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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,DRR162520,DRX153139,DRS083200,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 2 mpf zebrafish replicate5,SAMD00152468,,sample name:l02 5|age:2 month|biological replicate:5|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152468,DRX153139,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152468,,,,1264817800.0,6324089.0,DRR162520,0:100 1:100,A:351295111;C:280181229;G:281044764;T:352232836;N:63860,100,100,,,351295111,280181229,281044764,352232836,63860,DRX153139,DRS083200,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.93687,0.93419,0.07774,0.07776,0.7587,0.7609,0.56082,0.56748,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Liver,Liver and Biliary System
222,DRR162519,DRX153138,DRS083199,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 2 mpf zebrafish replicate4,SAMD00152467,,sample name:l02 4|age:2 month|biological replicate:4|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152467,DRX153138,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152467,,,,1762366200.0,8811831.0,DRR162519,0:100 1:100,A:481999545;C:397566169;G:399183135;T:483526493;N:90858,100,100,,,481999545,397566169,399183135,483526493,90858,DRX153138,DRS083199,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.93994,0.93528,0.06039,0.05936,0.75037,0.75394,0.52945,0.52961,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Liver,Liver and Biliary System
223,DRR162518,DRX153137,DRS083198,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 2 mpf zebrafish replicate3,SAMD00152466,,sample name:l02 3|age:2 month|biological replicate:3|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152466,DRX153137,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152466,,,,1464434200.0,7322171.0,DRR162518,0:100 1:100,A:400972247;C:330316514;G:329635959;T:403435022;N:74458,100,100,,,400972247,330316514,329635959,403435022,74458,DRX153137,DRS083198,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.94169,0.93517,0.075,0.07408,0.78541,0.78796,0.56483,0.56426,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Liver,Liver and Biliary System
224,DRR162517,DRX153136,DRS083197,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 2 mpf zebrafish replicate2,SAMD00152465,,sample name:l02 2|age:2 month|biological replicate:2|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152465,DRX153136,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152465,,,,1953667000.0,9768335.0,DRR162517,0:100 1:100,A:525411621;C:450279523;G:450410879;T:527464993;N:99984,100,100,,,525411621,450279523,450410879,527464993,99984,DRX153136,DRS083197,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.94424,0.93692,0.06451,0.06582,0.78358,0.79557,0.56036,0.57581,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Liver,Liver and Biliary System
225,DRR162516,DRX153135,DRS083196,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 2 mpf zebrafish replicate1,SAMD00152464,,sample name:l02 1|age:2 month|biological replicate:1|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152464,DRX153135,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152464,,,,1541676600.0,7708383.0,DRR162516,0:100 1:100,A:414776600;C:354650822;G:357258514;T:414910092;N:80572,100,100,,,414776600,354650822,357258514,414910092,80572,DRX153135,DRS083196,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.94346,0.93048,0.06888,0.06759,0.79086,0.79452,0.56037,0.55727,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Liver,Liver and Biliary System
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,SRR26078877,SRX21793726,SRS18895468,SRP461206,PRJNA1018104,Global liver transcriptome assay of WT  Igfbp7 null mutant and Igfbp7 LOE animals,PRJNA1018104,Other,The global increased expression of Insulin like growth factor binding protein 7 IGFBP7 has been detected in non alcoholic fatty liver disease NAFLD patients  however  its roles in NAFLD and the mechanism remain largely unclear. The goal of this study is to investigate the effect and mechanism of Igfbp7 using a zebrafish NAFLD model. The igfbp7 /  null zebrafish mutant and the Igfbp7 liver overexpressed LOE transgenic zebrafish based on Gal4/UAS system were generated by CRISPR/Cas9 and Tol2 transgenic technique  respectively. The zebrafish NAFLD models in wildtypes  igfbp7 /  mutants and Igfbp7 LOE fishes have been established by high fat diet feeding. The Igfbp7 dynamic expression and its effects on NAFLD progression have been detected and analyzed in both human NAFLD patients and zebrafish models. And the potential mechanism has been investigated through transcriptome analysis and subsequent detection and verification.,,,,wild type 1,WT replicate 1,,strain:wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 mpf|dev stage:adult|collection date:2021 10 09|geo loc name:China:Shanxi|sex:male|tissue:Liver|biomaterial provider:Zebrafish Facility of the Institute of Biomedical Sciences  Shanxi University|birth date:09 Jun 2021|birth location:China:Shanxi|breeding history:Fishes were fed 4 times per day with a high fat diet|breeding method:a high fat diet  in which 5% cholesterol was added to the standard diet feed type:Marvbeni C1  corresponding to 40 mg/fish/day|replicate:WT replicate=biological replicate1|BioSampleModel:Model organism or animal,,,,,,,,,wild type 1,WT1,WT1,wild type 1,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP461206,,,WT1_1.fq.gz WT1_2.fq.gz,fastq fastq,7170532200.0,23901774.0,WT1 1.fq.gz,0:150 1:150,A:1931584106;C:1658793663;G:1662799956;T:1917012316;N:342159,150,150,,,1931584106,1658793663,1662799956,1917012316,342159,SRX21793726,SRS18895468,SRA1713671,First Hospital of Shanxi Medical University|Department of Gastroenterology and Hepatology,First Hospital of Shanxi Medical University,2,0.93456,0.93372,0.06482,0.06467,0.77327,0.77266,0.52308,0.53023,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-09-16,Adult,Adult,Liver,Liver and Biliary System
28496,SRR26321412,SRX22029502,SRS19102283,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 1,R27,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R27,R27,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R27.fastq,fastq,23400.0,312.0,R27.fastq,0:75,A:7949;C:4612;G:4730;T:6100;N:9,75,,,,7949,4612,4730,6100,9,SRX22029502,SRS19102283,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.89642,,0.06772,,0.99827,,0.75,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28497,SRR26321413,SRX22029501,SRS19102284,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,1dpci 4,R22,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R22,R22,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R22.fastq,fastq,23400.0,312.0,R22.fastq,0:75,A:7470;C:4460;G:5063;T:6404;N:3,75,,,,7470,4460,5063,6404,3,SRX22029501,SRS19102284,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87073,,0.12167,,0.99801,,0.73157,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28498,SRR26321414,SRX22029500,SRS19102281,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,R21,R21,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R21,R21,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R21.fastq,fastq,23400.0,312.0,R21.fastq,0:75,A:7540;C:4349;G:4857;T:6646;N:8,75,,,,7540,4349,4857,6646,8,SRX22029500,SRS19102281,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.8839,,0.04494,,0.99768,,0.72769,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28499,SRR26321415,SRX22029499,SRS19102282,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,1dpci 2,R18,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R18,R18,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R18.fastq,fastq,23400.0,312.0,R18.fastq,0:75,A:7380;C:4430;G:5069;T:6518;N:3,75,,,,7380,4430,5069,6518,3,SRX22029499,SRS19102282,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87259,,0.11196,,0.99784,,0.69791,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28500,SRR26321416,SRX22029498,SRS19102280,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,1dpci 1,R17,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R17,R17,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R17.fastq,fastq,23400.0,312.0,R17.fastq,0:75,A:7322;C:4455;G:5111;T:6507;N:5,75,,,,7322,4455,5111,6507,5,SRX22029498,SRS19102280,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.90439,,0.12749,,0.99813,,0.71052,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28501,SRR26321417,SRX22029497,SRS19102279,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 5,R1,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R1,R1,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R1.fastq,fastq,23400.0,312.0,R1.fastq,0:75,A:7934;C:4560;G:4922;T:5980;N:4,75,,,,7934,4560,4922,5980,4,SRX22029497,SRS19102279,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87045,,0.10526,,0.99805,,0.71978,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28502,SRR26321418,SRX22029496,SRS19102277,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 4,R64,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R64,R64,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R64.fastq,fastq,23400.0,312.0,R64.fastq,0:75,A:7844;C:4626;G:4804;T:6126;N:0,75,,,,7844,4626,4804,6126,0,SRX22029496,SRS19102277,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.90119,,0.07509,,0.99839,,0.8,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28503,SRR26321419,SRX22029495,SRS19102278,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 3,R61,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R61,R61,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R61.fastq,fastq,23400.0,312.0,R61.fastq,0:75,A:7454;C:4556;G:4960;T:6425;N:5,75,,,,7454,4556,4960,6425,5,SRX22029495,SRS19102278,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.89098,,0.06015,,0.99813,,0.77102,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28504,SRR26321420,SRX22029494,SRS19102276,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,7dpci 4,30,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,30,30,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,30.fastq,fastq,23400.0,312.0,30.fastq,0:75,A:7732;C:4528;G:5150;T:5987;N:3,75,,,,7732,4528,5150,5987,3,SRX22029494,SRS19102276,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.88447,,0.13147,,0.99772,,0.71584,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28505,SRR26321421,SRX22029493,SRS19102275,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,R11,R11,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,R11,R11,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R11.fastq,fastq,23400.0,312.0,R11.fastq,0:75,A:7818;C:4507;G:5107;T:5956;N:12,75,,,,7818,4507,5107,5956,12,SRX22029493,SRS19102275,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.89345,,0.11475,,0.99847,,0.82258,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28506,SRR26321422,SRX22029492,SRS19102274,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,7dpci 2,31,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,31,31,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,31.fastq,fastq,23400.0,312.0,31.fastq,0:75,A:7470;C:4619;G:4802;T:6504;N:5,75,,,,7470,4619,4802,6504,5,SRX22029492,SRS19102274,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87699,,0.11111,,0.99829,,0.78918,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28507,SRR26321423,SRX22029491,SRS19102273,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,7dpci 1,R9,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,R9,R9,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R9.fastq,fastq,23400.0,312.0,R9.fastq,0:75,A:8130;C:4537;G:4809;T:5917;N:7,75,,,,8130,4537,4809,5917,7,SRX22029491,SRS19102273,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.83588,,0.05725,,0.99801,,0.68586,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28508,SRR26321424,SRX22029490,SRS19102272,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 4,R33,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R33,R33,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R33.fastq,fastq,23400.0,312.0,R33.fastq,0:75,A:7745;C:4421;G:4867;T:6360;N:7,75,,,,7745,4421,4867,6360,7,SRX22029490,SRS19102272,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87259,,0.07335,,0.99805,,0.71428,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28509,SRR26321425,SRX22029489,SRS19102271,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 3,R31,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R31,R31,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R31.fastq,fastq,23400.0,312.0,R31.fastq,0:75,A:7441;C:4483;G:5163;T:6313;N:0,75,,,,7441,4483,5163,6313,0,SRX22029489,SRS19102271,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.9,,0.05925,,0.9977,,0.68325,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28510,SRR26321426,SRX22029488,SRS19102270,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 2,R29,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R29,R29,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R29.fastq,fastq,23400.0,312.0,R29.fastq,0:75,A:7379;C:4698;G:5166;T:6156;N:1,75,,,,7379,4698,5166,6156,1,SRX22029488,SRS19102270,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.91016,,0.05859,,0.99797,,0.74528,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28511,SRR26321427,SRX22029487,SRS19102269,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 2,R62,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R62,R62,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R62.fastq,fastq,23400.0,312.0,R62.fastq,0:75,A:7383;C:4566;G:4713;T:6728;N:10,75,,,,7383,4566,4713,6728,10,SRX22029487,SRS19102269,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.91571,,0.05363,,0.99835,,0.77674,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28512,SRR26321428,SRX22029486,SRS19102268,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,Replicate 1 for SHAM,SHAM 1,R63,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia: Melbourne|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R63,R63,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R63.fastq,fastq,23400.0,312.0,R63.fastq,0:75,A:7516;C:4606;G:4765;T:6508;N:5,75,,,,7516,4606,4765,6508,5,SRX22029486,SRS19102268,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.90385,,0.0423,,0.99805,,0.72429,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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