zebrafish larvae at 6 dpf. tissue:Liver|genotype:AB|treatment:Lipofermata GSM8012205 GSM8012205: Liver 6dpf Lipofermata rep1; Danio rerio; RNA Seq GSM8012205 r1 GSM8012205 1 For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483191   loader:fastq load.py Lipofermata_1_R1.fastq.gz Lipofermata_1_R2.fastq.gz fastq fastq 3645146040.0 12070020.0 GSM8012205 r1 0:151 1:151 A:981366033;C:836975744;G:858564002;T:968208667;N:31594 151 151     981366033 836975744 858564002 968208667 31594 SRX23167487 SRS20117075 SRA1784007 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   Belgium 2024-01-11 Larval Larval Liver Liver and Biliary System
29819 29819 SRR27496349 SRX23167486 SRS20117074 SRP483191 PRJNA1063616 Protection from starvation induced liver atrophy. GSE252997 Transcriptome Analysis Starvation causes the accumulation of lipid droplets in the liver a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover cavefish are resistant to liver atrophy during starvation providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish surface fish and cavefish we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall our study identifies a conserved druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment no exogenous food was added. At 6 dpf the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.   pubmed:38467419   Liver 6dpf DMSO rep2 GSM8012204   source name:Liver|tissue:Liver|genotype:AB|treatment:DMSO|geo loc name:missing|collection date:missing Liver 6dpf DMSO rep2 Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome and counted using FeatureCounts. For normalization differential gene expression analysis and GO analysis iDEP version 0.951 was utilized with default parameters. For differential gene expression a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples. Liver Lipofermata or DMSO treatment for 48 hours For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture’s instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode. Zebrafish larvae at 6 dpf. tissue:Liver|genotype:AB|treatment:DMSO GSM8012204 GSM8012204: Liver 6dpf DMSO rep2; Danio rerio; RNA Seq GSM8012204 r1 GSM8012204 1 For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483191   loader:fastq load.py DMSO_2_R1.fastq.gz DMSO_2_R2.fastq.gz fastq fastq 3062768334.0 10141617.0 GSM8012204 r1 0:151 1:151 A:815902447;C:711030547;G:726159250;T:809648102;N:27988 151 151     815902447 711030547 726159250 809648102 27988 SRX23167486 SRS20117074 SRA1784007 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   Belgium 2024-01-11 Larval Larval Liver Liver and Biliary System
30605 30605 SRR27885298 SRX23547062 SRS20394839 SRP488393 PRJNA1073712 Danio rerio Raw sequence reads PRJNA1073712 Whole Genome Sequencing normal RNAseq of Danio rerio         Treat3   breed:AB|dev stage:7 dpf|collection date:2022 01 06|geo loc name:China: Wuhan|sex:not determined|tissue:liver|replicate:replicate=treat biolobical replicate 3|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio t3 t3 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP488393     treat3_1.fq.gz treat3_2.fq.gz fastq fastq 11227897200.0 37426324.0 treat3 1.fq.gz 0:150 1:150 A:2841991870;C:2760705502;G:2843113319;T:2781984816;N:101693 150 150     2841991870 2760705502 2843113319 2781984816 101693 SRX23547062 SRS20394839 SRA1798310 Wuhan University|School of Basic Medical Sciences Wuhan University 2 0.9395 0.93765 0.03042 0.02991 0.75943 0.76282 0.52931 0.52802 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-02-06 Larval Larval Liver Liver and Biliary System
30606 30606 SRR27885299 SRX23547061 SRS20394838 SRP488393 PRJNA1073712 Danio rerio Raw sequence reads PRJNA1073712 Whole Genome Sequencing normal RNAseq of Danio rerio         Control3   breed:AB|dev stage:7 dpf|collection date:2022 01 06|geo loc name:China: Wuhan|sex:not determined|tissue:liver|replicate:replicate=control biolobical replicate 3|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio c3 c3 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP488393     control3_1.fq.gz control3_2.fq.gz fastq fastq 13204860600.0 44016202.0 control3 1.fq.gz 0:150 1:150 A:3362002161;C:3237033953;G:3340888463;T:3264815850;N:120173 150 150     3362002161 3237033953 3340888463 3264815850 120173 SRX23547061 SRS20394838 SRA1798310 Wuhan University|School of Basic Medical Sciences Wuhan University 2 0.94114 0.94099 0.03313 0.0336 0.7611 0.76562 0.52598 0.54255 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-02-06 Larval Larval Liver Liver and Biliary System
30607 30607 SRR27885300 SRX23547060 SRS20394837 SRP488393 PRJNA1073712 Danio rerio Raw sequence reads PRJNA1073712 Whole Genome Sequencing normal RNAseq of Danio rerio         Treat2   breed:AB|dev stage:7 dpf|collection date:2022 01 02|geo loc name:China: Wuhan|sex:not determined|tissue:liver|replicate:replicate=treat biolobical replicate 2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio t2 t2 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP488393     treat2_1.fq.gz treat2_2.fq.gz fastq fastq 13686972300.0 45623241.0 treat2 1.fq.gz 0:150 1:150 A:3497540140;C:3330959709;G:3473656510;T:3384780397;N:35544 150 150     3497540140 3330959709 3473656510 3384780397 35544 SRX23547060 SRS20394837 SRA1798310 Wuhan University|School of Basic Medical Sciences Wuhan University 2 0.94978 0.9476 0.02247 0.02209 0.77508 0.78104 0.5376 0.54975 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-02-06 Larval Larval Liver Liver and Biliary System
30608 30608 SRR27885301 SRX23547059 SRS20394836 SRP488393 PRJNA1073712 Danio rerio Raw sequence reads PRJNA1073712 Whole Genome Sequencing normal RNAseq of Danio rerio         Control2   breed:AB|dev stage:7 dpf|collection date:2022 01 02|geo loc name:China: Wuhan|sex:not determined|tissue:liver|replicate:replicate=control biolobical replicate 2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio c2 c2 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP488393     control2_1.fq.gz control2_2.fq.gz fastq fastq 13075274400.0 43584248.0 control2 1.fq.gz 0:150 1:150 A:3297304643;C:3196925316;G:3364735785;T:3216273784;N:34872 150 150     3297304643 3196925316 3364735785 3216273784 34872 SRX23547059 SRS20394836 SRA1798310 Wuhan University|School of Basic Medical Sciences Wuhan University 2 0.94539 0.94301 0.02162 0.02151 0.78358 0.78886 0.53728 0.52362 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-02-06 Larval Larval Liver Liver and Biliary System

Next page

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");;