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
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
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
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
29816,SRR27496346,SRX23167489,SRS20117077,SRP483191,PRJNA1063616,Protection from starvation induced liver atrophy.,GSE252997,Transcriptome Analysis,Starvation causes the accumulation of lipid droplets in the liver  a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding  hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here  we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation  the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover  cavefish are resistant to liver atrophy during starvation  providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish  surface fish  and cavefish  we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further  down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis  suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall  our study identifies a conserved  druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment  no exogenous food was added. At 6 dpf  the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.,,pubmed:38467419,,Liver 6dpf DMSO rep1,GSM8012203,,source name:Liver|tissue:Liver|genotype:AB|treatment:DMSO|geo loc name:missing|collection date:missing,Liver 6dpf DMSO rep1,Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome  and counted using FeatureCounts. For normalization  differential gene expression analysis  and GO analysis  iDEP version 0.951 was utilized with default parameters. For differential gene expression  a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples.,Liver,Lipofermata or DMSO treatment for 48 hours,For RNA Seq  mRNA was isolated from livers at 6 dpf. For this  livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega  Z6110. mRNA was isolated from the lysed tissue by following the manufacture’s instruction. cDNA synthesis  library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods  e.g. measurement of volume and quantity  gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology  using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation  post first strand synthesis  the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next  the sequencing adapters were ligated to the DNA fragments  and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.,Zebrafish larvae at 6 dpf.,tissue:Liver|genotype:AB|treatment:DMSO,GSM8012203,GSM8012203: Liver 6dpf DMSO rep1; Danio rerio; RNA Seq,GSM8012203 r1,GSM8012203,1,For RNA Seq  mRNA was isolated from livers at 6 dpf. For this  livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega  Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis  library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods  e.g. measurement of volume and quantity  gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology  using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation  post first strand synthesis  the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next  the sequencing adapters were ligated to the DNA fragments  and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483191,,loader:fastq load.py,DMSO_1_R1.fastq.gz DMSO_1_R2.fastq.gz,fastq fastq,3947938488.0,13072644.0,GSM8012203 r1,0:151 1:151,A:1068152483;C:899059502;G:921482728;T:1059209932;N:33843,151,151,,,1068152483,899059502,921482728,1059209932,33843,SRX23167489,SRS20117077,SRA1784007,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Belgium,2024-01-11,Larval,Larval,Liver,Liver and Biliary System
29817,SRR27496347,SRX23167488,SRS20117076,SRP483191,PRJNA1063616,Protection from starvation induced liver atrophy.,GSE252997,Transcriptome Analysis,Starvation causes the accumulation of lipid droplets in the liver  a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding  hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here  we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation  the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover  cavefish are resistant to liver atrophy during starvation  providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish  surface fish  and cavefish  we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further  down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis  suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall  our study identifies a conserved  druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment  no exogenous food was added. At 6 dpf  the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.,,pubmed:38467419,,Liver 6dpf Lipofermata rep2,GSM8012206,,source name:Liver|tissue:Liver|genotype:AB|treatment:Lipofermata|geo loc name:missing|collection date:missing,Liver 6dpf Lipofermata rep2,Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome  and counted using FeatureCounts. For normalization  differential gene expression analysis  and GO analysis  iDEP version 0.951 was utilized with default parameters. For differential gene expression  a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples.,Liver,Lipofermata or DMSO treatment for 48 hours,For RNA Seq  mRNA was isolated from livers at 6 dpf. For this  livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega  Z6110. mRNA was isolated from the lysed tissue by following the manufacture’s instruction. cDNA synthesis  library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods  e.g. measurement of volume and quantity  gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology  using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation  post first strand synthesis  the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next  the sequencing adapters were ligated to the DNA fragments  and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.,Zebrafish larvae at 6 dpf.,tissue:Liver|genotype:AB|treatment:Lipofermata,GSM8012206,GSM8012206: Liver 6dpf Lipofermata rep2; Danio rerio; RNA Seq,GSM8012206 r1,GSM8012206,1,For RNA Seq  mRNA was isolated from livers at 6 dpf. For this  livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega  Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis  library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods  e.g. measurement of volume and quantity  gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology  using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation  post first strand synthesis  the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next  the sequencing adapters were ligated to the DNA fragments  and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483191,,loader:fastq load.py,Lipofermata_2_R1.fastq.gz Lipofermata_2_R2.fastq.gz,fastq fastq,3365739868.0,11144834.0,GSM8012206 r1,0:151 1:151,A:904693218;C:775639535;G:792394997;T:892981123;N:30995,151,151,,,904693218,775639535,792394997,892981123,30995,SRX23167488,SRS20117076,SRA1784007,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Belgium,2024-01-11,Larval,Larval,Liver,Liver and Biliary System
29818,SRR27496348,SRX23167487,SRS20117075,SRP483191,PRJNA1063616,Protection from starvation induced liver atrophy.,GSE252997,Transcriptome Analysis,Starvation causes the accumulation of lipid droplets in the liver  a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding  hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here  we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation  the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover  cavefish are resistant to liver atrophy during starvation  providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish  surface fish  and cavefish  we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further  down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis  suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall  our study identifies a conserved  druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment  no exogenous food was added. At 6 dpf  the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.,,pubmed:38467419,,Liver 6dpf Lipofermata rep1,GSM8012205,,source name:Liver|tissue:Liver|genotype:AB|treatment:Lipofermata|geo loc name:missing|collection date:missing,Liver 6dpf Lipofermata rep1,Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome  and counted using FeatureCounts. For normalization  differential gene expression analysis  and GO analysis  iDEP version 0.951 was utilized with default parameters. For differential gene expression  a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples.,Liver,Lipofermata or DMSO treatment for 48 hours,For RNA Seq  mRNA was isolated from livers at 6 dpf. For this  livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega  Z6110. mRNA was isolated from the lysed tissue by following the manufacture’s instruction. cDNA synthesis  library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods  e.g. measurement of volume and quantity  gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology  using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation  post first strand synthesis  the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next  the sequencing adapters were ligated to the DNA fragments  and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.,Zebrafish larvae at 6 dpf.,tissue:Liver|genotype:AB|treatment:Lipofermata,GSM8012205,GSM8012205: Liver 6dpf Lipofermata rep1; Danio rerio; RNA Seq,GSM8012205 r1,GSM8012205,1,For RNA Seq  mRNA was isolated from livers at 6 dpf. For this  livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega  Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis  library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods  e.g. measurement of volume and quantity  gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology  using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation  post first strand synthesis  the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next  the sequencing adapters were ligated to the DNA fragments  and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483191,,loader:fastq load.py,Lipofermata_1_R1.fastq.gz Lipofermata_1_R2.fastq.gz,fastq fastq,3645146040.0,12070020.0,GSM8012205 r1,0:151 1:151,A:981366033;C:836975744;G:858564002;T:968208667;N:31594,151,151,,,981366033,836975744,858564002,968208667,31594,SRX23167487,SRS20117075,SRA1784007,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Belgium,2024-01-11,Larval,Larval,Liver,Liver and Biliary System
29819,SRR27496349,SRX23167486,SRS20117074,SRP483191,PRJNA1063616,Protection from starvation induced liver atrophy.,GSE252997,Transcriptome Analysis,Starvation causes the accumulation of lipid droplets in the liver  a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding  hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here  we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation  the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover  cavefish are resistant to liver atrophy during starvation  providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish  surface fish  and cavefish  we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further  down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis  suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall  our study identifies a conserved  druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment  no exogenous food was added. At 6 dpf  the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.,,pubmed:38467419,,Liver 6dpf DMSO rep2,GSM8012204,,source name:Liver|tissue:Liver|genotype:AB|treatment:DMSO|geo loc name:missing|collection date:missing,Liver 6dpf DMSO rep2,Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome  and counted using FeatureCounts. For normalization  differential gene expression analysis  and GO analysis  iDEP version 0.951 was utilized with default parameters. For differential gene expression  a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples.,Liver,Lipofermata or DMSO treatment for 48 hours,For RNA Seq  mRNA was isolated from livers at 6 dpf. For this  livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega  Z6110. mRNA was isolated from the lysed tissue by following the manufacture’s instruction. cDNA synthesis  library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods  e.g. measurement of volume and quantity  gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology  using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation  post first strand synthesis  the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next  the sequencing adapters were ligated to the DNA fragments  and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.,Zebrafish larvae at 6 dpf.,tissue:Liver|genotype:AB|treatment:DMSO,GSM8012204,GSM8012204: Liver 6dpf DMSO rep2; Danio rerio; RNA Seq,GSM8012204 r1,GSM8012204,1,For RNA Seq  mRNA was isolated from livers at 6 dpf. For this  livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega  Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis  library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods  e.g. measurement of volume and quantity  gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology  using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation  post first strand synthesis  the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next  the sequencing adapters were ligated to the DNA fragments  and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483191,,loader:fastq load.py,DMSO_2_R1.fastq.gz DMSO_2_R2.fastq.gz,fastq fastq,3062768334.0,10141617.0,GSM8012204 r1,0:151 1:151,A:815902447;C:711030547;G:726159250;T:809648102;N:27988,151,151,,,815902447,711030547,726159250,809648102,27988,SRX23167486,SRS20117074,SRA1784007,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Belgium,2024-01-11,Larval,Larval,Liver,Liver and Biliary System
34933,SRR32455887,SRX27770376,SRS24149655,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a6 R 1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with hexagingerol and RSL3|replicate:replicate=Biological Replicate 10|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with hexagingerol and RSL3,a6 R 1,a6 R 1,Zebrafish hepatocytes treated with hexagingerol and RSL3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100779-a6_R_1.R1.raw.fastq.gz L1EIG0100779-a6_R_1.R2.raw.fastq.gz,fastq fastq,6312642580.0,20902790.0,L1EIG0100779 a6 R 1.R1.raw.fastq.gz,0:151 1:151,A:1737087421;C:1412742895;G:1434786235;T:1727525167;N:500862,151,151,,,1737087421,1412742895,1434786235,1727525167,500862,SRX27770376,SRS24149655,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34934,SRR32455888,SRX27770375,SRS24149654,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a6 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with hexagingerol|replicate:replicate=Biological Replicate 9|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with hexagingerol,a6 3,a6 3,Zebrafish hepatocytes treated with hexagingerol,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100778-a6_3.R1.raw.fastq.gz L1EIG0100778-a6_3.R2.raw.fastq.gz,fastq fastq,7105238258.0,23527279.0,L1EIG0100778 a6 3.R1.raw.fastq.gz,0:151 1:151,A:1967054238;C:1576589056;G:1603457184;T:1957568817;N:568963,151,151,,,1967054238,1576589056,1603457184,1957568817,568963,SRX27770375,SRS24149654,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34935,SRR32455889,SRX27770374,SRS24149653,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a6 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with hexagingerol|replicate:replicate=Biological Replicate 8|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with hexagingerol,a6 2,a6 2,Zebrafish hepatocytes treated with hexagingerol,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100777-a6_2.R1.raw.fastq.gz L1EIG0100777-a6_2.R2.raw.fastq.gz,fastq fastq,6411725760.0,21230880.0,L1EIG0100777 a6 2.R1.raw.fastq.gz,0:151 1:151,A:1774737720;C:1423197995;G:1445462269;T:1767813232;N:514544,151,151,,,1774737720,1423197995,1445462269,1767813232,514544,SRX27770374,SRS24149653,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34936,SRR32455890,SRX27770373,SRS24149652,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a6 1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with hexagingerol|replicate:replicate=Biological Replicate 7|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with hexagingerol,a6 1,a6 1,Zebrafish hepatocytes treated with hexagingerol,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100776-a6_1.R1.raw.fastq.gz L1EIG0100776-a6_1.R2.raw.fastq.gz,fastq fastq,6755539170.0,22369335.0,L1EIG0100776 a6 1.R1.raw.fastq.gz,0:151 1:151,A:1872149169;C:1498908791;G:1521034783;T:1862905844;N:540583,151,151,,,1872149169,1498908791,1521034783,1862905844,540583,SRX27770373,SRS24149652,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34937,SRR32455891,SRX27770372,SRS24149651,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,R 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with RSL3|replicate:replicate=Biological Replicate 6|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with RSL3,R 3,R 3,Zebrafish hepatocytes treated with RSL3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100775-R_3.R1.raw.fastq.gz L1EIG0100775-R_3.R2.raw.fastq.gz,fastq fastq,6942710314.0,22989107.0,L1EIG0100775 R 3.R1.raw.fastq.gz,0:151 1:151,A:1902580151;C:1560207132;G:1591149353;T:1888209871;N:563807,151,151,,,1902580151,1560207132,1591149353,1888209871,563807,SRX27770372,SRS24149651,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34938,SRR32455892,SRX27770371,SRS24149650,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,R 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with RSL3|replicate:replicate=Biological Replicate 5|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with RSL3,R 2,R 2,Zebrafish hepatocytes treated with RSL3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100774-R_2.R1.raw.fastq.gz L1EIG0100774-R_2.R2.raw.fastq.gz,fastq fastq,6762005292.0,22390746.0,L1EIG0100774 R 2.R1.raw.fastq.gz,0:151 1:151,A:1853419911;C:1519952383;G:1546410472;T:1841314407;N:908119,151,151,,,1853419911,1519952383,1546410472,1841314407,908119,SRX27770371,SRS24149650,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34939,SRR32455893,SRX27770370,SRS24149649,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,R 1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with RSL3|replicate:replicate=Biological Replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with RSL3,R 1,R 1,Zebrafish hepatocytes treated with RSL3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100773-R_1.R1.raw.fastq.gz L1EIG0100773-R_1.R2.raw.fastq.gz,fastq fastq,6895808204.0,22833802.0,L1EIG0100773 R 1.R1.raw.fastq.gz,0:151 1:151,A:1893971807;C:1546715304;G:1570984307;T:1883580575;N:556211,151,151,,,1893971807,1546715304,1570984307,1883580575,556211,SRX27770370,SRS24149649,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34940,SRR32455894,SRX27770369,SRS24149648,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a0 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Untreated zebrafish hepatocytes|replicate:replicate=Biological Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,Untreated zebrafish hepatocytes,a0 3,a0 3,Untreated zebrafish hepatocytes,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100772-a0_3.R1.raw.fastq.gz L1EIG0100772-a0_3.R2.raw.fastq.gz,fastq fastq,7075697524.0,23429462.0,L1EIG0100772 a0 3.R1.raw.fastq.gz,0:151 1:151,A:1948593052;C:1578581045;G:1609493554;T:1938462155;N:567718,151,151,,,1948593052,1578581045,1609493554,1938462155,567718,SRX27770369,SRS24149648,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34941,SRR32455895,SRX27770368,SRS24149647,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a6 R 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with hexagingerol and RSL3|replicate:replicate=Biological Replicate 12|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with hexagingerol and RSL3,a6 R 3,a6 R 3,Zebrafish hepatocytes treated with hexagingerol and RSL3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100781-a6_R_3.R1.raw.fastq.gz L1EIG0100781-a6_R_3.R2.raw.fastq.gz,fastq fastq,7116518260.0,23564630.0,L1EIG0100781 a6 R 3.R1.raw.fastq.gz,0:151 1:151,A:1964563996;C:1585337517;G:1611230029;T:1954816245;N:570473,151,151,,,1964563996,1585337517,1611230029,1954816245,570473,SRX27770368,SRS24149647,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34942,SRR32455896,SRX27770367,SRS24149646,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a6 R 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with hexagingerol and RSL3|replicate:replicate=Biological Replicate 11|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with hexagingerol and RSL3,a6 R 2,a6 R 2,Zebrafish hepatocytes treated with hexagingerol and RSL3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100780-a6_R_2.R1.raw.fastq.gz L1EIG0100780-a6_R_2.R2.raw.fastq.gz,fastq fastq,6799607916.0,22515258.0,L1EIG0100780 a6 R 2.R1.raw.fastq.gz,0:151 1:151,A:1876556721;C:1516219722;G:1543095947;T:1863186684;N:548842,151,151,,,1876556721,1516219722,1543095947,1863186684,548842,SRX27770367,SRS24149646,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34943,SRR32455897,SRX27770366,SRS24149645,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a0 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Untreated zebrafish hepatocytes|replicate:replicate=Biological Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,Untreated zebrafish hepatocytes,a0 2,a0 2,Untreated zebrafish hepatocytes,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100771-a0_2.R1.raw.fastq.gz L1EIG0100771-a0_2.R2.raw.fastq.gz,fastq fastq,7445923854.0,24655377.0,L1EIG0100771 a0 2.R1.raw.fastq.gz,0:151 1:151,A:2041975942;C:1667033398;G:1714016742;T:2022303021;N:594751,151,151,,,2041975942,1667033398,1714016742,2022303021,594751,SRX27770366,SRS24149645,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34944,SRR32455898,SRX27770365,SRS24149644,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a0 1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Untreated zebrafish hepatocytes|replicate:replicate=Biological Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,Untreated zebrafish hepatocytes,a0 1,a0 1,Untreated zebrafish hepatocytes,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100770-a0_1.R1.raw.fastq.gz L1EIG0100770-a0_1.R2.raw.fastq.gz,fastq fastq,7695172910.0,25480705.0,L1EIG0100770 a0 1.R1.raw.fastq.gz,0:151 1:151,A:2126497578;C:1711136637;G:1741192106;T:2115729594;N:616995,151,151,,,2126497578,1711136637,1741192106,2115729594,616995,SRX27770365,SRS24149644,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34958,SRR32588715,SRX27895236,SRS24266238,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from Danio rerio,C2 F2 F L22,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from liver,C2 F2 F L22,C2 F2 F L22,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m64467e_240816_172726.hifi_reads.flnc.fastq.gz,fastq,15103018596.0,3471157.0,m64467e 240816 172726.hifi reads.flnc.fastq.gz,0:4351.00,A:4102928612;C:3526979790;G:3455927740;T:4017182454;N:0,4351,,,,4102928612,3526979790,3455927740,4017182454,0,SRX27895236,SRS24266238,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Adult,Adult,Liver,Liver and Biliary System
34959,SRR32588716,SRX27895235,SRS24266237,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from Danio rerio,C2 F2 F L21,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from liver,C2 F2 F L21,C2 F2 F L21,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240913_130745_s1.skera.flnc.fastq.gz,fastq,91129501236.0,45094963.0,m84270 240913 130745 s1.skera.flnc.fastq.gz,0:2020.84,A:25808290124;C:20578070676;G:20740793271;T:24002347165;N:0,2020,,,,25808290124,20578070676,20740793271,24002347165,0,SRX27895235,SRS24266237,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Adult,Adult,Liver,Liver and Biliary System
34969,SRR32588726,SRX27895225,SRS24266223,SRP568323,PRJNA1232602,Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains,PRJNA1232602,Other,In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.,,,,Iso Seq RNA from Danio rerio,C2 F2 M L,,strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,Iso Seq RNA from liver,C2 F2 M L,C2 F2 M L,The long Read Sequencing libraries was sequenced using PacBio Sequel II,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,PACBIO_SMRT,Sequel II,,SRP568323,,,m84270_240911_170652_s2.skera.flnc.fastq.gz,fastq,103288926144.0,58528654.0,m84270 240911 170652 s2.skera.flnc.fastq.gz,0:1764.76,A:30548263427;C:22289732504;G:23327561779;T:27123368434;N:0,1764,,,,30548263427,22289732504,23327561779,27123368434,0,SRX27895225,SRS24266223,SRA2089085,National Human Genome Research Institute|Translational and Functional Genomics Branch,National Human Genome Research Institute National Human Genome Research Institute,,,,,,,,,,,,T,,long read,pacbio,pacbio_modern,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2025-03-06,Adult,Adult,Liver,Liver and Biliary System
35820,SRR33048250,SRX28313563,SRS24652528,SRP577496,PRJNA1248508,Transcriptome sequencing of hepatocytes with or without xxx during liver development in zebrafish,PRJNA1248508,Other,The hepatocytes and non hepatocytes within the livers of 3dpf  7 dpf  and adult transgenic Tgfabp10:GFP zebrafish were utilized for experimentation. Upon cessation of opercular movements  animals were euthanized via immersion in ice cold water for ten minutes. In this transgenic line  hepatocytes in the liver express GFP. Subsequently  liver tissues were subjected to enzymatic digestion using 1 mg Collagenase IV dissolved in 1 ml L 15 medium  incubated at room temperature for 20 minutes. Liver tissues were then transferred to Leibovitz L 15 medium with an osmolarity of 300 mOsm and pH adjusted to 7.35. Hepatocytes and non  hepatocytes were isolated through gentle trituration. The chamber was mounted onto the stage of an Olympus inverted microscope equipped with fluorescence capabilities  perfused with fresh L 15 medium for 5 minutes to rinse off debris. Calibrate flow cytometer Moflo XDP  Beckman  ensuring that the instrument settings such as voltage thresholds and compensation matrices are properly configured for GFP detection. Use beads calibrated for green fluorescent protein to adjust the photomultiplier tube voltages and other parameters. Prepare sterile sorting tubes filled with a suitable buffer to collect sorted cells. Pre chill if necessary. Use an argon laser typically at 488 nm for GFP excitation. Set appropriate filters to detect GFP emission  usually centred around 530 nm. Discriminate intact cells from cell fragments based on size and internal complexity. Balance purity and yield by adjusting sort speed and stringency of gating parameters. Follow strict cleaning protocols post sorting to avoid contamination. Isolated cells were collected utilizing flow cytometry  enabling precise sorting of GFP positive hepatocytes from GFP negative non hepatocytes. Approximately 400 hepatocytes and non hepatocytes were harvested from around 12 zebrafish  with 3 replicates per sample. The careful isolation procedures and subsequent sorting by flow cytometry facilitated acquisition of pure populations of hepatocytes and non hepatocytes  ensuring gene expression profiles and reliable downstream analyses of cellular composition.,,,,Adult GFP,The hepatocytes within the liver of adult transgenic Tgfabp10:GFP zebrafish,,strain:not applicable|isolate:not applicable|breed:hepatocytes|cultivar:transgenic Tgfabp10:GFP zebrafish|ecotype:not applicable|age:not collected|dev stage:Adult|collection date:2019 06 19|geo loc name:China: Sichuan|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,Adult GFP,ED19155414,ED19155414,library preparations were sequenced on an Illumina Novaseq platform and 150bp paired end reads were generated,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP577496,,,Adult_GFP_R1.fq.gz Adult_GFP_R2.fq.gz,fastq fastq,7663055700.0,25543519.0,Adult GFP R1.fq.gz,0:150 1:150,A:2211883588;C:1631375476;G:1646187061;T:2173545801;N:63774,150,150,,,2211883588,1631375476,1646187061,2173545801,63774,SRX28313563,SRS24652528,SRA2109063,Chengdu Medical College|School of Basic Medicine,Chengdu Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-04-09,Adult,Adult,Liver,Liver and Biliary System
35821,SRR33048251,SRX28313562,SRS24652529,SRP577496,PRJNA1248508,Transcriptome sequencing of hepatocytes with or without xxx during liver development in zebrafish,PRJNA1248508,Other,The hepatocytes and non hepatocytes within the livers of 3dpf  7 dpf  and adult transgenic Tgfabp10:GFP zebrafish were utilized for experimentation. Upon cessation of opercular movements  animals were euthanized via immersion in ice cold water for ten minutes. In this transgenic line  hepatocytes in the liver express GFP. Subsequently  liver tissues were subjected to enzymatic digestion using 1 mg Collagenase IV dissolved in 1 ml L 15 medium  incubated at room temperature for 20 minutes. Liver tissues were then transferred to Leibovitz L 15 medium with an osmolarity of 300 mOsm and pH adjusted to 7.35. Hepatocytes and non  hepatocytes were isolated through gentle trituration. The chamber was mounted onto the stage of an Olympus inverted microscope equipped with fluorescence capabilities  perfused with fresh L 15 medium for 5 minutes to rinse off debris. Calibrate flow cytometer Moflo XDP  Beckman  ensuring that the instrument settings such as voltage thresholds and compensation matrices are properly configured for GFP detection. Use beads calibrated for green fluorescent protein to adjust the photomultiplier tube voltages and other parameters. Prepare sterile sorting tubes filled with a suitable buffer to collect sorted cells. Pre chill if necessary. Use an argon laser typically at 488 nm for GFP excitation. Set appropriate filters to detect GFP emission  usually centred around 530 nm. Discriminate intact cells from cell fragments based on size and internal complexity. Balance purity and yield by adjusting sort speed and stringency of gating parameters. Follow strict cleaning protocols post sorting to avoid contamination. Isolated cells were collected utilizing flow cytometry  enabling precise sorting of GFP positive hepatocytes from GFP negative non hepatocytes. Approximately 400 hepatocytes and non hepatocytes were harvested from around 12 zebrafish  with 3 replicates per sample. The careful isolation procedures and subsequent sorting by flow cytometry facilitated acquisition of pure populations of hepatocytes and non hepatocytes  ensuring gene expression profiles and reliable downstream analyses of cellular composition.,,,,D7 GFP,The hepatocytes within the liver of 7 dpf transgenic Tgfabp10:GFP zebrafish,,strain:not applicable|isolate:not applicable|breed:hepatocytes|cultivar:transgenic Tgfabp10:GFP zebrafish|ecotype:not applicable|age:not collected|dev stage:7 dpf date:2019 06 19|geo loc name:China: Sichuan|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,D7 GFP,ED19155408,ED19155408,library preparations were sequenced on an Illumina Novaseq platform and 150bp paired end reads were generated,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP577496,,,D7_GFP_R1.fq.gz D7_GFP_R2.fq.gz,fastq fastq,7981076700.0,26603589.0,D7 GFP R1.fq.gz,0:150 1:150,A:2179536437;C:1804626545;G:1832481252;T:2164370673;N:61793,150,150,,,2179536437,1804626545,1832481252,2164370673,61793,SRX28313562,SRS24652529,SRA2109063,Chengdu Medical College|School of Basic Medicine,Chengdu Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-04-09,Larval,Larval,Liver,Liver and Biliary System
35822,SRR33048252,SRX28313561,SRS24652526,SRP577496,PRJNA1248508,Transcriptome sequencing of hepatocytes with or without xxx during liver development in zebrafish,PRJNA1248508,Other,The hepatocytes and non hepatocytes within the livers of 3dpf  7 dpf  and adult transgenic Tgfabp10:GFP zebrafish were utilized for experimentation. Upon cessation of opercular movements  animals were euthanized via immersion in ice cold water for ten minutes. In this transgenic line  hepatocytes in the liver express GFP. Subsequently  liver tissues were subjected to enzymatic digestion using 1 mg Collagenase IV dissolved in 1 ml L 15 medium  incubated at room temperature for 20 minutes. Liver tissues were then transferred to Leibovitz L 15 medium with an osmolarity of 300 mOsm and pH adjusted to 7.35. Hepatocytes and non  hepatocytes were isolated through gentle trituration. The chamber was mounted onto the stage of an Olympus inverted microscope equipped with fluorescence capabilities  perfused with fresh L 15 medium for 5 minutes to rinse off debris. Calibrate flow cytometer Moflo XDP  Beckman  ensuring that the instrument settings such as voltage thresholds and compensation matrices are properly configured for GFP detection. Use beads calibrated for green fluorescent protein to adjust the photomultiplier tube voltages and other parameters. Prepare sterile sorting tubes filled with a suitable buffer to collect sorted cells. Pre chill if necessary. Use an argon laser typically at 488 nm for GFP excitation. Set appropriate filters to detect GFP emission  usually centred around 530 nm. Discriminate intact cells from cell fragments based on size and internal complexity. Balance purity and yield by adjusting sort speed and stringency of gating parameters. Follow strict cleaning protocols post sorting to avoid contamination. Isolated cells were collected utilizing flow cytometry  enabling precise sorting of GFP positive hepatocytes from GFP negative non hepatocytes. Approximately 400 hepatocytes and non hepatocytes were harvested from around 12 zebrafish  with 3 replicates per sample. The careful isolation procedures and subsequent sorting by flow cytometry facilitated acquisition of pure populations of hepatocytes and non hepatocytes  ensuring gene expression profiles and reliable downstream analyses of cellular composition.,,,,D3 GFP,The hepatocytes within the liver of 3dpf transgenic Tgfabp10:GFP zebrafish,,strain:not applicable|isolate:not applicable|breed:hepatocytes|cultivar:transgenic Tgfabp10:GFP zebrafish|ecotype:not applicable|age:not collected|dev stage:3 dpf date:2019 06 19|geo loc name:China: Sichuan|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,D3 GFP,ED19155403,ED19155403,library preparations were sequenced on an Illumina Novaseq platform and 150bp paired end reads were generated,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP577496,,,D3_GFP_R1.fq.gz D3_GFP_R2.fq.gz,fastq fastq,5675477100.0,18918257.0,D3 GFP R1.fq.gz,0:150 1:150,A:1686172751;C:1174770916;G:1187685676;T:1626795743;N:52014,150,150,,,1686172751,1174770916,1187685676,1626795743,52014,SRX28313561,SRS24652526,SRA2109063,Chengdu Medical College|School of Basic Medicine,Chengdu Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-04-09,Larval,Larval,Liver,Liver and Biliary System
35823,SRR33048253,SRX28313560,SRS24652527,SRP577496,PRJNA1248508,Transcriptome sequencing of hepatocytes with or without xxx during liver development in zebrafish,PRJNA1248508,Other,The hepatocytes and non hepatocytes within the livers of 3dpf  7 dpf  and adult transgenic Tgfabp10:GFP zebrafish were utilized for experimentation. Upon cessation of opercular movements  animals were euthanized via immersion in ice cold water for ten minutes. In this transgenic line  hepatocytes in the liver express GFP. Subsequently  liver tissues were subjected to enzymatic digestion using 1 mg Collagenase IV dissolved in 1 ml L 15 medium  incubated at room temperature for 20 minutes. Liver tissues were then transferred to Leibovitz L 15 medium with an osmolarity of 300 mOsm and pH adjusted to 7.35. Hepatocytes and non  hepatocytes were isolated through gentle trituration. The chamber was mounted onto the stage of an Olympus inverted microscope equipped with fluorescence capabilities  perfused with fresh L 15 medium for 5 minutes to rinse off debris. Calibrate flow cytometer Moflo XDP  Beckman  ensuring that the instrument settings such as voltage thresholds and compensation matrices are properly configured for GFP detection. Use beads calibrated for green fluorescent protein to adjust the photomultiplier tube voltages and other parameters. Prepare sterile sorting tubes filled with a suitable buffer to collect sorted cells. Pre chill if necessary. Use an argon laser typically at 488 nm for GFP excitation. Set appropriate filters to detect GFP emission  usually centred around 530 nm. Discriminate intact cells from cell fragments based on size and internal complexity. Balance purity and yield by adjusting sort speed and stringency of gating parameters. Follow strict cleaning protocols post sorting to avoid contamination. Isolated cells were collected utilizing flow cytometry  enabling precise sorting of GFP positive hepatocytes from GFP negative non hepatocytes. Approximately 400 hepatocytes and non hepatocytes were harvested from around 12 zebrafish  with 3 replicates per sample. The careful isolation procedures and subsequent sorting by flow cytometry facilitated acquisition of pure populations of hepatocytes and non hepatocytes  ensuring gene expression profiles and reliable downstream analyses of cellular composition.,,,,D3 Cont,The non hepatocytes within the liver of 3dp transgenic Tgfabp10:GFP zebrafish,,strain:not applicable|isolate:not applicable|breed:non hepatocytes|cultivar:transgenic Tgfabp10:GFP zebrafish|ecotype:not applicable|age:not collected|dev stage:3 dpf date:2019 06 19|geo loc name:China: Sichuan|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,D3 Cont,ED19155405,ED19155405,library preparations were sequenced on an Illumina Novaseq platform and 150bp paired end reads were generated,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP577496,,,D3_Cont_R1.fq.gz D3_Cont_R2.fq.gz,fastq fastq,6351962700.0,21173209.0,D3 Cont R1.fq.gz,0:150 1:150,A:1820293872;C:1368447220;G:1385705833;T:1777459731;N:56044,150,150,,,1820293872,1368447220,1385705833,1777459731,56044,SRX28313560,SRS24652527,SRA2109063,Chengdu Medical College|School of Basic Medicine,Chengdu Medical College,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-04-09,Larval,Larval,Liver,Liver and Biliary System
36336,SRR390721,SRX112005,SRS282726,SRP009863,PRJNA151317,A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver,GSE34493,Transcriptome Analysis,We sequenced mRNA from each transgenic zebrafish line including WT  HBx  HCP  and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.,,,,mRNA from HBx+HCP transgenic line,GSM850201,,source name:zebrafish liver|phenotype:intrahepatic cholangiocarcinoma|strain:HBx+HCP transgenic|tissue:liver,mRNA from HBx+HCP transgenic line,HBx+HCP count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.,zebrafish liver,Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis,The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing  the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation  the sequencing run was performed by using SOLiD 3 System. Data analysis  was performed with SOLiD Analysis Tool Pipeline.,Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C.,phenotype:intrahepatic cholangiocarcinoma|strain:HBx+HCP transgenic|tissue:liver,GSM850201,GSM850201: mRNA from HBx+HCP transgenic line; Danio rerio; RNA Seq,GSM850201 1,GSM850201: mRNA from HBx+HCP transgenic line,1,,GEO Accession:GSM850201,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>,SRP009863,,,HBx+HCP.qual HBx+HCP.csfasta,SOLiD_native SOLiD_native,3946087000.0,78921740.0,GSM850201 r1,0:50,0:926148003;1:1112848138;2:1139608445;3:763770020;.:3712394,50,,,,,,,,,SRX112005,SRS282726,SRA048698,GEO,"Institute of Cellular and Organismic Biology, Academia Sinica",1,0.71816,,0.05681,,0.91727,,0.25279,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Taiwan,2011-12-16,Undetermined,Adult,Liver,Liver and Biliary System
36337,SRR390720,SRX112004,SRS282725,SRP009863,PRJNA151317,A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver,GSE34493,Transcriptome Analysis,We sequenced mRNA from each transgenic zebrafish line including WT  HBx  HCP  and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.,,,,mRNA from HCP transgenic line,GSM850200,,source name:zebrafish liver|phenotype:n1|strain:HCP transgenic|tissue:liver,mRNA from HCP transgenic line,HCP count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.,zebrafish liver,Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis,The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing  the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation  the sequencing run was performed by using SOLiD 3 System. Data analysis  was performed with SOLiD Analysis Tool Pipeline.,Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C.,phenotype:n1|strain:HCP transgenic|tissue:liver,GSM850200,GSM850200: mRNA from HCP transgenic line; Danio rerio; RNA Seq,GSM850200 1,GSM850200: mRNA from HCP transgenic line,1,,GEO Accession:GSM850200,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>,SRP009863,,,HCP.qual HCP.csfasta,SOLiD_native SOLiD_native,4104044600.0,82080892.0,GSM850200 r1,0:50,0:944238890;1:1172273582;2:1207771613;3:775967445;.:3793070,50,,,,,,,,,SRX112004,SRS282725,SRA048698,GEO,"Institute of Cellular and Organismic Biology, Academia Sinica",1,0.70132,,0.05286,,0.94422,,0.26785,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Taiwan,2011-12-16,Undetermined,Adult,Liver,Liver and Biliary System
36338,SRR390719,SRX112003,SRS282724,SRP009863,PRJNA151317,A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver,GSE34493,Transcriptome Analysis,We sequenced mRNA from each transgenic zebrafish line including WT  HBx  HCP  and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.,,,,mRNA from HBx transgenic line,GSM850199,,source name:zebrafish liver|phenotype:n1|strain:HBx transgenic|tissue:liver,mRNA from HBx transgenic line,HBx count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.,zebrafish liver,Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis,The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing  the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation  the sequencing run was performed by using SOLiD 3 System. Data analysis  was performed with SOLiD Analysis Tool Pipeline.,Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C.,phenotype:n1|strain:HBx transgenic|tissue:liver,GSM850199,GSM850199: mRNA from HBx transgenic line; Danio rerio; RNA Seq,GSM850199 1,GSM850199: mRNA from HBx transgenic line,1,,GEO Accession:GSM850199,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>,SRP009863,,,HBx.qual HBx.csfasta,SOLiD_native SOLiD_native,3783924950.0,75678499.0,GSM850199 r1,0:50,0:909506019;1:1055965468;2:1075994223;3:739008253;.:3450987,50,,,,,,,,,SRX112003,SRS282724,SRA048698,GEO,"Institute of Cellular and Organismic Biology, Academia Sinica",1,0.70675,,0.04174,,0.94146,,0.22954,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Taiwan,2011-12-16,Undetermined,Adult,Liver,Liver and Biliary System
36339,SRR390718,SRX112002,SRS282723,SRP009863,PRJNA151317,A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver,GSE34493,Transcriptome Analysis,We sequenced mRNA from each transgenic zebrafish line including WT  HBx  HCP  and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.,,,,mRNA from AB strain,GSM850198,,source name:zebrafish liver|phenotype:n1|strain:AB|tissue:liver,mRNA from AB strain,WT count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.,zebrafish liver,Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis,The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing  the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation  the sequencing run was performed by using SOLiD 3 System. Data analysis  was performed with SOLiD Analysis Tool Pipeline.,Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C.,phenotype:n1|strain:AB|tissue:liver,GSM850198,GSM850198: mRNA from AB strain; Danio rerio; RNA Seq,GSM850198 1,GSM850198: mRNA from AB strain,1,,GEO Accession:GSM850198,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>,SRP009863,,,WT.csfasta WT.qual,SOLiD_native SOLiD_native,5129652800.0,102593056.0,GSM850198 r1,0:50,0:1167298346;1:1421158274;2:1551481320;3:984758434;.:4956426,50,,,,,,,,,SRX112002,SRS282723,SRA048698,GEO,"Institute of Cellular and Organismic Biology, Academia Sinica",1,0.73072,,0.04843,,0.95574,,0.21796,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Taiwan,2011-12-16,Undetermined,Adult,Liver,Liver and Biliary System
36371,SRR498195,SRX148642,SRS334220,SRP013245,PRJNA167126,The zebrafish embryo as an alternative model for the evaluation of liver toxicity using histopathology and expression profiling,GSE38042,Transcriptome Analysis,The zebrafish is as a powerful vertebrate model system for modeling human disease including liver pathology. In ZFE  hepatic responses can be expected post exposure to hepatotoxicants  because hepatocytes are present from 36 hpf and at 72 hpf the liver is fully functioning. These characteristics make the whole ZFE an attractive alternative model for compound induced hepatotoxicity screening. Therefore  the main objective of this study is to further strengthen the applicability of whole ZFE as an alternative model for hepatotoxicity testing  with a special focus on the ability to identify gene expression responses in whole ZFE that are suggestive of hepatotoxicity. Deep sequence technology is applied to assess whether hepatotoxicity specific transcripts that are identified in livers of hepatotoxicant treated adult zebrafish can be detected in whole ZFE as well. Overall design: Whole zebrafish embryo and adult zebrafish are exposed for 48 hours to human hepatotoxicants. postwards  the adult liver is dissected and snap frozen untill processed for RNA isolation. The whole zebrafish embryos are pooled  one sample consists of 15 embryos  and are also snap frozen untill processed for RNA isolation. For every sample RNA is isolated according to the protocol of de Jong et al 2009. and then equal amounts of every sample is pooled. The two pools one for the adult zebrafish liver  the other for the whole zebrafish embryo are sequenced.,,,,Adult zebrafish liver,GSM932886,,source name:Adult zebrafish liver|tissue:liver|developmental stage:adult|treatment:exposed for 48h t2 xxx known human hepatotoxicants  including paraquat  acetaminophen  thioacetamide  cyclosporine A  17a ethynylestradiol  chlorpromazine  amiodar1  tetracycline and valproic acid,Adult zebrafish liver,Illumina Genome Analyzer pipeline. Genome build: Ensemble  Zv8  Release 59  August 2010. Supplementary files format and content: RPKM,Adult zebrafish liver,Zebrafish are exposed for 48h ttwo xxx known human hepatotoxicants  including paraquat  acetaminophen  thioacetamide  cyclosporine A  17a ethynylestradiol  chlorpromazine  amiodarone  tetracycline and valproic acid.,Whole zebrafish embryo and adult zebrafish are exposed for 48 hours to human hepatotoxicants. postwards  the adult liver is dissected and snap frozen untill processed for RNA isolation. The whole zebrafish embryos are pooled  one sample consists of 15 embryos  and are also snap frozen untill processed for RNA isolation. For every sample RNA is isolated according to the protocol of de Jong et al 2009. and then equal amounts of every sample is pooled. The two pools one for the adult zebrafish liver  the other for the whole zebrafish embryo are sequenced.,,tissue:liver|developmental stage:adult|treatment:exposed for 48h t2 xxx known human hepatotoxicants  including paraquat  acetaminophen  thioacetamide  cyclosporine A  17a ethynylestradiol  chlorpromazine  amiodar1  tetracycline and valproic acid,GSM932886,GSM932886: Adult zebrafish liver; Danio rerio; RNA Seq,GSM932886 2,GSM932886: Adult zebrafish liver,1,,GEO Accession:GSM932886,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP013245,,,s_1_2_sequence-ZFPOOL.txt s_1_1_sequence-ZFPOOL.txt,fastq fastq,928783500.0,9287835.0,GSM932886 r1,0:50 1:50,A:252619394;C:208590239;G:209788766;T:257119544;N:665557,50,50,,,252619394,208590239,209788766,257119544,665557,SRX148642,SRS334220,SRA052989,GEO,"Laboratory for Health Protection Research, National Institute of Public Health and the Environment (RIVM)",2,0.88557,0.88335,0.08801,0.0874,0.79131,0.79133,0.4709,0.47049,50,50,B,B,biological fallback assumption,illumina,early_illumina,unknown,random_priming,unknown,bulk,unknown,unknown,,Netherlands,2012-05-17,Adult,Adult,Liver,Liver and Biliary System
36506,SRR566696,SRX185761,SRS361914,SRP015680,PRJNA174800,Transcriptomic analyses of Myc induced zebrafish liver cancer,GSE40745,Transcriptome Analysis,To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.,,pubmed:23038063,source: liver tumor  M+D+,GSM1000561: M+D+ 2,GSM1000561,,genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline,M+D+ 2,The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,liver tumor  M+D+,Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.,Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.,,genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline,GSM1000561,GSM1000561: M+D+ 2; Danio rerio; RNA Seq,GSM1000561 1,,1,,GEO Accession:GSM1000561,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP015680,,,M+D+_2_QV.qual M+D+_2.csfasta,SOLiD_native SOLiD_native,1493416960.0,42669056.0,GSM1000561 r1,0:35,0:377247910;1:348861020;2:522134600;3:237405266;.:7768164,35,,,,,,,,,SRX185761,SRS361914,SRA058618,GEO,National University of Singapore,1,0.06244,,0.00306,,0.99567,,0.34618,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2012-09-10,Larval,Larval,Liver,Liver and Biliary System
36507,SRR566695,SRX185760,SRS361913,SRP015680,PRJNA174800,Transcriptomic analyses of Myc induced zebrafish liver cancer,GSE40745,Transcriptome Analysis,To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.,,pubmed:23038063,source: liver tumor  M+D+,GSM1000560: M+D+ 1,GSM1000560,,genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline,M+D+ 1,The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,liver tumor  M+D+,Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.,Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.,,genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline,GSM1000560,GSM1000560: M+D+ 1; Danio rerio; RNA Seq,GSM1000560 1,,1,,GEO Accession:GSM1000560,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP015680,,,,,1291539515.0,36901129.0,GSM1000560 r1,0:35,0:266006021;1:328523841;2:440474617;3:254266912;.:2268124,35,,,,,,,,,SRX185760,SRS361913,SRA058618,GEO,National University of Singapore,1,0.10629,,0.0044,,0.99239,,0.31953,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2012-09-10,Larval,Larval,Liver,Liver and Biliary System
36508,SRR566694,SRX185759,SRS361912,SRP015680,PRJNA174800,Transcriptomic analyses of Myc induced zebrafish liver cancer,GSE40745,Transcriptome Analysis,To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.,,pubmed:23038063,source: control liver  M D+,GSM1000559: M D+ 2,GSM1000559,,genotype:wildtype|tissue:liver|treatment:doxycycline,M D+ 2,The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver  M D+,Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.,Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.,,genotype:wildtype|tissue:liver|treatment:doxycycline,GSM1000559,GSM1000559: M D+ 2; Danio rerio; RNA Seq,GSM1000559 1,,1,,GEO Accession:GSM1000559,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP015680,,,M-D+_2_QV.qual,SOLiD_native,1438423910.0,41097826.0,GSM1000559 r1,0:35,0:353104627;1:349496969;2:433338629;3:275089557;.:27394128,35,,,,,,,,,SRX185759,SRS361912,SRA058618,GEO,National University of Singapore,1,0.04748,,0.00442,,0.99425,,0.53794,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2012-09-10,Larval,Larval,Liver,Liver and Biliary System
36509,SRR566693,SRX185758,SRS361911,SRP015680,PRJNA174800,Transcriptomic analyses of Myc induced zebrafish liver cancer,GSE40745,Transcriptome Analysis,To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.,,pubmed:23038063,source: control liver  M D+,GSM1000558: M D+ 1,GSM1000558,,genotype:wildtype|tissue:liver|treatment:doxycycline,M D+ 1,The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver  M D+,Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.,Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.,,genotype:wildtype|tissue:liver|treatment:doxycycline,GSM1000558,GSM1000558: M D+ 1; Danio rerio; RNA Seq,GSM1000558 1,,1,,GEO Accession:GSM1000558,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP015680,,,M-D+_1.csfasta,SOLiD_native,1284638285.0,36703951.0,GSM1000558 r1,0:35,0:328871758;1:317693850;2:402981931;3:233637468;.:1453278,35,,,,,,,,,SRX185758,SRS361911,SRA058618,GEO,National University of Singapore,1,0.10539,,0.00562,,0.99141,,0.37635,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2012-09-10,Larval,Larval,Liver,Liver and Biliary System
36510,SRR566692,SRX185757,SRS361910,SRP015680,PRJNA174800,Transcriptomic analyses of Myc induced zebrafish liver cancer,GSE40745,Transcriptome Analysis,To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.,,pubmed:23038063,source: control liver  M+D ,GSM1000557: M+D  2,GSM1000557,,genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1,M+D  2,The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver  M+D ,Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.,Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.,,genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1,GSM1000557,GSM1000557: M+D  2; Danio rerio; RNA Seq,GSM1000557 1,,1,,GEO Accession:GSM1000557,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP015680,,,M+D-_2_QV.qual,SOLiD_native,1404966080.0,40141888.0,GSM1000557 r1,0:35,0:371691603;1:354481639;2:405221861;3:271978812;.:1592165,35,,,,,,,,,SRX185757,SRS361910,SRA058618,GEO,National University of Singapore,1,0.07869,,0.00455,,0.99253,,0.51508,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2012-09-10,Larval,Larval,Liver,Liver and Biliary System
36511,SRR566691,SRX185756,SRS361909,SRP015680,PRJNA174800,Transcriptomic analyses of Myc induced zebrafish liver cancer,GSE40745,Transcriptome Analysis,To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.,,pubmed:23038063,source: control liver  M+D ,GSM1000556: M+D  1,GSM1000556,,genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1,M+D  1,The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver  M+D ,Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.,Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.,,genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1,GSM1000556,GSM1000556: M+D  1; Danio rerio; RNA Seq,GSM1000556 1,,1,,GEO Accession:GSM1000556,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP015680,,,M+D-_1_QV.qual M+D-_1.csfasta,SOLiD_native SOLiD_native,1286706820.0,36763052.0,GSM1000556 r1,0:35,0:252864341;1:338709089;2:436928155;3:256235022;.:1970213,35,,,,,,,,,SRX185756,SRS361909,SRA058618,GEO,National University of Singapore,1,0.12399,,0.00617,,0.98752,,0.50351,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2012-09-10,Larval,Larval,Liver,Liver and Biliary System
36512,SRR566690,SRX185755,SRS361908,SRP015680,PRJNA174800,Transcriptomic analyses of Myc induced zebrafish liver cancer,GSE40745,Transcriptome Analysis,To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.,,pubmed:23038063,source: control liver  M D ,GSM1000555: M D  2,GSM1000555,,genotype:wildtype|tissue:liver|treatment:n1,M D  2,The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver  M D ,Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.,Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.,,genotype:wildtype|tissue:liver|treatment:n1,GSM1000555,GSM1000555: M D  2; Danio rerio; RNA Seq,GSM1000555 1,,1,,GEO Accession:GSM1000555,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP015680,,,M-D-_2_QV.qual M-D-_2.csfasta,SOLiD_native SOLiD_native,1337952770.0,38227222.0,GSM1000555 r1,0:35,0:391863829;1:347720340;2:312814682;3:283542736;.:2011183,35,,,,,,,,,SRX185755,SRS361908,SRA058618,GEO,National University of Singapore,1,0.04605,,0.00365,,0.99494,,0.51825,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2012-09-10,Larval,Larval,Liver,Liver and Biliary System
36513,SRR566689,SRX185754,SRS361907,SRP015680,PRJNA174800,Transcriptomic analyses of Myc induced zebrafish liver cancer,GSE40745,Transcriptome Analysis,To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.,,pubmed:23038063,source: control liver  M D ,GSM1000554: M D  1,GSM1000554,,genotype:wildtype|tissue:liver|treatment:n1,M D  1,The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver  M D ,Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.,Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.,,genotype:wildtype|tissue:liver|treatment:n1,GSM1000554,GSM1000554: M D  1; Danio rerio; RNA Seq,GSM1000554 1,,1,,GEO Accession:GSM1000554,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP015680,,,M-D-_1.csfasta,SOLiD_native,1395143680.0,39861248.0,GSM1000554 r1,0:35,0:439852883;1:355203725;2:298639546;3:299770820;.:1676706,35,,,,,,,,,SRX185754,SRS361907,SRA058618,GEO,National University of Singapore,1,0.02094,,0.00123,,0.99784,,0.58426,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2012-09-10,Larval,Larval,Liver,Liver and Biliary System
37108,SRR924082,SRX316721,SRS472258,SRP026400,PRJNA210007,Genome wide identification of molecular pathways and biomarkers in response to arsenic exposure in zebrafish liver,GSE48427,Transcriptome Analysis,In the present study  we employed the RNA sequencing platform to examine the molecular response of zebrafish liver to arsenic exposure and carry out detailed transcriptomic analyses for further understanding of molecular toxicity. We found that several important biological processes were perturbed by arsenic exposure  including oxidation reduction  translation  iron ion transport  cell redox and homeostasis  as well as related pathways in metabolism and diseases. Furthermore  as there are currently no biomarker genes available for predicting arsenic exposure  we took the advantage of RNA sequencing platform to identify most suitable biomarker genes from top responsive genes to arsenic exposure. We first validated these top responsive genes by RT qPCR in zebrafish and then in Japanese medaka Oryzias latipes at individual fish level for more robustly responsive genes across different fish species. Overall design: Transcriptome profiling of arsenic treated sample and control sample were generated by deep sequencing using three prime RNA SAGE on the SOLiD system.,,pubmed:24176670;pubmed:23922661,,H2O treated zebrafish liver,GSM1177837,,source name:liver  control|genotype/variation:wildtype|tissue:liver|age:3 month|treatment:water control,H2O treated zebrafish liver,The SOLiD generated RNA Seq reads were 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maximum mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 58 Supplementary files format and content: Tab delimited text file. The mapped transcripts are listed with GI  RefSeq accession  and expression levels in TPM.,liver  control,3 mpf wildtype zebrafish were treated for 96 hrs. Sodium arsenate treatment was conducted in 3 L tanks with around 15 adults and water was changed every day.,Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.,,genotype/variation:wildtype|tissue:liver|age:3 month|treatment:water control,GSM1177837,GSM1177837: H2O treated zebrafish liver; Danio rerio; RNA Seq,GSM1177837,,1,Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.,GEO Accession:GSM1177837,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP026400,,,solid0518_20101014_Gong_1_SetA_F3_0_1H2O.csfasta solid0518_20101014_Gong_1_SetA_F3_QV_0_1H2O.qual,SOLiD_native SOLiD_native,477311205.0,13637463.0,GSM1177837 r1,0:35,0:176467601;1:101093405;2:105775125;3:93265462;.:709612,35,,,,,,,,,SRX316721,SRS472258,SRA091803,GEO,National University of Singapore,1,0.02019,,0.01385,,0.9973,,0.64062,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-06-28,Adult,Adult,Liver,Liver and Biliary System
37109,SRR924081,SRX316720,SRS454027,SRP026400,PRJNA210007,Genome wide identification of molecular pathways and biomarkers in response to arsenic exposure in zebrafish liver,GSE48427,Transcriptome Analysis,In the present study  we employed the RNA sequencing platform to examine the molecular response of zebrafish liver to arsenic exposure and carry out detailed transcriptomic analyses for further understanding of molecular toxicity. We found that several important biological processes were perturbed by arsenic exposure  including oxidation reduction  translation  iron ion transport  cell redox and homeostasis  as well as related pathways in metabolism and diseases. Furthermore  as there are currently no biomarker genes available for predicting arsenic exposure  we took the advantage of RNA sequencing platform to identify most suitable biomarker genes from top responsive genes to arsenic exposure. We first validated these top responsive genes by RT qPCR in zebrafish and then in Japanese medaka Oryzias latipes at individual fish level for more robustly responsive genes across different fish species. Overall design: Transcriptome profiling of arsenic treated sample and control sample were generated by deep sequencing using three prime RNA SAGE on the SOLiD system.,,pubmed:24176670;pubmed:23922661,,Arsenic treated zebrafish liver,GSM1177836,,source name:liver  arsenic|genotype/variation:wildtype|tissue:liver|age:3 month|treatment:arsenate sodium,Arsenic treated zebrafish liver,The SOLiD generated RNA Seq reads were 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maximum mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 58 Supplementary files format and content: Tab delimited text file. The mapped transcripts are listed with GI  RefSeq accession  and expression levels in TPM.,liver  arsenic,3 mpf wildtype zebrafish were treated for 96 hrs. Sodium arsenate treatment was conducted in 3 L tanks with around 15 adults and water was changed every day.,Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.,,genotype/variation:wildtype|tissue:liver|age:3 month|treatment:arsenate sodium,GSM1177836,GSM1177836: Arsenic treated zebrafish liver; Danio rerio; RNA Seq,GSM1177836,,1,Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.,GEO Accession:GSM1177836,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP026400,,,solid0518_20101014_Gong_1_SetA_F3_QV_2_2Arsenic.qual solid0518_20101014_Gong_1_SetA_F3_2_2Arsenic.csfasta,SOLiD_native SOLiD_native,477279215.0,13636549.0,GSM1177836 r1,0:35,0:135280436;1:121477647;2:102046207;3:117826846;.:648079,35,,,,,,,,,SRX316720,SRS454027,SRA091803,GEO,National University of Singapore,1,0.0161,,0.00302,,0.99334,,0.51629,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-06-28,Adult,Adult,Liver,Liver and Biliary System
37130,SRR952910,SRX335554,SRS470625,SRP028848,PRJNA215326,Transcriptomic analyses of TCDD treated zebrafish liver,GSE49915,Transcriptome Analysis,To fully understand molecular toxicity of TCDD in an in vivo animal model  adult zebrafish were exposed to TCDD at xxx nM for xxx h and the livers were sampled for RNA sequencing based transcriptomic profiling. A total of 1 058 differently expressed genes were identified based on fold change>2 and TPM transcripts per million >10. Among the top 20 up regulated genes  10 novel responsive genes were identified and verified by qRT PCR analysis on independent samples. Transcriptomic analysis indicated several deregulated pathways associated with cell cycle  endocrine disruptors  signal transduction and immune systems. Comparative analyses of TCDD induced transcriptomic changes between fish and mammalian models revealed that proteomic pathway is consistently up regulated while calcium signaling pathway and several immune related pathways are generally down regulated. Overall design: Transcriptome profiling of treated sample TCDD and control sample DMSO were generated by deep sequencing using three prime RNA SAGE with SOLiD system,,pubmed:24204792,,DMSO,GSM1209643,,source name:liver|tissue:liver|genotype:wildtype sibling|treatment:DMSO,DMSO,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Supplementary files format and content: The mapped transcripts were listed with GI and expression levels in TPM.,liver,3 mpf wildtype zebrafish were treated for 96 hrs. TCDD or DMSO treatment was conducted in 3 L tanks with around 15 adult and water was changed every day.,Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype:wildtype sibling|treatment:DMSO,GSM1209643,GSM1209643: DMSO; Danio rerio; RNA Seq,GSM1209643,,1,Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1209643,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP028848,,,solid0518_20101014_Gong_1_SetA_F3_0_2DMSO.csfasta solid0518_20101014_Gong_1_SetA_F3_QV_0_2DMSO.qual,SOLiD_native SOLiD_native,409327205.0,11695063.0,GSM1209643 r1,0:35,0:136723730;1:95263220;2:87949986;3:88818989;.:571280,35,,,,,,,,,SRX335554,SRS470625,SRA098000,GEO,National University of Singapore,1,0.01735,,0.00647,,0.9946,,0.51324,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-08-15,Adult,Adult,Liver,Liver and Biliary System
37131,SRR952909,SRX335553,SRS470624,SRP028848,PRJNA215326,Transcriptomic analyses of TCDD treated zebrafish liver,GSE49915,Transcriptome Analysis,To fully understand molecular toxicity of TCDD in an in vivo animal model  adult zebrafish were exposed to TCDD at xxx nM for xxx h and the livers were sampled for RNA sequencing based transcriptomic profiling. A total of 1 058 differently expressed genes were identified based on fold change>2 and TPM transcripts per million >10. Among the top 20 up regulated genes  10 novel responsive genes were identified and verified by qRT PCR analysis on independent samples. Transcriptomic analysis indicated several deregulated pathways associated with cell cycle  endocrine disruptors  signal transduction and immune systems. Comparative analyses of TCDD induced transcriptomic changes between fish and mammalian models revealed that proteomic pathway is consistently up regulated while calcium signaling pathway and several immune related pathways are generally down regulated. Overall design: Transcriptome profiling of treated sample TCDD and control sample DMSO were generated by deep sequencing using three prime RNA SAGE with SOLiD system,,pubmed:24204792,,TCDD,GSM1209642,,source name:liver|tissue:liver|genotype:wildtype sibling|treatment:TCDD,TCDD,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Supplementary files format and content: The mapped transcripts were listed with GI and expression levels in TPM.,liver,3 mpf wildtype zebrafish were treated for 96 hrs. TCDD or DMSO treatment was conducted in 3 L tanks with around 15 adult and water was changed every day.,Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype:wildtype sibling|treatment:TCDD,GSM1209642,GSM1209642: TCDD; Danio rerio; RNA Seq,GSM1209642,,1,Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1209642,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP028848,,,solid0518_20101014_Gong_1_SetA_F3_QV_1_2TCDD.qual solid0518_20101014_Gong_1_SetA_F3_1_2TCDD.csfasta,SOLiD_native SOLiD_native,627514895.0,17928997.0,GSM1209642 r1,0:35,0:214639659;1:142538233;2:131819822;3:137625000;.:892181,35,,,,,,,,,SRX335553,SRS470624,SRA098000,GEO,National University of Singapore,1,0.01773,,0.00917,,0.99646,,0.56398,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-08-15,Adult,Adult,Liver,Liver and Biliary System
37217,SRR1035240,SRX381137,SRS505529,SRP033231,PRJNA229468,Overexpression of UHRF1 drives DNA hypomethylation and hepatocellular carcinoma,GSE52605,Transcriptome Analysis,UHRF1 is an essential regulator of DNA methylation that is highly expressed in many cancers. Using transgenic zebrafish  cultured cells and human tumors  we demonstrate that UHRF1 is an oncogene. RNAseq was used to assess the variation in gene expression between control and experimental samples. Overall design: Total small RNA from 2 batches of Tgfabp10:has.UHRF1 GFPHigh and age matched Tgfabp10:nls mCherry control 5 dpf zebrafish livers was purified for preparation of high throughput sequencing libraries.,,pubmed:24486181,,mCherry cntr2,GSM1272461,,source name:Zebrafish 5 dpf liver|genotype/variation:Tgfabp10:nls mCherry|tissue:liver|development stage:5 dpf,mCherry cntr2,Illumina CASAVA version 1.7 used for basecalling Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al.  2008; Olson et al.  2008; Tam et al.  2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes genes and their quantile normalized frequencies.,Zebrafish 5 dpf liver,,Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible  bar coded adapters were ligated to both ends.,,genotype/variation:Tgfabp10:nls mCherry|tissue:liver|developmental stage:5 dpf,GSM1272461,GSM1272461: mCherry cntr2; Danio rerio; RNA Seq,GSM1272461,,1,Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible  bar coded adapters were ligated to both ends.,GEO Accession:GSM1272461,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP033231,,,mCherry_cntr2.fastq.gz,fastq,2132003100.0,21320031.0,GSM1272461 r1,0:100,A:536532013;C:533562250;G:522685362;T:536641910;N:2581565,100,,,,536532013,533562250,522685362,536641910,2581565,SRX381137,SRS505529,SRA111986,GEO,"sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai",1,0.88347,,0.04357,,0.81964,,0.52384,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2013-11-21,Larval,Larval,Liver,Liver and Biliary System
37218,SRR1035239,SRX381136,SRS505528,SRP033231,PRJNA229468,Overexpression of UHRF1 drives DNA hypomethylation and hepatocellular carcinoma,GSE52605,Transcriptome Analysis,UHRF1 is an essential regulator of DNA methylation that is highly expressed in many cancers. Using transgenic zebrafish  cultured cells and human tumors  we demonstrate that UHRF1 is an oncogene. RNAseq was used to assess the variation in gene expression between control and experimental samples. Overall design: Total small RNA from 2 batches of Tgfabp10:has.UHRF1 GFPHigh and age matched Tgfabp10:nls mCherry control 5 dpf zebrafish livers was purified for preparation of high throughput sequencing libraries.,,pubmed:24486181,,mCherry cntr1,GSM1272460,,source name:Zebrafish 5 dpf liver|genotype/variation:Tgfabp10:nls mCherry|tissue:liver|development stage:5 dpf,mCherry cntr1,Illumina CASAVA version 1.7 used for basecalling Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al.  2008; Olson et al.  2008; Tam et al.  2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes genes and their quantile normalized frequencies.,Zebrafish 5 dpf liver,,Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible  bar coded adapters were ligated to both ends.,,genotype/variation:Tgfabp10:nls mCherry|tissue:liver|developmental stage:5 dpf,GSM1272460,GSM1272460: mCherry cntr1; Danio rerio; RNA Seq,GSM1272460,,1,Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible  bar coded adapters were ligated to both ends.,GEO Accession:GSM1272460,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP033231,,,mCherry_cntr1.fastq.gz,fastq,2098395500.0,20983955.0,GSM1272460 r1,0:100,A:533756912;C:521877600;G:512200617;T:528020965;N:2539406,100,,,,533756912,521877600,512200617,528020965,2539406,SRX381136,SRS505528,SRA111986,GEO,"sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai",1,0.89445,,0.02866,,0.82426,,0.50861,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2013-11-21,Larval,Larval,Liver,Liver and Biliary System
37219,SRR1035238,SRX381135,SRS505527,SRP033231,PRJNA229468,Overexpression of UHRF1 drives DNA hypomethylation and hepatocellular carcinoma,GSE52605,Transcriptome Analysis,UHRF1 is an essential regulator of DNA methylation that is highly expressed in many cancers. Using transgenic zebrafish  cultured cells and human tumors  we demonstrate that UHRF1 is an oncogene. RNAseq was used to assess the variation in gene expression between control and experimental samples. Overall design: Total small RNA from 2 batches of Tgfabp10:has.UHRF1 GFPHigh and age matched Tgfabp10:nls mCherry control 5 dpf zebrafish livers was purified for preparation of high throughput sequencing libraries.,,pubmed:24486181,,UHRF1 hi B,GSM1272459,,source name:Zebrafish 5 dpf liver|genotype/variation:Tgfabp10:has.UHRF1 GFP|tissue:liver|development stage:5 dpf,UHRF1 hi B,Illumina CASAVA version 1.7 used for basecalling Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al.  2008; Olson et al.  2008; Tam et al.  2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes genes and their quantile normalized frequencies.,Zebrafish 5 dpf liver,,Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible  bar coded adapters were ligated to both ends.,,genotype/variation:Tgfabp10:has.UHRF1 GFP|tissue:liver|developmental stage:5 dpf,GSM1272459,GSM1272459: UHRF1 hi B; Danio rerio; RNA Seq,GSM1272459,,1,Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible  bar coded adapters were ligated to both ends.,GEO Accession:GSM1272459,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP033231,,,UHRF1_hi_B.fastq.gz,fastq,2127061900.0,21270619.0,GSM1272459 r1,0:100,A:540147604;C:542900044;G:522760277;T:518703604;N:2550371,100,,,,540147604,542900044,522760277,518703604,2550371,SRX381135,SRS505527,SRA111986,GEO,"sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai",1,0.7609,,0.0395,,0.77788,,0.51544,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2013-11-21,Larval,Larval,Liver,Liver and Biliary System
37220,SRR1035237,SRX381134,SRS505526,SRP033231,PRJNA229468,Overexpression of UHRF1 drives DNA hypomethylation and hepatocellular carcinoma,GSE52605,Transcriptome Analysis,UHRF1 is an essential regulator of DNA methylation that is highly expressed in many cancers. Using transgenic zebrafish  cultured cells and human tumors  we demonstrate that UHRF1 is an oncogene. RNAseq was used to assess the variation in gene expression between control and experimental samples. Overall design: Total small RNA from 2 batches of Tgfabp10:has.UHRF1 GFPHigh and age matched Tgfabp10:nls mCherry control 5 dpf zebrafish livers was purified for preparation of high throughput sequencing libraries.,,pubmed:24486181,,UHRF1 hi A,GSM1272458,,source name:Zebrafish 5 dpf liver|genotype/variation:Tgfabp10:has.UHRF1 GFP|tissue:liver|development stage:5 dpf,UHRF1 hi A,Illumina CASAVA version 1.7 used for basecalling Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al.  2008; Olson et al.  2008; Tam et al.  2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes genes and their quantile normalized frequencies.,Zebrafish 5 dpf liver,,Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible  bar coded adapters were ligated to both ends.,,genotype/variation:Tgfabp10:has.UHRF1 GFP|tissue:liver|developmental stage:5 dpf,GSM1272458,GSM1272458: UHRF1 hi A; Danio rerio; RNA Seq,GSM1272458,,1,Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible  bar coded adapters were ligated to both ends.,GEO Accession:GSM1272458,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP033231,,,UHRF1_hi_A.fastq.gz,fastq,2476218900.0,24762189.0,GSM1272458 r1,0:100,A:625575890;C:631605318;G:620422311;T:595617894;N:2997487,100,,,,625575890,631605318,620422311,595617894,2997487,SRX381134,SRS505526,SRA111986,GEO,"sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai",1,0.80154,,0.04243,,0.80409,,0.50831,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2013-11-21,Larval,Larval,Liver,Liver and Biliary System
37271,SRR1050719,SRX392663,SRS515660,SRP034513,PRJNA231764,Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer,GSE53342,Transcriptome Analysis,To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless  they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples  and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs  suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus  these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D   X M+D   X M D+  xmrk tumor sample X+M D+ and control samples X M D   X+M D   X M D+  were generated by deep sequencing  using three prime RNA SAGE on SOLiD system,,pubmed:24633177,,X+M D+,GSM1289483,,source name:liver tumor|tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:doxycycline,X+M D+,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,liver tumor,Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:doxycycline,GSM1289483,GSM1289483: X+M D+; Danio rerio; RNA Seq,GSM1289483,,1,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1289483,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP034513,,,X+M-D+.csfasta.gz X+M-D+.qual,SOLiD_native SOLiD_native,367532585.0,10500931.0,GSM1289483 r1,0:35,0:113917936;1:90770860;2:74839037;3:87267038;.:737714,35,,,,,,,,,SRX392663,SRS515660,SRA117588,GEO,National University of Singapore,1,0.03142,,0.01041,,0.99115,,0.47722,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-16,Adult,Adult,Liver,Liver and Biliary System
37272,SRR1050718,SRX392662,SRS515661,SRP034513,PRJNA231764,Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer,GSE53342,Transcriptome Analysis,To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless  they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples  and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs  suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus  these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D   X M+D   X M D+  xmrk tumor sample X+M D+ and control samples X M D   X+M D   X M D+  were generated by deep sequencing  using three prime RNA SAGE on SOLiD system,,pubmed:24633177,,X M+D+,GSM1289482,,source name:liver tumor|tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:doxycycline,X M+D+,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,liver tumor,Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:doxycycline,GSM1289482,GSM1289482: X M+D+; Danio rerio; RNA Seq,GSM1289482,,1,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1289482,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP034513,,,X-M+D+.csfasta.gz X-M+D+.qual,SOLiD_native SOLiD_native,524940885.0,14998311.0,GSM1289482 r1,0:35,0:177873348;1:126792787;2:107434769;3:111636161;.:1203820,35,,,,,,,,,SRX392662,SRS515661,SRA117588,GEO,National University of Singapore,1,0.04433,,0.02519,,0.99456,,0.5443,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-16,Adult,Adult,Liver,Liver and Biliary System
37273,SRR1050717,SRX392661,SRS515658,SRP034513,PRJNA231764,Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer,GSE53342,Transcriptome Analysis,To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless  they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples  and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs  suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus  these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D   X M+D   X M D+  xmrk tumor sample X+M D+ and control samples X M D   X+M D   X M D+  were generated by deep sequencing  using three prime RNA SAGE on SOLiD system,,pubmed:24633177,,X M D+,GSM1289481,,source name:control liver|tissue:liver|genotype:wildtype sibling|agent:doxycycline,X M D+,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver,Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype:wildtype sibling|agent:doxycycline,GSM1289481,GSM1289481: X M D+; Danio rerio; RNA Seq,GSM1289481,,1,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1289481,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP034513,,,X-M-D+.csfasta.gz X-M-D+.qual,SOLiD_native SOLiD_native,503677265.0,14390779.0,GSM1289481 r1,0:35,0:153190412;1:124381654;2:106372352;3:118615876;.:1116971,35,,,,,,,,,SRX392661,SRS515658,SRA117588,GEO,National University of Singapore,1,0.03136,,0.01201,,0.99356,,0.49598,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-16,Adult,Adult,Liver,Liver and Biliary System
37274,SRR1050716,SRX392660,SRS515659,SRP034513,PRJNA231764,Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer,GSE53342,Transcriptome Analysis,To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless  they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples  and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs  suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus  these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D   X M+D   X M D+  xmrk tumor sample X+M D+ and control samples X M D   X+M D   X M D+  were generated by deep sequencing  using three prime RNA SAGE on SOLiD system,,pubmed:24633177,,X+M D ,GSM1289480,,source name:control liver|tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:n1,X+M D ,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver,Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:n1,GSM1289480,GSM1289480: X+M D ; Danio rerio; RNA Seq,GSM1289480,,1,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1289480,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP034513,,,X+M-D-.csfasta.gz X+M-D-.qual,SOLiD_native SOLiD_native,634523960.0,18129256.0,GSM1289480 r1,0:35,0:234010528;1:135057441;2:132344184;3:131577105;.:1534702,35,,,,,,,,,SRX392660,SRS515659,SRA117588,GEO,National University of Singapore,1,0.06814,,0.05142,,0.99579,,0.6174,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-16,Adult,Adult,Liver,Liver and Biliary System
37275,SRR1050715,SRX392659,SRS515657,SRP034513,PRJNA231764,Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer,GSE53342,Transcriptome Analysis,To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless  they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples  and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs  suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus  these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D   X M+D   X M D+  xmrk tumor sample X+M D+ and control samples X M D   X+M D   X M D+  were generated by deep sequencing  using three prime RNA SAGE on SOLiD system,,pubmed:24633177,,X M+D ,GSM1289479,,source name:control liver|tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:n1,X M+D ,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver,Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:n1,GSM1289479,GSM1289479: X M+D ; Danio rerio; RNA Seq,GSM1289479,,1,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1289479,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP034513,,,X-M+D-.csfasta.gz X-M+D-.qual,SOLiD_native SOLiD_native,417548565.0,11929959.0,GSM1289479 r1,0:35,0:114209112;1:103552786;2:91302789;3:107590004;.:893874,35,,,,,,,,,SRX392659,SRS515657,SRA117588,GEO,National University of Singapore,1,0.02253,,0.00519,,0.99218,,0.61466,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-16,Adult,Adult,Liver,Liver and Biliary System