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
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
31986,SRR28894021,SRX24452441,SRS21206092,SRP505663,PRJNA1107798,liver,PRJNA1107798,Other,wt and elovl2 mutant liver,,,,,elovl2 4,,strain:elovl2 4|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,elovl2 4,8,8,liver,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq X,,SRP505663,,,elovl2-4,fastq,4367010000.0,29113400.0,elovl2 4.gz,0:150,A:1161921878;C:1015107709;G:1012841192;T:1177020487;N:118734,150,,,,1161921878,1015107709,1012841192,1177020487,118734,SRX24452441,SRS21206092,SRA1858809,Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology,Chinese Academy of Sciences (CAS),,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-05-04,Undetermined,Undetermined,Liver,Liver and Biliary System
31987,SRR28894022,SRX24452440,SRS21206091,SRP505663,PRJNA1107798,liver,PRJNA1107798,Other,wt and elovl2 mutant liver,,,,,elovl2 3,,strain:elovl2 3|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,elovl2 3,7,7,liver,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq X,,SRP505663,,,elovl2-3,fastq,5125533150.0,34170221.0,elovl2 3.gz,0:150,A:1365645170;C:1189846405;G:1184721703;T:1385180096;N:139776,150,,,,1365645170,1189846405,1184721703,1385180096,139776,SRX24452440,SRS21206091,SRA1858809,Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology,Chinese Academy of Sciences (CAS),,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-05-04,Undetermined,Undetermined,Liver,Liver and Biliary System
31988,SRR28894023,SRX24452439,SRS21206090,SRP505663,PRJNA1107798,liver,PRJNA1107798,Other,wt and elovl2 mutant liver,,,,,elovl2 2,,strain:elovl2 2|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,elovl2 2,6,6,liver,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq X,,SRP505663,,,elovl2-2,fastq,3261375750.0,21742505.0,elovl2 2.gz,0:150,A:878478836;C:747963062;G:743760185;T:891083235;N:90432,150,,,,878478836,747963062,743760185,891083235,90432,SRX24452439,SRS21206090,SRA1858809,Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology,Chinese Academy of Sciences (CAS),,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-05-04,Undetermined,Undetermined,Liver,Liver and Biliary System
31989,SRR28894024,SRX24452438,SRS21206089,SRP505663,PRJNA1107798,liver,PRJNA1107798,Other,wt and elovl2 mutant liver,,,,,elovl2 1,,strain:elovl2 1|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,elovl2 1,5,5,liver,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq X,,SRP505663,,,elovl2-1,fastq,3629422950.0,24196153.0,elovl2 1.gz,0:150,A:974034477;C:836070594;G:831068189;T:988151010;N:98680,150,,,,974034477,836070594,831068189,988151010,98680,SRX24452438,SRS21206089,SRA1858809,Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology,Chinese Academy of Sciences (CAS),,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-05-04,Undetermined,Undetermined,Liver,Liver and Biliary System
31990,SRR28894025,SRX24452437,SRS21206088,SRP505663,PRJNA1107798,liver,PRJNA1107798,Other,wt and elovl2 mutant liver,,,,,WT 4,,strain:WT 4|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,WT 4,4,4,liver,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq X,,SRP505663,,,WT-4,fastq,4037472900.0,26916486.0,WT 4.gz,0:150,A:1083383010;C:932278459;G:925831402;T:1095868616;N:111413,150,,,,1083383010,932278459,925831402,1095868616,111413,SRX24452437,SRS21206088,SRA1858809,Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology,Chinese Academy of Sciences (CAS),,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-05-04,Undetermined,Undetermined,Liver,Liver and Biliary System
31991,SRR28894026,SRX24452436,SRS21206087,SRP505663,PRJNA1107798,liver,PRJNA1107798,Other,wt and elovl2 mutant liver,,,,,WT 3,,strain:WT 3|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,WT 3,3,3,liver,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq X,,SRP505663,,,WT-3,fastq,3651994200.0,24346628.0,WT 3.gz,0:150,A:978819903;C:844506880;G:836704943;T:991863415;N:99059,150,,,,978819903,844506880,836704943,991863415,99059,SRX24452436,SRS21206087,SRA1858809,Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology,Chinese Academy of Sciences (CAS),,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-05-04,Undetermined,Undetermined,Liver,Liver and Biliary System
31992,SRR28894027,SRX24452435,SRS21206086,SRP505663,PRJNA1107798,liver,PRJNA1107798,Other,wt and elovl2 mutant liver,,,,,WT 2,,strain:WT 2|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,WT 2,2,2,liver,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq X,,SRP505663,,,WT-2,fastq,3845338950.0,25635593.0,WT 2.gz,0:150,A:1033991995;C:885977441;G:878907105;T:1046356459;N:105950,150,,,,1033991995,885977441,878907105,1046356459,105950,SRX24452435,SRS21206086,SRA1858809,Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology,Chinese Academy of Sciences (CAS),,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-05-04,Undetermined,Undetermined,Liver,Liver and Biliary System
31993,SRR28894028,SRX24452434,SRS21206085,SRP505663,PRJNA1107798,liver,PRJNA1107798,Other,wt and elovl2 mutant liver,,,,,WT 1,,strain:WT 1|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,WT 1,1,1,liver,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq X,,SRP505663,,,WT-1,fastq,3756883050.0,25045887.0,WT 1.gz,0:150,A:1005244721;C:868304979;G:865360007;T:1017811504;N:161839,150,,,,1005244721,868304979,865360007,1017811504,161839,SRX24452434,SRS21206085,SRA1858809,Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology,Chinese Academy of Sciences (CAS),,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-05-04,Undetermined,Undetermined,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
41593,SRR392106,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,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>,SRP009841,,,c1-2_1.fq c1-2_2.fq,fastq fastq,855494000.0,4502600.0,Control Sampe 1,0:100 1:90,A:217839807;C:202017646;G:207454208;T:227797566;N:384773,100,90,,,217839807,202017646,207454208,227797566,384773,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.87575,0.93454,0.06936,0.08546,0.82513,0.82306,0.49603,0.49334,100,90,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
41594,SRR392108,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,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>,SRP009841,,,c2-2_1.fq c2-2_2.fq,fastq fastq,1238874100.0,6520390.0,Control Sampe 2,0:100 1:90,A:316162781;C:292160612;G:299402161;T:330578118;N:570428,100,90,,,316162781,292160612,299402161,330578118,570428,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.89891,0.94864,0.03863,0.04738,0.8673,0.86531,0.28488,0.27076,100,90,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
41595,SRR392109,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,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>,SRP009841,,,c3-2_2.fq c3-2_1.fq,fastq fastq,2412101476.0,12830327.0,Control Sampe 3,0:100 1:88,A:611075174;C:569003408;G:589175071;T:641747898;N:1099925,100,88,,,611075174,569003408,589175071,641747898,1099925,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.87563,0.94341,0.03506,0.0441,0.83063,0.82795,0.41995,0.41226,100,88,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
41596,SRR392110,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,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>,SRP009841,,,v1_2.fq v1_1.fq,fastq fastq,1549099640.0,8153156.0,Case sampe 1,0:100 1:90,A:412607118;C:353282622;G:359371048;T:423373718;N:465134,100,90,,,412607118,353282622,359371048,423373718,465134,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.92368,0.9462,0.0604,0.06838,0.81249,0.81578,0.47008,0.4761,100,90,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
41597,SRR392111,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,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>,SRP009841,,,v2_1.fq v2_2.fq,fastq fastq,1465445712.0,7794924.0,Case sampe 2,0:100 1:88,A:387149663;C:337675800;G:340143929;T:400109622;N:366698,100,88,,,387149663,337675800,340143929,400109622,366698,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.92047,0.94711,0.05494,0.06325,0.81255,0.8143,0.48839,0.47383,100,88,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
41598,SRR402758,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,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>,SRP009841,,,v3_2.fq v3_1.fq,fastq fastq,1025249164.0,5453453.0,Case sampe 3,0:100 1:88,A:261599009;C:242254683;G:249423008;T:271717829;N:254635,100,88,,,261599009,242254683,249423008,271717829,254635,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.93668,0.95934,0.02982,0.03449,0.81347,0.8196,0.47392,0.47176,100,88,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
42533,SRR5742065,SRX2947031,SRS2306327,SRP110156,PRJNA391468,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE PLASTICIZER 2 ETHYLHEXYL PHTHALATE DEHP.,GSE100367,Transcriptome Analysis,We report the effects of exposure to the endocrine disurptor 2 ethylhexyl phthalate DEHP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and insulin resistance  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:29391432,,CL68,GSM2679611,,tissue:Liver|agent:5.8 nM 2 ethylhexyl phthalate,CL68,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 0.65 nM of 17α ethinylestradiol EE2  one tank contained 5.8 nM of 2 ethylhexyl phthalate DEHP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:5.8 nM 2 ethylhexyl phthalate,GSM2679611,GSM2679611: CL68; Danio rerio; RNA Seq,GSM2679611,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679611,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110156,,,M-CL68.fa.fastq.gz,fastq,65053254.0,1548887.0,GSM2679611 r1,0:42,A:16875146;C:13379903;G:16312762;T:18482630;N:2813,42,,,,16875146,13379903,16312762,18482630,2813,SRX2947031,SRS2306327,SRA579533,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42534,SRR5742064,SRX2947030,SRS2306326,SRP110156,PRJNA391468,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE PLASTICIZER 2 ETHYLHEXYL PHTHALATE DEHP.,GSE100367,Transcriptome Analysis,We report the effects of exposure to the endocrine disurptor 2 ethylhexyl phthalate DEHP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and insulin resistance  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:29391432,,CL67,GSM2679610,,tissue:Liver|agent:5.8 nM 2 ethylhexyl phthalate,CL67,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 0.65 nM of 17α ethinylestradiol EE2  one tank contained 5.8 nM of 2 ethylhexyl phthalate DEHP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:5.8 nM 2 ethylhexyl phthalate,GSM2679610,GSM2679610: CL67; Danio rerio; RNA Seq,GSM2679610,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679610,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110156,,,M-CL67.fa.fastq.gz,fastq,97951518.0,2332179.0,GSM2679610 r1,0:42,A:25604873;C:20781116;G:24203084;T:27358188;N:4257,42,,,,25604873,20781116,24203084,27358188,4257,SRX2947030,SRS2306326,SRA579533,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42535,SRR5742063,SRX2947029,SRS2306325,SRP110156,PRJNA391468,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE PLASTICIZER 2 ETHYLHEXYL PHTHALATE DEHP.,GSE100367,Transcriptome Analysis,We report the effects of exposure to the endocrine disurptor 2 ethylhexyl phthalate DEHP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and insulin resistance  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:29391432,,CL66,GSM2679609,,tissue:Liver|agent:0.65 nM Ethinylestradiol EE2,CL66,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 0.65 nM of 17α ethinylestradiol EE2  one tank contained 5.8 nM of 2 ethylhexyl phthalate DEHP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:0.65 nM Ethinylestradiol EE2,GSM2679609,GSM2679609: CL66; Danio rerio; RNA Seq,GSM2679609,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679609,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110156,,,M-CL66.fa.fastq.gz,fastq,79555644.0,1894182.0,GSM2679609 r1,0:42,A:20840478;C:16298564;G:19354919;T:23058169;N:3514,42,,,,20840478,16298564,19354919,23058169,3514,SRX2947029,SRS2306325,SRA579533,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42536,SRR5742062,SRX2947028,SRS2306324,SRP110156,PRJNA391468,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE PLASTICIZER 2 ETHYLHEXYL PHTHALATE DEHP.,GSE100367,Transcriptome Analysis,We report the effects of exposure to the endocrine disurptor 2 ethylhexyl phthalate DEHP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and insulin resistance  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:29391432,,CL65,GSM2679608,,tissue:Liver|agent:0.65 nM Ethinylestradiol EE2,CL65,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 0.65 nM of 17α ethinylestradiol EE2  one tank contained 5.8 nM of 2 ethylhexyl phthalate DEHP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:0.65 nM Ethinylestradiol EE2,GSM2679608,GSM2679608: CL65; Danio rerio; RNA Seq,GSM2679608,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679608,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110156,,,M-CL65.fa.fastq.gz,fastq,74658444.0,1777582.0,GSM2679608 r1,0:42,A:19262431;C:15422889;G:18345920;T:21623880;N:3324,42,,,,19262431,15422889,18345920,21623880,3324,SRX2947028,SRS2306324,SRA579533,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42537,SRR5742061,SRX2947027,SRS2306322,SRP110156,PRJNA391468,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE PLASTICIZER 2 ETHYLHEXYL PHTHALATE DEHP.,GSE100367,Transcriptome Analysis,We report the effects of exposure to the endocrine disurptor 2 ethylhexyl phthalate DEHP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and insulin resistance  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:29391432,,CL64,GSM2679607,,tissue:Liver|agent:Control,CL64,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 0.65 nM of 17α ethinylestradiol EE2  one tank contained 5.8 nM of 2 ethylhexyl phthalate DEHP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:Control,GSM2679607,GSM2679607: CL64; Danio rerio; RNA Seq,GSM2679607,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679607,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110156,,,M-CL64e.fa.fastq.gz,fastq,81941412.0,1950986.0,GSM2679607 r1,0:42,A:21427784;C:17542697;G:20002613;T:22964734;N:3584,42,,,,21427784,17542697,20002613,22964734,3584,SRX2947027,SRS2306322,SRA579533,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42538,SRR5742060,SRX2947026,SRS2306323,SRP110156,PRJNA391468,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE PLASTICIZER 2 ETHYLHEXYL PHTHALATE DEHP.,GSE100367,Transcriptome Analysis,We report the effects of exposure to the endocrine disurptor 2 ethylhexyl phthalate DEHP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and insulin resistance  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:29391432,,CL63,GSM2679606,,tissue:Liver|agent:Control,CL63,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 0.65 nM of 17α ethinylestradiol EE2  one tank contained 5.8 nM of 2 ethylhexyl phthalate DEHP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:Control,GSM2679606,GSM2679606: CL63; Danio rerio; RNA Seq,GSM2679606,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679606,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110156,,,M-CL63e.fa.fastq.gz,fastq,99418914.0,2367117.0,GSM2679606 r1,0:42,A:25465262;C:20166931;G:24797943;T:28984279;N:4499,42,,,,25465262,20166931,24797943,28984279,4499,SRX2947026,SRS2306323,SRA579533,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42539,SRR5742109,SRX2947056,SRS2306352,SRP110158,PRJNA391470,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE NON IONIC SURFACTANT NONYLPHENOL NP.,GSE100369,Transcriptome Analysis,We report the effects of exposure to the endocrine disruptor nonylphenol NP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and inflammation  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:30563618,,CL62,GSM2679636,,tissue:Liver|agent:100 nM Nonylphenol NP|Sex:male,CL62,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content:   tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 1000 nM of 17β estradiol E2  one tank contained 100 nM of nonylphenol NP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:100 nM Nonylphenol NP|Sex:Male,GSM2679636,GSM2679636: CL62; Danio rerio; RNA Seq,GSM2679636,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679636,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110158,,,M-CL62.fa.fastq.gz,fastq,122493672.0,2916516.0,GSM2679636 r1,0:42,A:31987859;C:24358295;G:32088563;T:34053478;N:5477,42,,,,31987859,24358295,32088563,34053478,5477,SRX2947056,SRS2306352,SRA579535,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42540,SRR5742108,SRX2947055,SRS2306351,SRP110158,PRJNA391470,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE NON IONIC SURFACTANT NONYLPHENOL NP.,GSE100369,Transcriptome Analysis,We report the effects of exposure to the endocrine disruptor nonylphenol NP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and inflammation  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:30563618,,CL61,GSM2679635,,tissue:Liver|agent:100 nM Nonylphenol NP|Sex:male,CL61,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content:   tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 1000 nM of 17β estradiol E2  one tank contained 100 nM of nonylphenol NP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:100 nM Nonylphenol NP|Sex:Male,GSM2679635,GSM2679635: CL61; Danio rerio; RNA Seq,GSM2679635,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679635,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110158,,,M-CL61.fa.fastq.gz,fastq,127229214.0,3029267.0,GSM2679635 r1,0:42,A:32179832;C:24929970;G:35004390;T:35109199;N:5823,42,,,,32179832,24929970,35004390,35109199,5823,SRX2947055,SRS2306351,SRA579535,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42541,SRR5742107,SRX2947054,SRS2306350,SRP110158,PRJNA391470,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE NON IONIC SURFACTANT NONYLPHENOL NP.,GSE100369,Transcriptome Analysis,We report the effects of exposure to the endocrine disruptor nonylphenol NP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and inflammation  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:30563618,,CL58,GSM2679634,,tissue:Liver|agent:1000 nM Estradiol E2|Sex:male,CL58,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content:   tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 1000 nM of 17β estradiol E2  one tank contained 100 nM of nonylphenol NP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:1000 nM Estradiol E2|Sex:Male,GSM2679634,GSM2679634: CL58; Danio rerio; RNA Seq,GSM2679634,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679634,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110158,,,,,12874554.0,306537.0,GSM2679634 r1,0:42,A:3406277;C:2909885;G:3212543;T:3345323;N:526,42,,,,3406277,2909885,3212543,3345323,526,SRX2947054,SRS2306350,SRA579535,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42542,SRR5742106,SRX2947053,SRS2306349,SRP110158,PRJNA391470,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE NON IONIC SURFACTANT NONYLPHENOL NP.,GSE100369,Transcriptome Analysis,We report the effects of exposure to the endocrine disruptor nonylphenol NP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and inflammation  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:30563618,,CL57,GSM2679633,,tissue:Liver|agent:1000 nM Estradiol E2|Sex:male,CL57,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content:   tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 1000 nM of 17β estradiol E2  one tank contained 100 nM of nonylphenol NP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:1000 nM Estradiol E2|Sex:Male,GSM2679633,GSM2679633: CL57; Danio rerio; RNA Seq,GSM2679633,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679633,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110158,,,M-CL57.fa.fastq.gz,fastq,173445972.0,4129666.0,GSM2679633 r1,0:42,A:45882794;C:30528182;G:45001451;T:52025714;N:7831,42,,,,45882794,30528182,45001451,52025714,7831,SRX2947053,SRS2306349,SRA579535,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42543,SRR5742105,SRX2947052,SRS2306348,SRP110158,PRJNA391470,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE NON IONIC SURFACTANT NONYLPHENOL NP.,GSE100369,Transcriptome Analysis,We report the effects of exposure to the endocrine disruptor nonylphenol NP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and inflammation  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:30563618,,CL60,GSM2679632,,tissue:Liver|agent:Control|Sex:male,CL60,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content:   tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 1000 nM of 17β estradiol E2  one tank contained 100 nM of nonylphenol NP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:Control|Sex:Male,GSM2679632,GSM2679632: CL60; Danio rerio; RNA Seq,GSM2679632,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679632,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110158,,,M-CL60.fa.fastq.gz,fastq,118617576.0,2824228.0,GSM2679632 r1,0:42,A:31502482;C:23344593;G:29696129;T:34068892;N:5480,42,,,,31502482,23344593,29696129,34068892,5480,SRX2947052,SRS2306348,SRA579535,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42544,SRR5742104,SRX2947051,SRS2306347,SRP110158,PRJNA391470,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE NON IONIC SURFACTANT NONYLPHENOL NP.,GSE100369,Transcriptome Analysis,We report the effects of exposure to the endocrine disruptor nonylphenol NP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and inflammation  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:30563618,,CL59,GSM2679631,,tissue:Liver|agent:Control|Sex:male,CL59,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content:   tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 1000 nM of 17β estradiol E2  one tank contained 100 nM of nonylphenol NP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:Control|Sex:Male,GSM2679631,GSM2679631: CL59; Danio rerio; RNA Seq,GSM2679631,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679631,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110158,,,M-CL59.fa.fastq.gz,fastq,157464720.0,3749160.0,GSM2679631 r1,0:42,A:41134035;C:28837910;G:40629565;T:46856242;N:6968,42,,,,41134035,28837910,40629565,46856242,6968,SRX2947051,SRS2306347,SRA579535,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
45005,SRR6411470,SRX3504485,SRS2782039,SRP127390,PRJNA427283,RNA profiling of the liver and gut tissues in zebrafish Danio rerio [mRNA],GSE108435,Transcriptome Analysis,Compared to other fish models  miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However  this field of research is in its infancy and the function of several dre miRNAs  as well as their tissue specific expression profile  are yet to be defined.   In this study  the liver and gut were dissected wildtype/untreated fish  total and small RNA were extracted  mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis  known and putative novel miRNAs were identified. Finally  we constructed a “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of transcriptome in an in vivo model organism in two defined tissues  liver and gut.,parent bioproject:PRJNA427275,pubmed:30386173,,Liver 2 mRNA,GSM2898182,,source name:Liver|Sex:male|tissue:Liver,Liver 2 mRNA,Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the DESEQ2 output for the gut vs liver Comparison.  Columns to the right of the Base Mean column represent standard DEseq2 output.  Gut 1  Gut 2  Liver 1 and Liver 2 contain raw count data for the two gut and two liver RNAseq libraries respectively. The ensembl gene id  external gene name  description represent zebrafish gene identifiers. The human homologs as determined by Ensembl homology are described using the following human gene identifiers  hsapiens homolog ensembl gene  hgnc symbol  Human description and Human entrez geneid,Liver,Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C  and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra  Germany.  Fish were acclimated for one week prior to extracting the tissues  i.e. liver and intestine. Tissue samples were  immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,Sex:male|tissue:Liver,GSM2898182,GSM2898182: Liver 2 mRNA; Danio rerio; RNA Seq,GSM2898182,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2898182,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP127390,,,Liver_2.fastq.gz,fastq,2174570997.0,42638647.0,GSM2898182 r1,0:51,A:548366346;C:555137400;G:541707378;T:528997203;N:362670,51,,,,548366346,555137400,541707378,528997203,362670,SRX3504485,SRS2782039,SRA641251,GEO,"Walton RS311, Pathology, Medical University of South Carolina",1,0.91804,,0.03093,,0.88493,,0.59674,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,United States,2017-12-22,Undetermined,Undetermined,Liver,Liver and Biliary System
45006,SRR6411469,SRX3504484,SRS2782038,SRP127390,PRJNA427283,RNA profiling of the liver and gut tissues in zebrafish Danio rerio [mRNA],GSE108435,Transcriptome Analysis,Compared to other fish models  miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However  this field of research is in its infancy and the function of several dre miRNAs  as well as their tissue specific expression profile  are yet to be defined.   In this study  the liver and gut were dissected wildtype/untreated fish  total and small RNA were extracted  mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis  known and putative novel miRNAs were identified. Finally  we constructed a “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of transcriptome in an in vivo model organism in two defined tissues  liver and gut.,parent bioproject:PRJNA427275,pubmed:30386173,,Liver 1 mRNA,GSM2898181,,source name:Liver|Sex:male|tissue:Liver,Liver 1 mRNA,Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: Tab delimited .txt files include the DESEQ2 output for the gut vs liver Comparison.  Columns to the right of the Base Mean column represent standard DEseq2 output.  Gut 1  Gut 2  Liver 1 and Liver 2 contain raw count data for the two gut and two liver RNAseq libraries respectively. The ensembl gene id  external gene name  description represent zebrafish gene identifiers. The human homologs as determined by Ensembl homology are described using the following human gene identifiers  hsapiens homolog ensembl gene  hgnc symbol  Human description and Human entrez geneid,Liver,Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C  and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 . Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra  Germany.  Fish were acclimated for one week prior to extracting the tissues  i.e. liver and intestine. Tissue samples were  immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,Sex:male|tissue:Liver,GSM2898181,GSM2898181: Liver 1 mRNA; Danio rerio; RNA Seq,GSM2898181,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2898181,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP127390,,,Liver_1.fastq.gz,fastq,2401461582.0,47087482.0,GSM2898181 r1,0:51,A:602921605;C:569179122;G:609802884;T:619142202;N:415769,51,,,,602921605,569179122,609802884,619142202,415769,SRX3504484,SRS2782038,SRA641251,GEO,"Walton RS311, Pathology, Medical University of South Carolina",1,0.92109,,0.03525,,0.87874,,0.58277,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,trueseq,bulk,unknown,unknown,,United States,2017-12-22,Undetermined,Undetermined,Liver,Liver and Biliary System
60681,SRR12464066,SRX8958322,SRS7214898,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  4h  high conc  1,Cu04H1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:400 𝜇M|exposure time:4 hour|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Cu  4h  high conc  1,Cu04H1,Cu04H1,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu04H1_1.fq.gz Cu04H1_2.fq.gz,fastq fastq,7003880700.0,23346269.0,Cu04H1 1.fq.gz,0:150 1:150,A:1920900910;C:1604303204;G:1600464252;T:1878079528;N:132806,150,150,,,1920900910,1604303204,1600464252,1878079528,132806,SRX8958322,SRS7214898,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.92657,0.93897,0.07932,0.07947,0.74779,0.74716,0.50743,0.50423,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60682,SRR12464067,SRX8958321,SRS7214897,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  4h  medium conc  3,Cu04M3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:200 𝜇M|exposure time:4 hour|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Cu  4h  medium conc  3,Cu04M3,Cu04M3,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu04M3_1.fq.gz Cu04M3_2.fq.gz,fastq fastq,9311961600.0,31039872.0,Cu04M3 1.fq.gz,0:150 1:150,A:2521044874;C:2155085879;G:2154940773;T:2480737727;N:152347,150,150,,,2521044874,2155085879,2154940773,2480737727,152347,SRX8958321,SRS7214897,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.94147,0.9418,0.07192,0.07189,0.7432,0.74367,0.50788,0.49928,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60683,SRR12464068,SRX8958320,SRS7214896,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  4h  medium conc  2,Cu04M2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:200 𝜇M|exposure time:4 hour|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Cu  4h  medium conc  2,Cu04M2,Cu04M2,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu04M2_1.fq.gz Cu04M2_2.fq.gz,fastq fastq,6639588300.0,22131961.0,Cu04M2 1.fq.gz,0:150 1:150,A:1818278396;C:1524674487;G:1507680893;T:1788846191;N:108333,150,150,,,1818278396,1524674487,1507680893,1788846191,108333,SRX8958320,SRS7214896,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.9394,0.94372,0.082,0.0816,0.74332,0.74365,0.51233,0.51313,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60684,SRR12464069,SRX8958319,SRS7214895,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  4h  medium conc  1,Cu04M1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:200 𝜇M|exposure time:4 hour|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Cu  4h  medium conc  1,Cu04M1,Cu04M1,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu04M1_1.fq.gz Cu04M1_2.fq.gz,fastq fastq,7584984600.0,25283282.0,Cu04M1 1.fq.gz,0:150 1:150,A:2075644421;C:1739589944;G:1737598862;T:2032027277;N:124096,150,150,,,2075644421,1739589944,1737598862,2032027277,124096,SRX8958319,SRS7214895,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.9296,0.93997,0.07473,0.07536,0.74511,0.74558,0.50129,0.49967,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60685,SRR12464070,SRX8958318,SRS7214894,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  4h  low conc  3,Cu04L3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:100 𝜇M|exposure time:4 hour|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Cu  4h  low conc  3,Cu04L3,Cu04L3,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu04L3_1.fq.gz Cu04L3_2.fq.gz,fastq fastq,7930255200.0,26434184.0,Cu04L3 1.fq.gz,0:150 1:150,A:2164769170;C:1823398164;G:1819510632;T:2122447886;N:129348,150,150,,,2164769170,1823398164,1819510632,2122447886,129348,SRX8958318,SRS7214894,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93484,0.94118,0.0742,0.0751,0.74353,0.74357,0.50572,0.50084,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60686,SRR12464071,SRX8958317,SRS7214893,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  24h  high conc  3,Cd24H3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:20 𝜇M|exposure time:24 hour|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Cd  24h  high conc  3,Cd24H3,Cd24H3,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd24H3_1.fq.gz Cd24H3_2.fq.gz,fastq fastq,7931077500.0,26436925.0,Cd24H3 1.fq.gz,0:150 1:150,A:2172426173;C:1811683820;G:1811584780;T:2135299072;N:83655,150,150,,,2172426173,1811683820,1811584780,2135299072,83655,SRX8958317,SRS7214893,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93019,0.93104,0.08707,0.08636,0.76295,0.76402,0.51617,0.51238,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60687,SRR12464072,SRX8958316,SRS7214892,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  24h  high conc  2,Cd24H2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:20 𝜇M|exposure time:24 hour|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Cd  24h  high conc  2,Cd24H2,Cd24H2,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd24H2_1.fq.gz Cd24H2_2.fq.gz,fastq fastq,6751596300.0,22505321.0,Cd24H2 1.fq.gz,0:150 1:150,A:1849899166;C:1543397241;G:1542481409;T:1815746751;N:71733,150,150,,,1849899166,1543397241,1542481409,1815746751,71733,SRX8958316,SRS7214892,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.92587,0.93096,0.08638,0.08727,0.76577,0.76721,0.51617,0.51271,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60688,SRR12464073,SRX8958315,SRS7214891,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  24h  high conc  1,Cd24H1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:20 𝜇M|exposure time:24 hour|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Cd  24h  high conc  1,Cd24H1,Cd24H1,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd24H1_1.fq.gz Cd24H1_2.fq.gz,fastq fastq,6529785000.0,21765950.0,Cd24H1 1.fq.gz,0:150 1:150,A:1786700889;C:1493209174;G:1493580286;T:1756226630;N:68021,150,150,,,1786700889,1493209174,1493580286,1756226630,68021,SRX8958315,SRS7214891,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.92995,0.93214,0.08695,0.08724,0.76305,0.76378,0.48653,0.51285,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60689,SRR12464074,SRX8958314,SRS7214890,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  24h  medium conc  3,Cd24M3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:10 𝜇M|exposure time:24 hour|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Cd  24h  medium conc  3,Cd24M3,Cd24M3,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd24M3_1.fq.gz Cd24M3_2.fq.gz,fastq fastq,6300490800.0,21001636.0,Cd24M3 1.fq.gz,0:150 1:150,A:1687657129;C:1474456299;G:1477052957;T:1661258516;N:65899,150,150,,,1687657129,1474456299,1477052957,1661258516,65899,SRX8958314,SRS7214890,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.9452,0.94442,0.0676,0.0674,0.75848,0.75816,0.49395,0.50011,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60690,SRR12464075,SRX8958313,SRS7214889,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  24h  medium conc  2,Cd24M2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:10 𝜇M|exposure time:24 hour|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Cd  24h  medium conc  2,Cd24M2,Cd24M2,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd24M2_1.fq.gz Cd24M2_2.fq.gz,fastq fastq,6309228900.0,21030763.0,Cd24M2 1.fq.gz,0:150 1:150,A:1724109303;C:1446177699;G:1444603181;T:1694271760;N:66957,150,150,,,1724109303,1446177699,1444603181,1694271760,66957,SRX8958313,SRS7214889,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93428,0.93668,0.07835,0.07831,0.7571,0.75716,0.5075,0.50775,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60691,SRR12464076,SRX8958312,SRS7214888,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  24h  medium conc  1,Cd24M1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:10 𝜇M|exposure time:24 hour|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Cd  24h  medium conc  1,Cd24M1,Cd24M1,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd24M1_1.fq.gz Cd24M1_2.fq.gz,fastq fastq,7053528900.0,23511763.0,Cd24M1 1.fq.gz,0:150 1:150,A:1925683207;C:1618807671;G:1617901587;T:1891062329;N:74106,150,150,,,1925683207,1618807671,1617901587,1891062329,74106,SRX8958312,SRS7214888,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93587,0.93698,0.0769,0.07706,0.75824,0.75783,0.50886,0.50955,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60692,SRR12464077,SRX8958311,SRS7214887,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  24h  low conc  3,Cd24L3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:5 𝜇M|exposure time:24 hour|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Cd  24h  low conc  3,Cd24L3,Cd24L3,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd24L3_1.fq.gz Cd24L3_2.fq.gz,fastq fastq,7182969300.0,23943231.0,Cd24L3 1.fq.gz,0:150 1:150,A:1958186782;C:1650988467;G:1651994653;T:1921723572;N:75826,150,150,,,1958186782,1650988467,1651994653,1921723572,75826,SRX8958311,SRS7214887,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93535,0.93646,0.07828,0.07841,0.7488,0.75006,0.50128,0.50206,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60693,SRR12464078,SRX8958310,SRS7214886,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  24h  low conc  2,Cd24L2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:5 𝜇M|exposure time:24 hour|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Cd  24h  low conc  2,Cd24L2,Cd24L2,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd24L2_1.fq.gz Cd24L2_2.fq.gz,fastq fastq,8169704100.0,27232347.0,Cd24L2 1.fq.gz,0:150 1:150,A:2229274048;C:1876679266;G:1874470596;T:2189195334;N:84856,150,150,,,2229274048,1876679266,1874470596,2189195334,84856,SRX8958310,SRS7214886,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93693,0.93845,0.07907,0.0792,0.74838,0.74862,0.5002,0.50222,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60694,SRR12464079,SRX8958309,SRS7214885,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  4h  low conc  2,Cu04L2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:100 𝜇M|exposure time:4 hour|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Cu  4h  low conc  2,Cu04L2,Cu04L2,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu04L2_1.fq.gz Cu04L2_2.fq.gz,fastq fastq,7679080800.0,25596936.0,Cu04L2 1.fq.gz,0:150 1:150,A:2093339412;C:1768011985;G:1769763221;T:2047841208;N:124974,150,150,,,2093339412,1768011985,1769763221,2047841208,124974,SRX8958309,SRS7214885,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.92773,0.93977,0.07517,0.07553,0.74349,0.7429,0.50721,0.50562,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60695,SRR12464080,SRX8958308,SRS7214884,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  24h  low conc  1,Cd24L1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:5 𝜇M|exposure time:24 hour|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Cd  24h  low conc  1,Cd24L1,Cd24L1,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd24L1_1.fq.gz Cd24L1_2.fq.gz,fastq fastq,6543011700.0,21810039.0,Cd24L1 1.fq.gz,0:150 1:150,A:1784568350;C:1505031282;G:1504210365;T:1749132357;N:69346,150,150,,,1784568350,1505031282,1504210365,1749132357,69346,SRX8958308,SRS7214884,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93622,0.9374,0.07821,0.07782,0.74854,0.75026,0.50128,0.49785,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60696,SRR12464081,SRX8958307,SRS7214883,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  24h  Control  3,Cd24C3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:0 𝜇M|exposure time:24 hour|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Cd  24h  Control  3,Cd24C3,Cd24C3,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd24C3_1.fq.gz Cd24C3_2.fq.gz,fastq fastq,6292133100.0,20973777.0,Cd24C3 1.fq.gz,0:150 1:150,A:1725238483;C:1434877155;G:1435128127;T:1696828149;N:61186,150,150,,,1725238483,1434877155,1435128127,1696828149,61186,SRX8958307,SRS7214883,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93136,0.93296,0.0931,0.09347,0.73821,0.73807,0.49783,0.49618,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60697,SRR12464082,SRX8958306,SRS7214882,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  24h  Control  2,Cd24C2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:0 𝜇M|exposure time:24 hour|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Cd  24h  Control  2,Cd24C2,Cd24C2,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd24C2_1.fq.gz Cd24C2_2.fq.gz,fastq fastq,7548357000.0,25161190.0,Cd24C2 1.fq.gz,0:150 1:150,A:2069197560;C:1724688670;G:1721367614;T:2033030032;N:73124,150,150,,,2069197560,1724688670,1721367614,2033030032,73124,SRX8958306,SRS7214882,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93095,0.93108,0.09112,0.09167,0.74038,0.73998,0.49961,0.49374,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60698,SRR12464083,SRX8958305,SRS7214881,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  24h  Control  1,Cd24C1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:0 𝜇M|exposure time:24 hour|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Cd  24h  Control  1,Cd24C1,Cd24C1,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd24C1_1.fq.gz Cd24C1_2.fq.gz,fastq fastq,6968558700.0,23228529.0,Cd24C1 1.fq.gz,0:150 1:150,A:1906033588;C:1594789197;G:1593487780;T:1874180520;N:67615,150,150,,,1906033588,1594789197,1593487780,1874180520,67615,SRX8958305,SRS7214881,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93431,0.93408,0.09146,0.09154,0.73945,0.7401,0.50123,0.50233,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60699,SRR12464084,SRX8958304,SRS7214880,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  4h  high conc  3,Cd04H3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:20 𝜇M|exposure time:4 hour|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Cd  4h  high conc  3,Cd04H3,Cd04H3,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd04H3_1.fq.gz Cd04H3_2.fq.gz,fastq fastq,7121092500.0,23736975.0,Cd04H3 1.fq.gz,0:150 1:150,A:1957455665;C:1624607106;G:1622412265;T:1916480227;N:137237,150,150,,,1957455665,1624607106,1622412265,1916480227,137237,SRX8958304,SRS7214880,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.9261,0.93654,0.08607,0.087,0.74292,0.74361,0.50617,0.50631,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60700,SRR12464085,SRX8958303,SRS7214879,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  4h  high conc  2,Cd04H2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:20 𝜇M|exposure time:4 hour|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Cd  4h  high conc  2,Cd04H2,Cd04H2,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd04H2_1.fq.gz Cd04H2_2.fq.gz,fastq fastq,9498276300.0,31660921.0,Cd04H2 1.fq.gz,0:150 1:150,A:2590034359;C:2186143092;G:2181335900;T:2540655312;N:107637,150,150,,,2590034359,2186143092,2181335900,2540655312,107637,SRX8958303,SRS7214879,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93303,0.94057,0.07671,0.07724,0.74499,0.74434,0.4854,0.49948,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60701,SRR12464086,SRX8958302,SRS7214878,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  4h  high conc  1,Cd04H1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:20 𝜇M|exposure time:4 hour|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Cd  4h  high conc  1,Cd04H1,Cd04H1,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd04H1_1.fq.gz Cd04H1_2.fq.gz,fastq fastq,6374323500.0,21247745.0,Cd04H1 1.fq.gz,0:150 1:150,A:1748564842;C:1457309967;G:1455225044;T:1713120050;N:103597,150,150,,,1748564842,1457309967,1455225044,1713120050,103597,SRX8958302,SRS7214878,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.92496,0.93705,0.07909,0.08089,0.74801,0.7475,0.48754,0.50007,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60702,SRR12464087,SRX8958301,SRS7214877,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  4h  medium conc  3,Cd04M3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:10 𝜇M|exposure time:4 hour|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Cd  4h  medium conc  3,Cd04M3,Cd04M3,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd04M3_1.fq.gz Cd04M3_2.fq.gz,fastq fastq,7250817000.0,24169390.0,Cd04M3 1.fq.gz,0:150 1:150,A:1975158071;C:1668946082;G:1669123266;T:1937471306;N:118275,150,150,,,1975158071,1668946082,1669123266,1937471306,118275,SRX8958301,SRS7214877,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.92921,0.94037,0.07548,0.07656,0.7432,0.74341,0.50788,0.50908,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60703,SRR12464088,SRX8958300,SRS7214876,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  4h  medium conc  2,Cd04M2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:10 𝜇M|exposure time:4 hour|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Cd  4h  medium conc  2,Cd04M2,Cd04M2,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd04M2_1.fq.gz Cd04M2_2.fq.gz,fastq fastq,5986656300.0,19955521.0,Cd04M2 1.fq.gz,0:150 1:150,A:1632193964;C:1376716486;G:1376758629;T:1600889469;N:97752,150,150,,,1632193964,1376716486,1376758629,1600889469,97752,SRX8958300,SRS7214876,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93086,0.93921,0.07851,0.07889,0.74306,0.74219,0.50414,0.50764,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60704,SRR12464089,SRX8958299,SRS7214875,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  4h  medium conc  1,Cd04M1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:10 𝜇M|exposure time:4 hour|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Cd  4h  medium conc  1,Cd04M1,Cd04M1,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd04M1_1.fq.gz Cd04M1_2.fq.gz,fastq fastq,8145084600.0,27150282.0,Cd04M1 1.fq.gz,0:150 1:150,A:2219745498;C:1873092762;G:1873188281;T:2178924139;N:133920,150,150,,,2219745498,1873092762,1873188281,2178924139,133920,SRX8958299,SRS7214875,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93327,0.94067,0.07521,0.07584,0.74343,0.74375,0.50609,0.50813,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60705,SRR12464090,SRX8958298,SRS7214873,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  4h  low conc  1,Cu04L1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:100 𝜇M|exposure time:4 hour|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Cu  4h  low conc  1,Cu04L1,Cu04L1,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu04L1_1.fq.gz Cu04L1_2.fq.gz,fastq fastq,7700652600.0,25668842.0,Cu04L1 1.fq.gz,0:150 1:150,A:2092998833;C:1777194945;G:1777348880;T:2052984473;N:125469,150,150,,,2092998833,1777194945,1777348880,2052984473,125469,SRX8958298,SRS7214873,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93475,0.94043,0.07693,0.0773,0.74337,0.74268,0.49877,0.50092,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60706,SRR12464091,SRX8958297,SRS7214874,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  4h  low conc  3,Cd04L3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:5 𝜇M|exposure time:4 hour|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Cd  4h  low conc  3,Cd04L3,Cd04L3,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd04L3_1.fq.gz Cd04L3_2.fq.gz,fastq fastq,7609995900.0,25366653.0,Cd04L3 1.fq.gz,0:150 1:150,A:2066204844;C:1758177655;G:1757534707;T:2027954978;N:123716,150,150,,,2066204844,1758177655,1757534707,2027954978,123716,SRX8958297,SRS7214874,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93542,0.94079,0.07206,0.07236,0.74353,0.74357,0.50023,0.49884,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60707,SRR12464092,SRX8958296,SRS7214872,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  4h  low conc  2,Cd04L2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:5 𝜇M|exposure time:4 hour|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Cd  4h  low conc  2,Cd04L2,Cd04L2,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd04L2_1.fq.gz Cd04L2_2.fq.gz,fastq fastq,7790751300.0,25969171.0,Cd04L2 1.fq.gz,0:150 1:150,A:2130740107;C:1787877582;G:1788480420;T:2083526423;N:126768,150,150,,,2130740107,1787877582,1788480420,2083526423,126768,SRX8958296,SRS7214872,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.92628,0.93854,0.07244,0.07369,0.74261,0.74215,0.50888,0.50454,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60708,SRR12464093,SRX8958295,SRS7214871,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  4h  low conc  1,Cd04L1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:5 𝜇M|exposure time:4 hour|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Cd  4h  low conc  1,Cd04L1,Cd04L1,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd04L1_1.fq.gz Cd04L1_2.fq.gz,fastq fastq,7554535200.0,25181784.0,Cd04L1 1.fq.gz,0:150 1:150,A:2063575853;C:1736004021;G:1738118789;T:2016713446;N:123091,150,150,,,2063575853,1736004021,1738118789,2016713446,123091,SRX8958295,SRS7214871,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.92231,0.93828,0.07452,0.07615,0.74422,0.74353,0.5072,0.50776,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60709,SRR12464094,SRX8958294,SRS7214870,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  4h  Control  3,Cd04C3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:0 𝜇M|exposure time:4 hour|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Cd  4h  Control  3,Cd04C3,Cd04C3,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd04C3_1.fq.gz Cd04C3_2.fq.gz,fastq fastq,10363610100.0,34545367.0,Cd04C3 1.fq.gz,0:150 1:150,A:2810002669;C:2399449606;G:2399732935;T:2754255569;N:169321,150,150,,,2810002669,2399449606,2399732935,2754255569,169321,SRX8958294,SRS7214870,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93681,0.94219,0.07036,0.07084,0.7444,0.7459,0.50321,0.50522,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60710,SRR12464095,SRX8958293,SRS7214869,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  4h  Control  2,Cd04C2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:0 𝜇M|exposure time:4 hour|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Cd  4h  Control  2,Cd04C2,Cd04C2,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd04C2_1.fq.gz Cd04C2_2.fq.gz,fastq fastq,7643585700.0,25478619.0,Cd04C2 1.fq.gz,0:150 1:150,A:2099471996;C:1747003369;G:1744815908;T:2052169932;N:124495,150,150,,,2099471996,1747003369,1744815908,2052169932,124495,SRX8958293,SRS7214869,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.92262,0.93744,0.07731,0.07844,0.74444,0.74474,0.50906,0.50918,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60711,SRR12464096,SRX8958292,SRS7214868,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cd  4h  Control  1,Cd04C1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Cadmium|exposure concentration:0 𝜇M|exposure time:4 hour|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Cd  4h  Control  1,Cd04C1,Cd04C1,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cd04C1_1.fq.gz Cd04C1_2.fq.gz,fastq fastq,8466189300.0,28220631.0,Cd04C1 1.fq.gz,0:150 1:150,A:2313955140;C:1945278944;G:1941101156;T:2265716752;N:137308,150,150,,,2313955140,1945278944,1941101156,2265716752,137308,SRX8958292,SRS7214868,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93026,0.94067,0.07493,0.07516,0.7447,0.74468,0.49885,0.49972,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60712,SRR12464097,SRX8958291,SRS7214867,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  24h  high conc  3,Cu24H3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:400 𝜇M|exposure time:24 hour|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Cu  24h  high conc  3,Cu24H3,Cu24H3,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu24H3_1.fq.gz Cu24H3_2.fq.gz,fastq fastq,8062718400.0,26875728.0,Cu24H3 1.fq.gz,0:150 1:150,A:2198924138;C:1851816167;G:1850403807;T:2161494665;N:79623,150,150,,,2198924138,1851816167,1850403807,2161494665,79623,SRX8958291,SRS7214867,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93761,0.93722,0.08653,0.08644,0.74592,0.74637,0.50236,0.50346,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60713,SRR12464098,SRX8958290,SRS7214866,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  24h  high conc  2,Cu24H2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:400 𝜇M|exposure time:24 hour|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Cu  24h  high conc  2,Cu24H2,Cu24H2,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu24H2_1.fq.gz Cu24H2_2.fq.gz,fastq fastq,7424113800.0,24747046.0,Cu24H2 1.fq.gz,0:150 1:150,A:2026245376;C:1703715558;G:1702752737;T:1991327908;N:72221,150,150,,,2026245376,1703715558,1702752737,1991327908,72221,SRX8958290,SRS7214866,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93786,0.93803,0.08685,0.08655,0.74521,0.74619,0.50692,0.50746,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60714,SRR12464099,SRX8958289,SRS7214865,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  24h  high conc  1,Cu24H1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:400 𝜇M|exposure time:24 hour|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Cu  24h  high conc  1,Cu24H1,Cu24H1,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu24H1_1.fq.gz Cu24H1_2.fq.gz,fastq fastq,7003793700.0,23345979.0,Cu24H1 1.fq.gz,0:150 1:150,A:1910815962;C:1607426692;G:1607503938;T:1877978595;N:68513,150,150,,,1910815962,1607426692,1607503938,1877978595,68513,SRX8958289,SRS7214865,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93882,0.93882,0.08463,0.08466,0.74442,0.74537,0.49301,0.50238,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60715,SRR12464100,SRX8958288,SRS7214864,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  24h  medium conc  3,Cu24M3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:200 𝜇M|exposure time:24 hour|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Cu  24h  medium conc  3,Cu24M3,Cu24M3,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu24M3_1.fq.gz Cu24M3_2.fq.gz,fastq fastq,6747502500.0,22491675.0,Cu24M3 1.fq.gz,0:150 1:150,A:1847167108;C:1542696218;G:1540500063;T:1817073070;N:66041,150,150,,,1847167108,1542696218,1540500063,1817073070,66041,SRX8958288,SRS7214864,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93818,0.93754,0.0927,0.09225,0.74592,0.74643,0.49978,0.50038,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60716,SRR12464101,SRX8958287,SRS7214863,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  4h  Control  3,Cu04C3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:0 𝜇M|exposure time:4 hour|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Cu  4h  Control  3,Cu04C3,Cu04C3,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu04C3_1.fq.gz Cu04C3_2.fq.gz,fastq fastq,7563405000.0,25211350.0,Cu04C3 1.fq.gz,0:150 1:150,A:2071044188;C:1733568718;G:1735003713;T:2023665503;N:122878,150,150,,,2071044188,1733568718,1735003713,2023665503,122878,SRX8958287,SRS7214863,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.92346,0.9368,0.07661,0.07778,0.74215,0.74192,0.49887,0.50221,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60717,SRR12464102,SRX8958286,SRS7214862,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  24h  medium conc  2,Cu24M2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:200 𝜇M|exposure time:24 hour|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Cu  24h  medium conc  2,Cu24M2,Cu24M2,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu24M2_1.fq.gz Cu24M2_2.fq.gz,fastq fastq,6852587700.0,22841959.0,Cu24M2 1.fq.gz,0:150 1:150,A:1877852428;C:1566024569;G:1564412926;T:1844231182;N:66595,150,150,,,1877852428,1566024569,1564412926,1844231182,66595,SRX8958286,SRS7214862,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93696,0.93784,0.09157,0.09101,0.74732,0.74832,0.49096,0.49762,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60718,SRR12464103,SRX8958285,SRS7214861,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  24h  medium conc  1,Cu24M1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:200 𝜇M|exposure time:24 hour|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Cu  24h  medium conc  1,Cu24M1,Cu24M1,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu24M1_1.fq.gz Cu24M1_2.fq.gz,fastq fastq,9277924800.0,30926416.0,Cu24M1 1.fq.gz,0:150 1:150,A:2533946307;C:2126739869;G:2128075728;T:2489072913;N:89983,150,150,,,2533946307,2126739869,2128075728,2489072913,89983,SRX8958285,SRS7214861,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93722,0.93775,0.09123,0.09093,0.74651,0.74834,0.49541,0.49516,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60719,SRR12464104,SRX8958284,SRS7214859,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  24h  low conc  3,Cu24L3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:100 𝜇M|exposure time:24 hour|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Cu  24h  low conc  3,Cu24L3,Cu24L3,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu24L3_1.fq.gz Cu24L3_2.fq.gz,fastq fastq,6425719200.0,21419064.0,Cu24L3 1.fq.gz,0:150 1:150,A:1761211078;C:1466865811;G:1467738179;T:1729841194;N:62938,150,150,,,1761211078,1466865811,1467738179,1729841194,62938,SRX8958284,SRS7214859,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93551,0.93542,0.09461,0.09518,0.74639,0.74842,0.49657,0.47932,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60720,SRR12464105,SRX8958283,SRS7214860,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  24h  low conc  2,Cu24L2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:100 𝜇M|exposure time:24 hour|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Cu  24h  low conc  2,Cu24L2,Cu24L2,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu24L2_1.fq.gz Cu24L2_2.fq.gz,fastq fastq,6264532500.0,20881775.0,Cu24L2 1.fq.gz,0:150 1:150,A:1712506412;C:1435822770;G:1435257896;T:1680885259;N:60163,150,150,,,1712506412,1435822770,1435257896,1680885259,60163,SRX8958283,SRS7214860,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93729,0.93659,0.09213,0.09194,0.74653,0.74787,0.49933,0.50044,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60721,SRR12464106,SRX8958282,SRS7214858,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  24h  low conc  1,Cu24L1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:100 𝜇M|exposure time:24 hour|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Cu  24h  low conc  1,Cu24L1,Cu24L1,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu24L1_1.fq.gz Cu24L1_2.fq.gz,fastq fastq,6109442100.0,20364807.0,Cu24L1 1.fq.gz,0:150 1:150,A:1673071441;C:1395675190;G:1395483910;T:1645184975;N:26584,150,150,,,1673071441,1395675190,1395483910,1645184975,26584,SRX8958282,SRS7214858,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93049,0.93616,0.09515,0.09517,0.74645,0.74554,0.49052,0.49167,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60722,SRR12464107,SRX8958281,SRS7214857,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  24h  Control  3,Cu24C3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:0 𝜇M|exposure time:24 hour|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Cu  24h  Control  3,Cu24C3,Cu24C3,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu24C3_1.fq.gz Cu24C3_2.fq.gz,fastq fastq,7390587300.0,24635291.0,Cu24C3 1.fq.gz,0:150 1:150,A:2025856661;C:1686924859;G:1685511106;T:1992262065;N:32609,150,150,,,2025856661,1686924859,1685511106,1992262065,32609,SRX8958281,SRS7214857,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.92905,0.93221,0.09146,0.09182,0.73852,0.73843,0.49874,0.49873,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60723,SRR12464108,SRX8958280,SRS7214856,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  24h  Control  2,Cu24C2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:0 𝜇M|exposure time:24 hour|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Cu  24h  Control  2,Cu24C2,Cu24C2,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu24C2_1.fq.gz Cu24C2_2.fq.gz,fastq fastq,7104172800.0,23680576.0,Cu24C2 1.fq.gz,0:150 1:150,A:1943975740;C:1626361241;G:1625834553;T:1907931921;N:69345,150,150,,,1943975740,1626361241,1625834553,1907931921,69345,SRX8958280,SRS7214856,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93367,0.93524,0.08872,0.08916,0.73933,0.74002,0.50298,0.50459,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60724,SRR12464109,SRX8958279,SRS7214855,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  24h  Control  1,Cu24C1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:0 𝜇M|exposure time:24 hour|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Cu  24h  Control  1,Cu24C1,Cu24C1,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu24C1_1.fq.gz Cu24C1_2.fq.gz,fastq fastq,7342388700.0,24474629.0,Cu24C1 1.fq.gz,0:150 1:150,A:2010077606;C:1682033717;G:1680283202;T:1969901289;N:92886,150,150,,,2010077606,1682033717,1680283202,1969901289,92886,SRX8958279,SRS7214855,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.9339,0.9337,0.09174,0.09154,0.73919,0.73979,0.49512,0.49462,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60725,SRR12464110,SRX8958278,SRS7214853,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  4h  high conc  3,Cu04H3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:400 𝜇M|exposure time:4 hour|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Cu  4h  high conc  3,Cu04H3,Cu04H3,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu04H3_1.fq.gz Cu04H3_2.fq.gz,fastq fastq,7382973300.0,24609911.0,Cu04H3 1.fq.gz,0:150 1:150,A:2001736057;C:1709010181;G:1706622068;T:1965483865;N:121129,150,150,,,2001736057,1709010181,1706622068,1965483865,121129,SRX8958278,SRS7214853,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.9371,0.94074,0.07327,0.07283,0.74673,0.74698,0.49743,0.50165,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60726,SRR12464111,SRX8958277,SRS7214854,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  4h  high conc  2,Cu04H2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:400 𝜇M|exposure time:4 hour|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Cu  4h  high conc  2,Cu04H2,Cu04H2,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu04H2_1.fq.gz Cu04H2_2.fq.gz,fastq fastq,7838636700.0,26128789.0,Cu04H2 1.fq.gz,0:150 1:150,A:2152232608;C:1791667341;G:1788330412;T:2106278370;N:127969,150,150,,,2152232608,1791667341,1788330412,2106278370,127969,SRX8958277,SRS7214854,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.92207,0.93686,0.07643,0.0786,0.74696,0.7472,0.48976,0.49644,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60727,SRR12464112,SRX8958276,SRS7214852,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  4h  Control  2,Cu04C2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:0 𝜇M|exposure time:4 hour|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Cu  4h  Control  2,Cu04C2,Cu04C2,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu04C2_1.fq.gz Cu04C2_2.fq.gz,fastq fastq,6505001100.0,21683337.0,Cu04C2 1.fq.gz,0:150 1:150,A:1777161101;C:1494901821;G:1486199815;T:1746632300;N:106063,150,150,,,1777161101,1494901821,1486199815,1746632300,106063,SRX8958276,SRS7214852,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93373,0.93881,0.08245,0.08302,0.74121,0.74128,0.49934,0.50123,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
60728,SRR12464113,SRX8958275,SRS7214851,SRP277864,PRJNA657386,Danio rerio Transcriptome or Gene expression,PRJNA657386,Other,ZFL zebrafish liver cell line were exposed to various concentration of Copper chloride and cadmium chloride. The cells' RNA was collected and sent to RNA Seq.,,,,Cu  4h  Control  1,Cu04C1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:not applicable|tissue:liver|cell line:ZFL|sample type:cell culture|metal exposure:Copper|exposure concentration:0 𝜇M|exposure time:4 hour|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Cu  4h  Control  1,Cu04C1,Cu04C1,Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP277864,,,Cu04C1_1.fq.gz Cu04C1_2.fq.gz,fastq fastq,6825766500.0,22752555.0,Cu04C1 1.fq.gz,0:150 1:150,A:1850217538;C:1580452896;G:1578576220;T:1816408898;N:110948,150,150,,,1850217538,1580452896,1578576220,1816408898,110948,SRX8958275,SRS7214851,SRA1113719,The Chinese University of Hong Kong|School of Life Science,The Chinese University of Hong Kong,2,0.93745,0.94217,0.07189,0.0718,0.74101,0.74071,0.5027,0.50093,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2020-08-18,Undetermined,Undetermined,Liver,Liver and Biliary System
63904,SRR14213389,SRX10579907,SRS8684375,SRP314470,PRJNA721381,RNA Seq from zebrafish adult tissues,GSE171906,Transcriptome Analysis,The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.,,pubmed:34556579,,Liver3,GSM5237131,,source name:zebrafish liver|genotype:wild type|tissue:liver|strain:TLAB,Liver3,Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM,zebrafish liver,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|tissue:liver|strain:TLAB,GSM5237131,GSM5237131: Liver3; Danio rerio; RNA Seq,GSM5237131,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM5237131,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP314470,,,Liver3.fastq,fastq,1604374400.0,16043744.0,GSM5237131 r1,0:100,A:396446313;C:391073013;G:386394199;T:430400186;N:60689,100,,,,396446313,391073013,386394199,430400186,60689,SRX10579907,SRS8684375,SRA1217576,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.95853,,0.05369,,0.82144,,0.51934,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2021-04-12,Undetermined,Undetermined,Liver,Liver and Biliary System
63905,SRR14213388,SRX10579906,SRS8684374,SRP314470,PRJNA721381,RNA Seq from zebrafish adult tissues,GSE171906,Transcriptome Analysis,The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.,,pubmed:34556579,,Liver2,GSM5237130,,source name:zebrafish liver|genotype:wild type|tissue:liver|strain:TLAB,Liver2,Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM,zebrafish liver,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|tissue:liver|strain:TLAB,GSM5237130,GSM5237130: Liver2; Danio rerio; RNA Seq,GSM5237130,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM5237130,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP314470,,,Liver2.fastq,fastq,1705166200.0,17051662.0,GSM5237130 r1,0:100,A:412873546;C:422223229;G:416651408;T:453353011;N:65006,100,,,,412873546,422223229,416651408,453353011,65006,SRX10579906,SRS8684374,SRA1217576,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.95555,,0.05508,,0.8116,,0.55916,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2021-04-12,Undetermined,Undetermined,Liver,Liver and Biliary System
63906,SRR14213387,SRX10579905,SRS8684373,SRP314470,PRJNA721381,RNA Seq from zebrafish adult tissues,GSE171906,Transcriptome Analysis,The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.,,pubmed:34556579,,Liver1,GSM5237129,,source name:zebrafish liver|genotype:wild type|tissue:liver|strain:TLAB,Liver1,Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM,zebrafish liver,,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|tissue:liver|strain:TLAB,GSM5237129,GSM5237129: Liver1; Danio rerio; RNA Seq,GSM5237129,,1,Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina,GEO Accession:GSM5237129,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP314470,,,Liver1.fastq,fastq,1390903100.0,13909031.0,GSM5237129 r1,0:100,A:345678288;C:336452200;G:334456650;T:374262402;N:53560,100,,,,345678288,336452200,334456650,374262402,53560,SRX10579905,SRS8684373,SRA1217576,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.95915,,0.045,,0.83869,,0.58153,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2021-04-12,Undetermined,Undetermined,Liver,Liver and Biliary System
67832,SRR17375072,SRX13549231,SRS11443005,SRP352824,PRJNA793009,Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells,GSE192740,Other,Analysis of CITE seq data   Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45  cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar  from healthy and steatotic human livers  from hamster liver  pig liver  chicken liver  monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers  NAFLD mouse livers  healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45  cells derived from mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar. Liver CD45+ and CD45  cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver  mouse StSt capsule  mouse NAFLD liver   human non steatotic liver  human steatotic liver,parent bioproject:PRJNA793005,pubmed:35021063;pubmed:36304458,,Zebrafish 002 Whole Liver Cells Zebrafish,GSM5764413,,tissue:Liver|shortfilename:CS131|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:1241,Zebrafish 002 Whole Liver Cells Zebrafish,Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse  hg19 Human  GRCz10 Zebrafish  MesAur1.0.100 Hamster  GRCg6a.96 Chicken  Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene – and if present – antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object,Liver,,All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.,,shortfilename:CS131|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:1241,GSM5764413,GSM5764413: Zebrafish 002 Whole Liver Cells Zebrafish; Danio rerio; RNA Seq,GSM5764413,,1,All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.,GEO Accession:GSM5764413,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP352824,,,CS131_R1.fastq.gz CS131_R2.fastq.gz,fastq fastq,27410113115.0,230337085.0,GSM5764413 r1,0:28 1:91,A:7502899227;C:6375936516;G:6281396027;T:7241238684;N:8642661,28,91,,,7502899227,6375936516,6281396027,7241238684,8642661,SRX13549231,SRS11443005,SRA1349905,GEO,"VIB Inflammation Research Center, VIB-University of Ghent",2,0.00522,0.93004,0.00164,0.0692,0.99476,0.85098,0.48648,0.60903,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2021-12-29,Undetermined,Undetermined,Liver,Liver and Biliary System
67833,SRR17375071,SRX13549230,SRS11443004,SRP352824,PRJNA793009,Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells,GSE192740,Other,Analysis of CITE seq data   Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45  cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar  from healthy and steatotic human livers  from hamster liver  pig liver  chicken liver  monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers  NAFLD mouse livers  healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45  cells derived from mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar. Liver CD45+ and CD45  cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver  mouse StSt capsule  mouse NAFLD liver   human non steatotic liver  human steatotic liver,parent bioproject:PRJNA793005,pubmed:35021063;pubmed:36304458,,Zebrafish 001 Whole Liver Cells Zebrafish,GSM5764412,,tissue:Liver|shortfilename:CS130|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:2256,Zebrafish 001 Whole Liver Cells Zebrafish,Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse  hg19 Human  GRCz10 Zebrafish  MesAur1.0.100 Hamster  GRCg6a.96 Chicken  Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene – and if present – antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object,Liver,,All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.,,shortfilename:CS130|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:2256,GSM5764412,GSM5764412: Zebrafish 001 Whole Liver Cells Zebrafish; Danio rerio; RNA Seq,GSM5764412,,1,All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.,GEO Accession:GSM5764412,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP352824,,,CS130_R1.fastq.gz CS130_R2.fastq.gz,fastq fastq,29028764681.0,243939199.0,GSM5764412 r1,0:28 1:91,A:7990080958;C:6832189305;G:6802247428;T:7395232074;N:9014916,28,91,,,7990080958,6832189305,6802247428,7395232074,9014916,SRX13549230,SRS11443004,SRA1349905,GEO,"VIB Inflammation Research Center, VIB-University of Ghent",2,0.00621,0.93648,0.00152,0.07051,0.99466,0.85036,0.33907,0.45636,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2021-12-29,Undetermined,Undetermined,Liver,Liver and Biliary System
67834,SRR17375070,SRX13549229,SRS11443003,SRP352824,PRJNA793009,Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells,GSE192740,Other,Analysis of CITE seq data   Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45  cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar  from healthy and steatotic human livers  from hamster liver  pig liver  chicken liver  monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers  NAFLD mouse livers  healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45  cells derived from mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar. Liver CD45+ and CD45  cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver  mouse StSt capsule  mouse NAFLD liver   human non steatotic liver  human steatotic liver,parent bioproject:PRJNA793005,pubmed:35021063;pubmed:36304458,,Zebrafish 002 Liver mpeg1.1+ cells Zebrafish,GSM5764411,,tissue:Liver|shortfilename:CS129|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:4126,Zebrafish 002 Liver mpeg1.1+ cells Zebrafish,Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse  hg19 Human  GRCz10 Zebrafish  MesAur1.0.100 Hamster  GRCg6a.96 Chicken  Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene – and if present – antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object,Liver,,All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.,,shortfilename:CS129|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:4126,GSM5764411,GSM5764411: Zebrafish 002 Liver mpeg1.1+ cells Zebrafish; Danio rerio; RNA Seq,GSM5764411,,1,All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.,GEO Accession:GSM5764411,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP352824,,,CS129_R1.fastq.gz CS129_R2.fastq.gz,fastq fastq,37123150869.0,311959251.0,GSM5764411 r1,0:28 1:91,A:10576275333;C:7976755033;G:8122940005;T:10435522767;N:11657731,28,91,,,10576275333,7976755033,8122940005,10435522767,11657731,SRX13549229,SRS11443003,SRA1349905,GEO,"VIB Inflammation Research Center, VIB-University of Ghent",2,0.00585,0.89093,0.00199,0.20548,0.99269,0.82597,0.42801,0.61509,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2021-12-29,Undetermined,Undetermined,Liver,Liver and Biliary System
67835,SRR17375069,SRX13549228,SRS11443002,SRP352824,PRJNA793009,Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells,GSE192740,Other,Analysis of CITE seq data   Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45  cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar  from healthy and steatotic human livers  from hamster liver  pig liver  chicken liver  monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers  NAFLD mouse livers  healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45  cells derived from mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar. Liver CD45+ and CD45  cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver  mouse StSt capsule  mouse NAFLD liver   human non steatotic liver  human steatotic liver,parent bioproject:PRJNA793005,pubmed:35021063;pubmed:36304458,,Zebrafish 001 Liver mpeg1.1+ cells Zebrafish,GSM5764410,,tissue:Liver|shortfilename:CS128|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:1229,Zebrafish 001 Liver mpeg1.1+ cells Zebrafish,Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse  hg19 Human  GRCz10 Zebrafish  MesAur1.0.100 Hamster  GRCg6a.96 Chicken  Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene – and if present – antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object,Liver,,All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.,,shortfilename:CS128|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:1229,GSM5764410,GSM5764410: Zebrafish 001 Liver mpeg1.1+ cells Zebrafish; Danio rerio; RNA Seq,GSM5764410,,1,All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.,GEO Accession:GSM5764410,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP352824,,,CS128_R1.fastq.gz CS128_R2.fastq.gz,fastq fastq,38316694094.0,321989026.0,GSM5764410 r1,0:28 1:91,A:10814226120;C:8293271134;G:8575797871;T:10621330197;N:12068772,28,91,,,10814226120,8293271134,8575797871,10621330197,12068772,SRX13549228,SRS11443002,SRA1349905,GEO,"VIB Inflammation Research Center, VIB-University of Ghent",2,0.00626,0.88237,0.00215,0.18876,0.99249,0.83049,0.41451,0.59559,28,91,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2021-12-29,Undetermined,Undetermined,Liver,Liver and Biliary System