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110 rows where devstage_curation_coarse = "Juvenile" and tissue_curation_coarse = "Liver and Biliary System"

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tissue_curation_coarse 1

  • Liver and Biliary System · 110 ✖

tissue_curation 1

technology 1

experiment.library_strategy 1

experiment.library_source 1

devstage_curation_coarse 1

  • Juvenile · 110 ✖

devstage_curation 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
221 221 DRR162520 DRX153139 DRS083200 DRP004696 PRJDB7713 Age associated transcriptome analysis in 5 tissues of zebrafish DRP004696 Transcriptome Analysis We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.       liver sample from 2 mpf zebrafish replicate5 SAMD00152468   sample name:l02 5|age:2 month|biological replicate:5|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152468 DRX153139 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152468       1264817800.0 6324089.0 DRR162520 0:100 1:100 A:351295111;C:280181229;G:281044764;T:352232836;N:63860 100 100     351295111 280181229 281044764 352232836 63860 DRX153139 DRS083200 DRA007711 UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo 2 0.93687 0.93419 0.07774 0.07776 0.7587 0.7609 0.56082 0.56748 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Juvenile Juvenile Liver Liver and Biliary System
222 222 DRR162519 DRX153138 DRS083199 DRP004696 PRJDB7713 Age associated transcriptome analysis in 5 tissues of zebrafish DRP004696 Transcriptome Analysis We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.       liver sample from 2 mpf zebrafish replicate4 SAMD00152467   sample name:l02 4|age:2 month|biological replicate:4|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152467 DRX153138 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152467       1762366200.0 8811831.0 DRR162519 0:100 1:100 A:481999545;C:397566169;G:399183135;T:483526493;N:90858 100 100     481999545 397566169 399183135 483526493 90858 DRX153138 DRS083199 DRA007711 UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo 2 0.93994 0.93528 0.06039 0.05936 0.75037 0.75394 0.52945 0.52961 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Juvenile Juvenile Liver Liver and Biliary System
223 223 DRR162518 DRX153137 DRS083198 DRP004696 PRJDB7713 Age associated transcriptome analysis in 5 tissues of zebrafish DRP004696 Transcriptome Analysis We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.       liver sample from 2 mpf zebrafish replicate3 SAMD00152466   sample name:l02 3|age:2 month|biological replicate:3|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152466 DRX153137 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152466       1464434200.0 7322171.0 DRR162518 0:100 1:100 A:400972247;C:330316514;G:329635959;T:403435022;N:74458 100 100     400972247 330316514 329635959 403435022 74458 DRX153137 DRS083198 DRA007711 UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo 2 0.94169 0.93517 0.075 0.07408 0.78541 0.78796 0.56483 0.56426 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Juvenile Juvenile Liver Liver and Biliary System
224 224 DRR162517 DRX153136 DRS083197 DRP004696 PRJDB7713 Age associated transcriptome analysis in 5 tissues of zebrafish DRP004696 Transcriptome Analysis We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.       liver sample from 2 mpf zebrafish replicate2 SAMD00152465   sample name:l02 2|age:2 month|biological replicate:2|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152465 DRX153136 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152465       1953667000.0 9768335.0 DRR162517 0:100 1:100 A:525411621;C:450279523;G:450410879;T:527464993;N:99984 100 100     525411621 450279523 450410879 527464993 99984 DRX153136 DRS083197 DRA007711 UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo 2 0.94424 0.93692 0.06451 0.06582 0.78358 0.79557 0.56036 0.57581 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Juvenile Juvenile Liver Liver and Biliary System
225 225 DRR162516 DRX153135 DRS083196 DRP004696 PRJDB7713 Age associated transcriptome analysis in 5 tissues of zebrafish DRP004696 Transcriptome Analysis We performed transcriptome analysis for brain gill heart liver and muscle from 2 month 7 month 16 month and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al. 2014.       liver sample from 2 mpf zebrafish replicate1 SAMD00152464   sample name:l02 1|age:2 month|biological replicate:1|tissue:liver                 Illumina HiSeq 2000 paired end sequencing of SAMD00152464 DRX153135 1 1 Illumina TruSeq Stranded mRNA HT Kit   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004696 Illumina HiSeq 2000 paired end sequencing of SAMD00152464       1541676600.0 7708383.0 DRR162516 0:100 1:100 A:414776600;C:354650822;G:357258514;T:414910092;N:80572 100 100     414776600 354650822 357258514 414910092 80572 DRX153135 DRS083196 DRA007711 UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo 2 0.94346 0.93048 0.06888 0.06759 0.79086 0.79452 0.56037 0.55727 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Japan 2018-12-24 Juvenile Juvenile Liver Liver and Biliary System
31932 31932 SRR28776262 SRX24341224 SRS21101374 SRP503449 PRJNA1103351 Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration PRJNA1103351 Other Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.       Ablated 3 Ablated rep3   strain:AB|age:2 mpf date:2015 06 11|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Tgins:flag NTR|treatment:Metronidazole|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish hepatocytes P2276 105 P2276 105 RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP503449     5_150903_BC7FRTANXX_P2276_105_1.fastq.gz 5_150903_BC7FRTANXX_P2276_105_2.fastq.gz fastq fastq 12443422824.0 49378662.0 5 150903 BC7FRTANXX P2276 105 1.fastq.gz 0:126 1:126 A:3354062616;C:2842732118;G:2899611331;T:3337717349;N:9299410 126 126     3354062616 2842732118 2899611331 3337717349 9299410 SRX24341224 SRS21101374 SRA1851016 Karolinska Institutet|Cell and Molecular Biology Karolinska Institutet                       B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Sweden 2024-04-23 Juvenile Juvenile Liver Liver and Biliary System
31933 31933 SRR28776263 SRX24341223 SRS21101373 SRP503449 PRJNA1103351 Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration PRJNA1103351 Other Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.       Ablated 2 Ablated rep2   strain:AB|age:2 mpf date:2015 06 09|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Tgins:flag NTR|treatment:Metronidazole|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish hepatocytes P2276 103 P2276 103 RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP503449     5_150903_BC7FRTANXX_P2276_103_1.fastq.gz 5_150903_BC7FRTANXX_P2276_103_2.fastq.gz fastq fastq 12508569612.0 49637181.0 5 150903 BC7FRTANXX P2276 103 1.fastq.gz 0:126 1:126 A:3285561592;C:2941406523;G:2987518362;T:3285515692;N:8567443 126 126     3285561592 2941406523 2987518362 3285515692 8567443 SRX24341223 SRS21101373 SRA1851016 Karolinska Institutet|Cell and Molecular Biology Karolinska Institutet                       B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Sweden 2024-04-23 Juvenile Juvenile Liver Liver and Biliary System
31934 31934 SRR28776264 SRX24341222 SRS21101372 SRP503449 PRJNA1103351 Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration PRJNA1103351 Other Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.       Ablated 1 Ablated rep1   strain:AB|age:2 mpf date:2015 06 04|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Tgins:flag NTR|treatment:Metronidazole|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish hepatocytes P2276 101 P2276 101 RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP503449     5_150903_BC7FRTANXX_P2276_101_1.fastq.gz 5_150903_BC7FRTANXX_P2276_101_2.fastq.gz fastq fastq 12536188812.0 49746781.0 5 150903 BC7FRTANXX P2276 101 1.fastq.gz 0:126 1:126 A:3281688237;C:2958476935;G:3022979051;T:3265495888;N:7548701 126 126     3281688237 2958476935 3022979051 3265495888 7548701 SRX24341222 SRS21101372 SRA1851016 Karolinska Institutet|Cell and Molecular Biology Karolinska Institutet                       B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Sweden 2024-04-23 Juvenile Juvenile Liver Liver and Biliary System
31935 31935 SRR28776265 SRX24341221 SRS21101375 SRP503449 PRJNA1103351 Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration PRJNA1103351 Other Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.       Control 2 Control rep2   strain:AB|age:2 mpf date:2015 06 11|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Wild type|treatment:Metronidazole|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish hepatocytes P2276 106 P2276 106 RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP503449     5_150903_BC7FRTANXX_P2276_106_1.fastq.gz 5_150903_BC7FRTANXX_P2276_106_2.fastq.gz fastq fastq 11797087680.0 46813840.0 5 150903 BC7FRTANXX P2276 106 1.fastq.gz 0:126 1:126 A:3087253274;C:2787897503;G:2841312816;T:3072716302;N:7907785 126 126     3087253274 2787897503 2841312816 3072716302 7907785 SRX24341221 SRS21101375 SRA1851016 Karolinska Institutet|Cell and Molecular Biology Karolinska Institutet                       B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Sweden 2024-04-23 Juvenile Juvenile Liver Liver and Biliary System
31936 31936 SRR28776266 SRX24341220 SRS21101371 SRP503449 PRJNA1103351 Characterization of liver pancreas crosstalk following beta cell loss reveals a role for the molybdenum cofactor in beta cell regeneration PRJNA1103351 Other Understanding beta cell regeneration and how inter organ communication can contribute to that is crucial for developing new approaches for diabetes treatment. With this dataste we characterized the hepatocyte beta cell axis and how it can contribute to beta cell regeneration in a zebrafish model of beta cell loss. This data provide a transcriptomics analysis of isolated hepatocytes following beta cell ablation.       Control 1 Control rep1   strain:AB|age:2 mpf date:2015 06 09|geo loc name:Sweden|sex:mixed|tissue:Liver|cell type:Hepatocytes|collected by:Christos Karampelias|genotype:Wild type|treatment:Metronidazole|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish hepatocytes P2276 104 P2276 104 RNA was extracted from the sorted cells using the RNAqueous micro total isolation kit. The quality of the RNA was assessed and the first control sample was discarded as the RIN value was too low. Libraries were prepared using the TRUSeq stranded mRNA kit Illumina and sequenced on an Illumina HiSeq2500 instrument.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina HiSeq 2500   SRP503449     5_150903_BC7FRTANXX_P2276_104_1.fastq.gz 5_150903_BC7FRTANXX_P2276_104_2.fastq.gz fastq fastq 13294186416.0 52754708.0 5 150903 BC7FRTANXX P2276 104 1.fastq.gz 0:126 1:126 A:3544892164;C:3073022881;G:3106419492;T:3559768207;N:10083672 126 126     3544892164 3073022881 3106419492 3559768207 10083672 SRX24341220 SRS21101371 SRA1851016 Karolinska Institutet|Cell and Molecular Biology Karolinska Institutet                       B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   Sweden 2024-04-23 Juvenile Juvenile Liver Liver and Biliary System
34397 34397 SRR31719829 SRX27082407 SRS23541575 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb overexpression normal diet for 35 days RNAseq MASLD HepGOE ND rep2 HepGOE ND rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 10|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGOE zebrafish of normal diet. HepGOE ND rep2 HepGOE ND rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGOE_ND_rep2_1.fq.gz RNAseq_MASLD_HepGOE_ND_rep2_2.fq.gz fastq fastq 7177536600.0 23925122.0 RNAseq MASLD HepGOE ND rep2 1.fq.gz 0:150 1:150 A:1917334205;C:1668595888;G:1703080664;T:1887679182;N:846661 150 150     1917334205 1668595888 1703080664 1887679182 846661 SRX27082407 SRS23541575 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34398 34398 SRR31719830 SRX27082406 SRS23541574 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb overexpression normal diet for 35 days RNAseq MASLD HepGOE ND rep1 HepGOE ND rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 9|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGOE zebrafish of normal diet. HepGOE ND rep1 HepGOE ND rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGOE_ND_rep1_1.fq.gz RNAseq_MASLD_HepGOE_ND_rep1_2.fq.gz fastq fastq 6621268500.0 22070895.0 RNAseq MASLD HepGOE ND rep1 1.fq.gz 0:150 1:150 A:1711419517;C:1595902037;G:1611514825;T:1702282385;N:149736 150 150     1711419517 1595902037 1611514825 1702282385 149736 SRX27082406 SRS23541574 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34399 34399 SRR31719831 SRX27082405 SRS23541573 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb knockout high fat high cholesterol diet for 35 days RNAseq MASLD HepGKO HFC rep2 HepGKO HFC rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 8|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGKO zebrafish of high fat high cholesterol diet. HepGKO HFC rep2 HepGKO HFC rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGKO_HFC_rep2_1.fq.gz RNAseq_MASLD_HepGKO_HFC_rep2_2.fq.gz fastq fastq 5901646500.0 19672155.0 RNAseq MASLD HepGKO HFC rep2 1.fq.gz 0:150 1:150 A:1547939419;C:1401111812;G:1425197669;T:1527300198;N:97402 150 150     1547939419 1401111812 1425197669 1527300198 97402 SRX27082405 SRS23541573 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34400 34400 SRR31719832 SRX27082404 SRS23541572 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb knockout high fat high cholesterol diet for 35 days RNAseq MASLD HepGKO HFC rep1 HepGKO HFC rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 7|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGKO zebrafish of high fat high cholesterol diet. HepGKO HFC rep1 HepGKO HFC rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGKO_HFC_rep1_1.fq.gz RNAseq_MASLD_HepGKO_HFC_rep1_2.fq.gz fastq fastq 6484178700.0 21613929.0 RNAseq MASLD HepGKO HFC rep1 1.fq.gz 0:150 1:150 A:1692850957;C:1545705390;G:1573644279;T:1671871368;N:106706 150 150     1692850957 1545705390 1573644279 1671871368 106706 SRX27082404 SRS23541572 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34401 34401 SRR31719833 SRX27082403 SRS23541571 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb knockout normal diet for 35 days RNAseq MASLD HepGKO ND rep2 HepGKO ND rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 6|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGKO zebrafish of normal diet. HepGKO ND rep2 HepGKO ND rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGKO_ND_rep2_1.fq.gz RNAseq_MASLD_HepGKO_ND_rep2_2.fq.gz fastq fastq 6436941000.0 21456470.0 RNAseq MASLD HepGKO ND rep2 1.fq.gz 0:150 1:150 A:1671402056;C:1543860294;G:1570976721;T:1650596456;N:105473 150 150     1671402056 1543860294 1570976721 1650596456 105473 SRX27082403 SRS23541571 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34402 34402 SRR31719834 SRX27082402 SRS23541570 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb knockout normal diet for 35 days RNAseq MASLD HepGKO ND rep1 HepGKO ND rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 5|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGKO zebrafish of normal diet. HepGKO ND rep1 HepGKO ND rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGKO_ND_rep1_1.fq.gz RNAseq_MASLD_HepGKO_ND_rep1_2.fq.gz fastq fastq 6386174700.0 21287249.0 RNAseq MASLD HepGKO ND rep1 1.fq.gz 0:150 1:150 A:1662767742;C:1527603435;G:1545756971;T:1649944714;N:101838 150 150     1662767742 1527603435 1545756971 1649944714 101838 SRX27082402 SRS23541570 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34403 34403 SRR31719835 SRX27082401 SRS23541569 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     WT zebrafish high fat high cholesterol diet for 35 days RNAseq MASLD WT HFC rep2 WT HFC rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in WT zebrafish of high fat high cholesterol diet. WT HFC rep2 WT HFC rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_WT_HFC_rep2_1.fq.gz RNAseq_MASLD_WT_HFC_rep2_2.fq.gz fastq fastq 7088163900.0 23627213.0 RNAseq MASLD WT HFC rep2 1.fq.gz 0:150 1:150 A:1904609517;C:1635475353;G:1664944747;T:1882978732;N:155551 150 150     1904609517 1635475353 1664944747 1882978732 155551 SRX27082401 SRS23541569 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34404 34404 SRR31719836 SRX27082400 SRS23541568 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     WT zebrafish high fat high cholesterol diet for 35 days RNAseq MASLD WT HFC rep1 WT HFC rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in WT zebrafish of high fat high cholesterol diet. WT HFC rep1 WT HFC rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_WT_HFC_rep1_1.fq.gz RNAseq_MASLD_WT_HFC_rep1_2.fq.gz fastq fastq 7053396600.0 23511322.0 RNAseq MASLD WT HFC rep1 1.fq.gz 0:150 1:150 A:1862942395;C:1655266768;G:1688002812;T:1847030526;N:154099 150 150     1862942395 1655266768 1688002812 1847030526 154099 SRX27082400 SRS23541568 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34405 34405 SRR31719837 SRX27082399 SRS23541567 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb overexpression high fat high cholesterol diet for 35 days RNAseq MASLD HepGOE HFC rep2 HepGOE HFC rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 12|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGOE zebrafish of high fat high cholesterol diet. HepGOE HFC rep2 HepGOE HFC rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGOE_HFC_rep2_1.fq.gz RNAseq_MASLD_HepGOE_HFC_rep2_2.fq.gz fastq fastq 7004757600.0 23349192.0 RNAseq MASLD HepGOE HFC rep2 1.fq.gz 0:150 1:150 A:1846708800;C:1647727254;G:1676955416;T:1833207397;N:158733 150 150     1846708800 1647727254 1676955416 1833207397 158733 SRX27082399 SRS23541567 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34406 34406 SRR31719838 SRX27082398 SRS23541566 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     hepatocyte specific gmfb overexpression high fat high cholesterol diet for 35 days RNAseq MASLD HepGOE HFC rep1 HepGOE HFC rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 11|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in HepGOE zebrafish of high fat high cholesterol diet. HepGOE HFC rep1 HepGOE HFC rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_HepGOE_HFC_rep1_1.fq.gz RNAseq_MASLD_HepGOE_HFC_rep1_2.fq.gz fastq fastq 8211524400.0 27371748.0 RNAseq MASLD HepGOE HFC rep1 1.fq.gz 0:150 1:150 A:2217820195;C:1876471113;G:1906298333;T:2210753213;N:181546 150 150     2217820195 1876471113 1906298333 2210753213 181546 SRX27082398 SRS23541566 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34407 34407 SRR31719839 SRX27082397 SRS23541565 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     WT zebrafish normal diet for 35 days RNAseq MASLD WT ND rep2 WT ND rep2   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in WT zebrafish of normal diet. WT ND rep2 WT ND rep2 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_WT_ND_rep2_1.fq.gz RNAseq_MASLD_WT_ND_rep2_2.fq.gz fastq fastq 6966786300.0 23222621.0 RNAseq MASLD WT ND rep2 1.fq.gz 0:150 1:150 A:1855652140;C:1619780884;G:1651213951;T:1839982276;N:157049 150 150     1855652140 1619780884 1651213951 1839982276 157049 SRX27082397 SRS23541565 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
34408 34408 SRR31719840 SRX27082396 SRS23541564 SRP551495 PRJNA1198392 RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD PRJNA1198392 Other Glia maturation factor beta Gmfb an actin filament debrancher was first identified in the brain and has more recently been associated with liver diseases. However the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.     WT zebrafish normal diet for 35 days RNAseq MASLD WT ND rep1 WT ND rep1   strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal                 Transcriptome of liver tissues in WT zebrafish of normal diet. WT ND rep1 WT ND rep1 Total RNA was extracted from liver tissue for RNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP551495     RNAseq_MASLD_WT_ND_rep1_1.fq.gz RNAseq_MASLD_WT_ND_rep1_2.fq.gz fastq fastq 7149668700.0 23832229.0 RNAseq MASLD WT ND rep1 1.fq.gz 0:150 1:150 A:1869145140;C:1695095352;G:1726444600;T:1858824841;N:158767 150 150     1869145140 1695095352 1726444600 1858824841 158767 SRX27082396 SRS23541564 SRA2034386 Southern Medical University|Biomedical Research Center Southern Medical University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-12-15 Juvenile Juvenile Liver Liver and Biliary System
42181 42181 SRR5482153 SRX2765568 SRS2149771 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Large harvested line biological replicate 1 F2 offspring originating from wild caught population LS1 F2   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2008|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F2 individuals LS1 F2 LS1 F2 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     LS1-F2-10_FCC4CMHACXX_L1_WHZEBagiNCADRAAPEI-205_1.fq.gz LS1-F2-1_FCC4BKHACXX_L7_WHZEBagiNCAARAAPEI-201_1.fq.gz LS1-F2-5_FCC4BKHACXX_L7_WHZEBagiNCABRAAPEI-202_1.fq.gz LS1-F2-8_FCC4BKHACXX_L7_WHZEBagiNCACRAAPEI-203_1.fq.gz fastq fastq fastq fastq 12496905120.0 255038880.0 LS1 F2 10 FCC4CMHACXX L1 WHZEBagiNCADRAAPEI 205 1.fq.gz 0:49 A:3275093505;C:2981786839;G:2904373605;T:3334855308;N:795863 49       3275093505 2981786839 2904373605 3334855308 795863 SRX2765568 SRS2149771 SRA557107 University of Turku|Biology University of Turku 1 0.88577   0.04599   0.76469   0.48703   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42182 42182 SRR5482152 SRX2765567 SRS2149770 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Large harvested line biological replicate 2 F2 offspring originating from wild caught population LS2 F2   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2008|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F2 individuals LS2 F2 LS2 F2 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     LS2-F2-10_FCC4CMHACXX_L4_WHZEBagiNCALRAAPEI-213_1.fq.gz LS2-F2-11_FCC4CMHACXX_L4_WHZEBagiNCAMRAAPEI-214_1.fq.gz LS2-F2-14_FCC4C2AACXX_L1_WHZEBagiNCANRAAPEI-215_1.fq.gz LS2-F2-9_FCC4CMHACXX_L4_WHZEBagiNCAKRAAPEI-212_1.fq.gz fastq fastq fastq fastq 11108547205.0 226705045.0 LS2 F2 9 FCC4CMHACXX L4 WHZEBagiNCAKRAAPEI 212 1.fq.gz 0:49 A:2930693084;C:2628276474;G:2564131315;T:2984423047;N:1023285 49       2930693084 2628276474 2564131315 2984423047 1023285 SRX2765567 SRS2149770 SRA557107 University of Turku|Biology University of Turku 1 0.90013   0.04677   0.81251   0.44762   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42183 42183 SRR5482151 SRX2765565 SRS2149769 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Random harvested line biological replicate 1 F2 offspring originating from wild caught population RS1 F2   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2008|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F2 individuals RS1 F2 RS1 F2 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     RS1-F2-14_FCC4C2AACXX_L2_WHZEBagiNCAURAAPEI-223_1.fq.gz RS1-F2-16_FCC4C2AACXX_L2_WHZEBagiNCAVRAAPEI-225_1.fq.gz RS1-F2-17_FCC4C2AACXX_L3_WHZEBagiNCAWRAAPEI-227_1.fq.gz RS1-F2-19_FCC4C2AACXX_L3_WHZEBagiNCAXRAAPEI-201_1.fq.gz fastq fastq fastq fastq 12074501894.0 246418406.0 RS1 F2 16 FCC4C2AACXX L2 WHZEBagiNCAVRAAPEI 225 1.fq.gz 0:49 A:3199737416;C:2851335695;G:2767557430;T:3254746975;N:1124378 49       3199737416 2851335695 2767557430 3254746975 1124378 SRX2765565 SRS2149769 SRA557107 University of Turku|Biology University of Turku 1 0.87838   0.05071   0.81663   0.55417   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42184 42184 SRR5482150 SRX2765564 SRS2149768 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Random harvested line biological replicate 2 F2 offspring originating from wild caught population RS2 F2   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2008|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F2 individuals RS2 F2 RS2 F2 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     RS2-F2-3_FCC4CMHACXX_L2_WHZEBagiNCBFRAAPEI-210_1.fq.gz RS2-F2-6-2_FCC4CMHACXX_L2_WHZEBagiNCBGRAAPEI-211_1.fq.gz RS2-F2-8_FCC4CMHACXX_L2_WHZEBagiNCBHRABPEI-212_1.fq.gz RS2-F2-9_FCC4CMHACXX_L3_WHZEBagiNCBIRABPEI-213_1.fq.gz fastq fastq fastq fastq 11923597525.0 243338725.0 RS2 F2 9 FCC4CMHACXX L3 WHZEBagiNCBIRABPEI 213 1.fq.gz 0:49 A:3132507165;C:2819390547;G:2776793842;T:3193588286;N:1317685 49       3132507165 2819390547 2776793842 3193588286 1317685 SRX2765564 SRS2149768 SRA557107 University of Turku|Biology University of Turku 1 0.90986   0.05269   0.814   0.36827   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42185 42185 SRR5482149 SRX2765563 SRS2149767 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Large harvested line biological replicate 1 F5 offspring originating from wild caught population LS1 F5   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2010|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F5 individuals LS1 F5 LS1 F5 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     LS1-15_FCC4C3HACXX_L1_WHZEBagiNBANRAAPEI-215_1.fq.gz LS1-2_FCC4BJ2ACXX_L5_WHZEBagiNBABRAAPEI-202_1.fq.gz LS1-6_FCC4BJ2ACXX_L6_WHZEBagiNBAFRAAPEI-207_1.fq.gz LS1-8_FCC4BJ2ACXX_L8_WHZEBagiNBAJRAAPEI-211_1.fq.gz fastq fastq fastq fastq 12776192331.0 260738619.0 LS1 2 FCC4BJ2ACXX L5 WHZEBagiNBABRAAPEI 202 1.fq.gz 0:49 A:3371838433;C:3025006624;G:2934135898;T:3444117388;N:1093988 49       3371838433 3025006624 2934135898 3444117388 1093988 SRX2765563 SRS2149767 SRA557107 University of Turku|Biology University of Turku 1 0.88482   0.04932   0.813   0.51224   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42186 42186 SRR5482148 SRX2765562 SRS2149766 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Large harvested line biological replicate 2 F5 offspring originating from wild caught population LS2 F5   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2010|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F5 individuals LS2 F5 LS2 F5 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     LS2-10_FCC4BJ2ACXX_L8_WHZEBagiNBAKRAAPEI-212_1.fq.gz LS2-11_FCC4C3HACXX_L1_WHZEBagiNBAORAAPEI-216_1.fq.gz LS2-1_FCC4BJ2ACXX_L5_WHZEBagiNBACRAAPEI-203_1.fq.gz LS2-7_FCC4BVYACXX_L1_WHZEBagiNBAGRAAPEI-208_1.fq.gz fastq fastq fastq fastq 11941143935.0 243696815.0 LS2 10 FCC4BJ2ACXX L8 WHZEBagiNBAKRAAPEI 212 1.fq.gz 0:49 A:3165540142;C:2817777586;G:2733117846;T:3223679054;N:1029307 49       3165540142 2817777586 2733117846 3223679054 1029307 SRX2765562 SRS2149766 SRA557107 University of Turku|Biology University of Turku 1 0.87119   0.04752   0.80251   0.55444   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42187 42187 SRR5482147 SRX2765561 SRS2149765 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Random harvested line biological replicate 1 F5 offspring originating from wild caught population RS1 F5   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2010|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F5 individuals RS1 F5 RS1 F5 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     RS1-10_FCC4BJ2ACXX_L8_WHZEBagiNBALRAAPEI-213_1.fq.gz RS1-2_FCC4Y2GACXX_L4_WHZEBagiNCBPRABPEI-221_1.fq.gz RS1-3_FCC4BJ2ACXX_L6_WHZEBagiNBADRAAPEI-205_1.fq.gz RS1-6_FCC4BV7ACXX_L1_WHZEBagiNBAHRAAPEI-209_1.fq.gz fastq fastq fastq fastq 12149652753.0 247952097.0 RS1 6 FCC4BV7ACXX L1 WHZEBagiNBAHRAAPEI 209 1.fq.gz 0:49 A:3177681868;C:2907323525;G:2822484622;T:3241144133;N:1018605 49       3177681868 2907323525 2822484622 3241144133 1018605 SRX2765561 SRS2149765 SRA557107 University of Turku|Biology University of Turku 1 0.90495   0.04625   0.80028   0.56443   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42188 42188 SRR5482146 SRX2765560 SRS2149764 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Random harvested line biological replicate 2 F5 offspring originating from wild caught population RS2 F5   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2010|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F5 individuals RS2 F5 RS2 F5 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     RS2-10_FCC4BVYACXX_L1_WHZEBagiNBAIRAAPEI-210_1.fq.gz RS2-13_FCC4C3HACXX_L1_WHZEBagiNBAMRAAPEI-214_1.fq.gz RS2-2_FCC4BJ2ACXX_L5_WHZEBagiNBAARAAPEI-201_1.fq.gz RS2-3_FCC4C19ACXX_L5_WHZEBagiNBAERAAPEI-206_1.fq.gz fastq fastq fastq fastq 11262796951.0 229852999.0 RS2 13 FCC4C3HACXX L1 WHZEBagiNBAMRAAPEI 214 1.fq.gz 0:49 A:2931626627;C:2710523895;G:2627211912;T:2992545637;N:888880 49       2931626627 2710523895 2627211912 2992545637 888880 SRX2765560 SRS2149764 SRA557107 University of Turku|Biology University of Turku 1 0.88588   0.04266   0.8112   0.52927   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42189 42189 SRR5482145 SRX2765559 SRS2149763 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Large harvested line biological replicate 1 F11 offspring originating from wild caught population LS1 F11   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2014|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F11 individuals LS1 F11 LS1 F11 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     LS1-F11B-11_FCC4CMHACXX_L1_WHZEBagiNCAERAAPEI-206_1.fq.gz LS1-F11B-13_FCC4CMHACXX_L1_WHZEBagiNCAFRAAPEI-207_1.fq.gz LS1-F11B-16_FCC4C19ACXX_L1_WHZEBagiNCAGRBAPEI-208_1.fq.gz LS1-F11B-17_FCC4BKHACXX_L8_WHZEBagiNCAHRAAPEI-209_1.fq.gz fastq fastq fastq fastq 11326213584.0 231147216.0 LS1 F11B 16 FCC4C19ACXX L1 WHZEBagiNCAGRBAPEI 208 1.fq.gz 0:49 A:2982223592;C:2693407623;G:2622876703;T:3026833843;N:871823 49       2982223592 2693407623 2622876703 3026833843 871823 SRX2765559 SRS2149763 SRA557107 University of Turku|Biology University of Turku 1 0.90202   0.04273   0.78273   0.51238   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42190 42190 SRR5482144 SRX2765558 SRS2149762 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Large harvested line biological replicate 2 F11 offspring originating from wild caught population LS2 F11   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2014|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F11 individuals LS2 F11 LS2 F11 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     LS2-F11B-1_FCC4C2AACXX_L1_WHZEBagiNCAORAAPEI-216_1.fq.gz LS2-F11B-2_FCC4C2AACXX_L1_WHZEBagiNCAPRAAPEI-218_1.fq.gz LS2-F11B-5_FCC4CMHACXX_L5_WHZEBagiNCAQRAAPEI-219_1.fq.gz LS2-F11B-7_FCC4CMHACXX_L5_WHZEBagiNCARRAAPEI-220_1.fq.gz fastq fastq fastq fastq 12030571875.0 245521875.0 LS2 F11B 7 FCC4CMHACXX L5 WHZEBagiNCARRAAPEI 220 1.fq.gz 0:49 A:3149792862;C:2871072895;G:2795019949;T:3213514581;N:1171588 49       3149792862 2871072895 2795019949 3213514581 1171588 SRX2765558 SRS2149762 SRA557107 University of Turku|Biology University of Turku 1 0.91893   0.036   0.77429   0.38962   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42191 42191 SRR5482143 SRX2765557 SRS2149760 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Random harvested line biological replicate 1 F11 offspring originating from wild caught population RS1 F11   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2014|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F11 individuals RS1 F11 RS1 F11 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     RS1-F11B-21_FCC4C2AACXX_L3_WHZEBagiNCAYRAAPEI-202_1.fq.gz RS1-F11B-23_FCC4C2AACXX_L4_WHZEBagiNCAZRAAPEI-203_1.fq.gz RS1-F11B-27_FCC4C2AACXX_L4_WHZEBagiNCBARAAPEI-205_1.fq.gz RS1-F11B-29_FCC4C2AACXX_L4_WHZEBagiNCBBRAAPEI-206_1.fq.gz fastq fastq fastq fastq 11947679555.0 243830195.0 RS1 F11B 21 FCC4C2AACXX L3 WHZEBagiNCAYRAAPEI 202 1.fq.gz 0:49 A:3159477117;C:2827401119;G:2753495798;T:3206143470;N:1162051 49       3159477117 2827401119 2753495798 3206143470 1162051 SRX2765557 SRS2149760 SRA557107 University of Turku|Biology University of Turku 1 0.87877   0.04488   0.77445   0.50852   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
42192 42192 SRR5482142 SRX2765556 SRS2149761 SRP105243 PRJNA383986 Danio rerio Raw sequence reads PRJNA383986 Other The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.       Danio rerio: Random harvested line biological replicate 2 F11 offspring originating from wild caught population RS2 F11   breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2014|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F11 individuals RS2 F11 RS2 F11 Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000   SRP105243     RS2-F11B-34_FCC4CMHACXX_L3_WHZEBagiNCBJRABPEI-214_1.fq.gz RS2-F11B-36_FCC4CMHACXX_L3_WHZEBagiNCBKRABPEI-215_1.fq.gz RS2-F11B-38_FCC4BY1ACXX_L1_WHZEBagiNCBLRABPEI-216_1.fq.gz RS2-F11B-40_FCC4BY1ACXX_L1_WHZEBagiNCBMRABPEI-218_1.fq.gz fastq fastq fastq fastq 10619740698.0 216729402.0 RS2 F11B 38 FCC4BY1ACXX L1 WHZEBagiNCBLRABPEI 216 1.fq.gz 0:49 A:2799661065;C:2501316593;G:2465115836;T:2852970598;N:676606 49       2799661065 2501316593 2465115836 2852970598 676606 SRX2765556 SRS2149761 SRA557107 University of Turku|Biology University of Turku 1 0.8851   0.04865   0.80407   0.54962   49   B   usable mapping rate illumina hiseq_era unknown other unknown bulk unknown unknown   Finland 2017-12-04 Juvenile Juvenile Liver Liver and Biliary System
53175 53175 SRR9708005 SRX6465919 SRS5126684 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week HBx Srcp53 DIO sample 2 GSM3954323   source name:8week HBx Srcp53 Overfed|strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Overfed 8week HBx Srcp53 DIO sample 2 Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week HBx Srcp53 Overfed The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Overfed GSM3954323 GSM3954323: 8week HBx Srcp53 DIO sample 2; Danio rerio; RNA Seq GSM3954323   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954323 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     TriDIO11_1.fq.gz TriDIO11_2.fq.gz fastq fastq 4249297200.0 14164324.0 GSM3954323 r1 0:150 1:150 A:1118373146;C:1004287869;G:1022623288;T:1103209208;N:803689 150 150     1118373146 1004287869 1022623288 1103209208 803689 SRX6465919 SRS5126684 SRA922815 GEO National Chiao Tung University 2 0.93432 0.93585 0.02504 0.0252 0.84147 0.84404 0.40759 0.40621 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System
53176 53176 SRR9708004 SRX6465918 SRS5126685 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week HBx Srcp53 DIO sample 1 GSM3954322   source name:8week HBx Srcp53 Overfed|strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Overfed 8week HBx Srcp53 DIO sample 1 Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week HBx Srcp53 Overfed The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Overfed GSM3954322 GSM3954322: 8week HBx Srcp53 DIO sample 1; Danio rerio; RNA Seq GSM3954322   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954322 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     TriDIO7_1.fq.gz TriDIO7_2.fq.gz fastq fastq 4138104000.0 13793680.0 GSM3954322 r1 0:150 1:150 A:1083497193;C:982815449;G:997572851;T:1073433464;N:785043 150 150     1083497193 982815449 997572851 1073433464 785043 SRX6465918 SRS5126685 SRA922815 GEO National Chiao Tung University 2 0.93773 0.93872 0.02225 0.02227 0.83976 0.8434 0.33808 0.33225 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System
53177 53177 SRR9708003 SRX6465917 SRS5126683 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week HBx Srcp53 NOR sample 2 GSM3954321   source name:8week HBx Srcp53 Normal diet|strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Normal diet 8week HBx Srcp53 NOR sample 2 Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week HBx Srcp53 Normal diet The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Normal diet GSM3954321 GSM3954321: 8week HBx Srcp53 NOR sample 2; Danio rerio; RNA Seq GSM3954321   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954321 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     TriNOR11_1.fq.gz TriNOR11_2.fq.gz fastq fastq 4268302500.0 14227675.0 GSM3954321 r1 0:150 1:150 A:1117539537;C:1013234805;G:1028678990;T:1108041769;N:807399 150 150     1117539537 1013234805 1028678990 1108041769 807399 SRX6465917 SRS5126683 SRA922815 GEO National Chiao Tung University 2 0.9398 0.9404 0.01665 0.01644 0.84691 0.84981 0.23273 0.23748 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System
53178 53178 SRR9708002 SRX6465916 SRS5126682 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week HBx Srcp53 NOR sample 1 GSM3954320   source name:8week HBx Srcp53 Normal diet|strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Normal diet 8week HBx Srcp53 NOR sample 1 Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week HBx Srcp53 Normal diet The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Normal diet GSM3954320 GSM3954320: 8week HBx Srcp53 NOR sample 1; Danio rerio; RNA Seq GSM3954320   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954320 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     TriNOR3_1.fq.gz TriNOR3_2.fq.gz fastq fastq 4035527100.0 13451757.0 GSM3954320 r1 0:150 1:150 A:1048654192;C:965234637;G:981448091;T:1039436158;N:754022 150 150     1048654192 965234637 981448091 1039436158 754022 SRX6465916 SRS5126682 SRA922815 GEO National Chiao Tung University 2 0.9318 0.93291 0.01634 0.01669 0.83155 0.83431 0.26548 0.26993 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System
53179 53179 SRR9708001 SRX6465915 SRS5126681 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week Srcp53 FAT GSM3954319   source name:8week Srcp53 High fat diet|strain/background:AB|genotype/variation:Srcp53 |tissue:Liver|diet:High fat diet 8week Srcp53 FAT Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week Srcp53 High fat diet The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:Srcp53 |tissue:Liver|diet:High fat diet GSM3954319 GSM3954319: 8week Srcp53 FAT; Danio rerio; RNA Seq GSM3954319   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954319 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     Src_FAT4_1.fq.gz Src_FAT4_2.fq.gz fastq fastq 4095939900.0 13653133.0 GSM3954319 r1 0:150 1:150 A:1080000914;C:966449452;G:980758473;T:1067958610;N:772451 150 150     1080000914 966449452 980758473 1067958610 772451 SRX6465915 SRS5126681 SRA922815 GEO National Chiao Tung University 2 0.9214 0.92115 0.02194 0.02143 0.86425 0.86679 0.19828 0.19948 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System
53180 53180 SRR9708000 SRX6465914 SRS5126680 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week Srcp53 DIO GSM3954318   source name:8week Srcp53 Overfed|strain/background:AB|genotype/variation:Srcp53 |tissue:Liver|diet:Overfed 8week Srcp53 DIO Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week Srcp53 Overfed The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:Srcp53 |tissue:Liver|diet:Overfed GSM3954318 GSM3954318: 8week Srcp53 DIO; Danio rerio; RNA Seq GSM3954318   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954318 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     SrcDIO11_1.fq.gz SrcDIO11_2.fq.gz fastq fastq 4295950800.0 14319836.0 GSM3954318 r1 0:150 1:150 A:1118680365;C:1026334652;G:1040877221;T:1109247541;N:811021 150 150     1118680365 1026334652 1040877221 1109247541 811021 SRX6465914 SRS5126680 SRA922815 GEO National Chiao Tung University 2 0.93615 0.93765 0.01871 0.01885 0.87097 0.87369 0.29136 0.29027 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System
53181 53181 SRR9707999 SRX6465913 SRS5126679 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week Srcp53 NOR sample 2 GSM3954317   source name:8week Srcp53 Normal diet|strain/background:AB|genotype/variation:Srcp53 |tissue:Liver|diet:Normal diet 8week Srcp53 NOR sample 2 Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week Srcp53 Normal diet The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:Srcp53 |tissue:Liver|diet:Normal diet GSM3954317 GSM3954317: 8week Srcp53 NOR sample 2; Danio rerio; RNA Seq GSM3954317   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954317 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     Src_NOR9_1.fq.gz Src_NOR9_2.fq.gz fastq fastq 3230924400.0 10769748.0 GSM3954317 r1 0:150 1:150 A:849542686;C:763912445;G:775517170;T:841572201;N:379898 150 150     849542686 763912445 775517170 841572201 379898 SRX6465913 SRS5126679 SRA922815 GEO National Chiao Tung University 2 0.92205 0.92321 0.02638 0.02642 0.83248 0.83546 0.33062 0.32957 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System
53182 53182 SRR9707998 SRX6465912 SRS5126677 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week Srcp53 NOR sample 1 GSM3954316   source name:8week Srcp53 Normal diet|strain/background:AB|genotype/variation:Srcp53 |tissue:Liver|diet:Normal diet 8week Srcp53 NOR sample 1 Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week Srcp53 Normal diet The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:Srcp53 |tissue:Liver|diet:Normal diet GSM3954316 GSM3954316: 8week Srcp53 NOR sample 1; Danio rerio; RNA Seq GSM3954316   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954316 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     Src_NOR5_1.fq.gz Src_NOR5_2.fq.gz fastq fastq 3622050600.0 12073502.0 GSM3954316 r1 0:150 1:150 A:952640423;C:856805394;G:867903368;T:944017329;N:684086 150 150     952640423 856805394 867903368 944017329 684086 SRX6465912 SRS5126677 SRA922815 GEO National Chiao Tung University 2 0.93859 0.9386 0.02248 0.02285 0.85638 0.85853 0.25471 0.26321 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System
53183 53183 SRR9707997 SRX6465911 SRS5126678 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week HBxp53 FAT GSM3954315   source name:8week HBxp53 High fat diet|strain/background:AB|genotype/variation:HBxp53 |tissue:Liver|diet:High fat diet 8week HBxp53 FAT Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week HBxp53 High fat diet The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:HBxp53 |tissue:Liver|diet:High fat diet GSM3954315 GSM3954315: 8week HBxp53 FAT; Danio rerio; RNA Seq GSM3954315   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954315 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     HBxFAT12_1.fq.gz HBxFAT12_2.fq.gz fastq fastq 3496192800.0 11653976.0 GSM3954315 r1 0:150 1:150 A:913664496;C:831395771;G:845661828;T:904814682;N:656023 150 150     913664496 831395771 845661828 904814682 656023 SRX6465911 SRS5126678 SRA922815 GEO National Chiao Tung University 2 0.93627 0.93829 0.01608 0.0163 0.87203 0.87588 0.20914 0.20793 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System
53184 53184 SRR9707996 SRX6465910 SRS5126676 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week HBxp53 DIO GSM3954314   source name:8week HBxp53 Overfed|strain/background:AB|genotype/variation:HBxp53 |tissue:Liver|diet:Overfed 8week HBxp53 DIO Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week HBxp53 Overfed The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:HBxp53 |tissue:Liver|diet:Overfed GSM3954314 GSM3954314: 8week HBxp53 DIO; Danio rerio; RNA Seq GSM3954314   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954314 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     HBxDIO13_1.fq.gz HBxDIO13_2.fq.gz fastq fastq 4161988500.0 13873295.0 GSM3954314 r1 0:150 1:150 A:1100750154;C:978574151;G:993521613;T:1088360923;N:781659 150 150     1100750154 978574151 993521613 1088360923 781659 SRX6465910 SRS5126676 SRA922815 GEO National Chiao Tung University 2 0.91603 0.91663 0.02493 0.02524 0.85867 0.86137 0.24463 0.2477 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System
53185 53185 SRR9707995 SRX6465909 SRS5126675 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week HBxp53 NOR sample 2 GSM3954313   source name:8week HBxp53 Normal diet|strain/background:AB|genotype/variation:HBxp53 |tissue:Liver|diet:Normal diet 8week HBxp53 NOR sample 2 Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week HBxp53 Normal diet The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:HBxp53 |tissue:Liver|diet:Normal diet GSM3954313 GSM3954313: 8week HBxp53 NOR sample 2; Danio rerio; RNA Seq GSM3954313   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954313 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     HBxNOR15_1.fq.gz HBxNOR15_2.fq.gz fastq fastq 3412777800.0 11375926.0 GSM3954313 r1 0:150 1:150 A:897716581;C:805966386;G:818686771;T:889764566;N:643496 150 150     897716581 805966386 818686771 889764566 643496 SRX6465909 SRS5126675 SRA922815 GEO National Chiao Tung University 2 0.92812 0.92863 0.02875 0.02888 0.85626 0.85918 0.32689 0.32969 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System
53186 53186 SRR9707994 SRX6465908 SRS5126674 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week HBxp53 NOR sample 1 GSM3954312   source name:8week HBxp53 Normal diet|strain/background:AB|genotype/variation:HBxp53 |tissue:Liver|diet:Normal diet 8week HBxp53 NOR sample 1 Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week HBxp53 Normal diet The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:HBxp53 |tissue:Liver|diet:Normal diet GSM3954312 GSM3954312: 8week HBxp53 NOR sample 1; Danio rerio; RNA Seq GSM3954312   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954312 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     HBx_NOR2_1.fq.gz HBx_NOR2_2.fq.gz fastq fastq 3251877900.0 10839593.0 GSM3954312 r1 0:150 1:150 A:853585195;C:770775549;G:781707938;T:845195300;N:613918 150 150     853585195 770775549 781707938 845195300 613918 SRX6465908 SRS5126674 SRA922815 GEO National Chiao Tung University 2 0.93901 0.93913 0.02224 0.02245 0.86766 0.87089 0.23209 0.23176 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System
53187 53187 SRR9707993 SRX6465907 SRS5126672 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week WT FAT GSM3954311   source name:8week WT High fat diet|strain/background:AB|genotype/variation:WT|tissue:Liver|diet:High fat diet 8week WT FAT Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week WT High fat diet The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:WT|tissue:Liver|diet:High fat diet GSM3954311 GSM3954311: 8week WT FAT; Danio rerio; RNA Seq GSM3954311   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954311 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     WT_FAT12_1.fq.gz WT_FAT12_2.fq.gz fastq fastq 3748358400.0 12494528.0 GSM3954311 r1 0:150 1:150 A:984937396;C:887127956;G:901610349;T:973974336;N:708363 150 150     984937396 887127956 901610349 973974336 708363 SRX6465907 SRS5126672 SRA922815 GEO National Chiao Tung University 2 0.92386 0.92371 0.0296 0.02954 0.85021 0.85313 0.26314 0.25996 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System
53188 53188 SRR9707992 SRX6465906 SRS5126673 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week WT DIO GSM3954310   source name:8week WT Overfed|strain/background:AB|genotype/variation:WT|tissue:Liver|diet:Overfed 8week WT DIO Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week WT Overfed The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:WT|tissue:Liver|diet:Overfed GSM3954310 GSM3954310: 8week WT DIO; Danio rerio; RNA Seq GSM3954310   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954310 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     WT_DIO16_1.fq.gz WT_DIO16_2.fq.gz fastq fastq 4022575800.0 13408586.0 GSM3954310 r1 0:150 1:150 A:1061317698;C:947922063;G:961268985;T:1051306042;N:761012 150 150     1061317698 947922063 961268985 1051306042 761012 SRX6465906 SRS5126673 SRA922815 GEO National Chiao Tung University 2 0.92971 0.93058 0.02073 0.02033 0.86334 0.86645 0.22401 0.22308 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System
53189 53189 SRR9707991 SRX6465905 SRS5126671 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week WT NOR sample 2 GSM3954309   source name:8week WT Normal diet|strain/background:AB|genotype/variation:WT|tissue:Liver|diet:Normal diet 8week WT NOR sample 2 Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week WT Normal diet The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:WT|tissue:Liver|diet:Normal diet GSM3954309 GSM3954309: 8week WT NOR sample 2; Danio rerio; RNA Seq GSM3954309   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954309 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     WT_NOR20_1.fq.gz WT_NOR20_2.fq.gz fastq fastq 3481565100.0 11605217.0 GSM3954309 r1 0:150 1:150 A:922872893;C:816859095;G:828168259;T:912998471;N:666382 150 150     922872893 816859095 828168259 912998471 666382 SRX6465905 SRS5126671 SRA922815 GEO National Chiao Tung University 2 0.92796 0.92775 0.02044 0.0205 0.85058 0.85372 0.24017 0.24546 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System
53190 53190 SRR9707990 SRX6465904 SRS5126670 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week WT NOR sample 1 GSM3954308   source name:8week WT Normal diet|strain/background:AB|genotype/variation:WT|tissue:Liver|diet:Normal diet 8week WT NOR sample 1 Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week WT Normal diet The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:WT|tissue:Liver|diet:Normal diet GSM3954308 GSM3954308: 8week WT NOR sample 1; Danio rerio; RNA Seq GSM3954308   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954308 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     WT_NOR2_1.fq.gz WT_NOR2_2.fq.gz fastq fastq 4215976200.0 14053254.0 GSM3954308 r1 0:150 1:150 A:1099428840;C:1005939535;G:1020758972;T:1089047539;N:801314 150 150     1099428840 1005939535 1020758972 1089047539 801314 SRX6465904 SRS5126670 SRA922815 GEO National Chiao Tung University 2 0.92522 0.92502 0.02531 0.02547 0.87113 0.8734 0.28382 0.28497 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System
56067 56067 SRR10868218 SRX7538241 SRS5976905 SRP241164 PRJNA600413 Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome GSE143416 Transcriptome Analysis Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male with…   pubmed:33163595   WDFL rep2 GSM4259038   source name:Withdrawal Female Liver 2|strain:short fin 'AB' strain|condition:Withdrawal|Sex:female|tissue:Liver WDFL rep2 Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues Withdrawal Female Liver 2 For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects. Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank. strain:short fin 'AB' strain|condition:Withdrawal|Sex:Female|tissue:Liver GSM4259038 GSM4259038: WDFL rep2; Danio rerio; RNA Seq GSM4259038   1 Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. GEO Accession:GSM4259038 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP241164     WDFL2_R2.fastq.gz WDFL2_R1.fastq.gz fastq fastq 5978725600.0 29893628.0 GSM4259038 r1 0:100 1:100 A:1574223203;C:1415058444;G:1415352341;T:1571279633;N:2811979 100 100     1574223203 1415058444 1415352341 1571279633 2811979 SRX7538241 SRS5976905 SRA1023469 GEO CSIR Centre for Cellular and Molecular biology 2 0.97373 0.9727 0.02754 0.0273 0.83717 0.84053 0.20675 0.20492 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   India 2020-01-10 Juvenile Juvenile Liver Liver and Biliary System
56068 56068 SRR10868217 SRX7538240 SRS5976904 SRP241164 PRJNA600413 Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome GSE143416 Transcriptome Analysis Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male with…   pubmed:33163595   WDFL rep1 GSM4259037   source name:Withdrawal Female Liver 1|strain:short fin 'AB' strain|condition:Withdrawal|Sex:female|tissue:Liver WDFL rep1 Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues Withdrawal Female Liver 1 For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects. Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank. strain:short fin 'AB' strain|condition:Withdrawal|Sex:Female|tissue:Liver GSM4259037 GSM4259037: WDFL rep1; Danio rerio; RNA Seq GSM4259037   1 Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. GEO Accession:GSM4259037 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP241164     WDFL1_R1.fastq.gz WDFL1_R2.fastq.gz fastq fastq 8803793400.0 44018967.0 GSM4259037 r1 0:100 1:100 A:2301352863;C:2094763989;G:2089744439;T:2313772264;N:4159845 100 100     2301352863 2094763989 2089744439 2313772264 4159845 SRX7538240 SRS5976904 SRA1023469 GEO CSIR Centre for Cellular and Molecular biology 2 0.97269 0.97147 0.02717 0.02755 0.83948 0.84206 0.20335 0.20575 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   India 2020-01-10 Juvenile Juvenile Liver Liver and Biliary System
56069 56069 SRR10868216 SRX7538239 SRS5976903 SRP241164 PRJNA600413 Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome GSE143416 Transcriptome Analysis Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male with…   pubmed:33163595   WDML rep2 GSM4259036   source name:Withdrawal Male Liver 2|strain:short fin 'AB' strain|condition:Withdrawal|Sex:male|tissue:Liver WDML rep2 Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues Withdrawal Male Liver 2 For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects. Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank. strain:short fin 'AB' strain|condition:Withdrawal|Sex:Male|tissue:Liver GSM4259036 GSM4259036: WDML rep2; Danio rerio; RNA Seq GSM4259036   1 Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. GEO Accession:GSM4259036 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP241164     WDML2_R2.fastq.gz WDML2_R1.fastq.gz fastq fastq 7015689200.0 35078446.0 GSM4259036 r1 0:100 1:100 A:1779798478;C:1742766511;G:1769340834;T:1720182359;N:3601018 100 100     1779798478 1742766511 1769340834 1720182359 3601018 SRX7538239 SRS5976903 SRA1023469 GEO CSIR Centre for Cellular and Molecular biology 2 0.94907 0.94528 0.03016 0.03069 0.79628 0.79859 0.53607 0.53294 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   India 2020-01-10 Juvenile Juvenile Liver Liver and Biliary System
56070 56070 SRR10868215 SRX7538238 SRS5976902 SRP241164 PRJNA600413 Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome GSE143416 Transcriptome Analysis Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male with…   pubmed:33163595   WDML rep1 GSM4259035   source name:Withdrawal Male Liver 1|strain:short fin 'AB' strain|condition:Withdrawal|Sex:male|tissue:Liver WDML rep1 Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues Withdrawal Male Liver 1 For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects. Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank. strain:short fin 'AB' strain|condition:Withdrawal|Sex:Male|tissue:Liver GSM4259035 GSM4259035: WDML rep1; Danio rerio; RNA Seq GSM4259035   1 Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. GEO Accession:GSM4259035 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP241164     WDML1_R1.fastq.gz WDML1_R2.fastq.gz fastq fastq 7147989000.0 35739945.0 GSM4259035 r1 0:100 1:100 A:1780372303;C:1815362554;G:1862406693;T:1686233575;N:3613875 100 100     1780372303 1815362554 1862406693 1686233575 3613875 SRX7538238 SRS5976902 SRA1023469 GEO CSIR Centre for Cellular and Molecular biology 2 0.93918 0.93766 0.02982 0.02971 0.80535 0.80913 0.52958 0.52331 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   India 2020-01-10 Juvenile Juvenile Liver Liver and Biliary System
56071 56071 SRR10868214 SRX7538237 SRS5976901 SRP241164 PRJNA600413 Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome GSE143416 Transcriptome Analysis Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male with…   pubmed:33163595   ALFL rep2 GSM4259034   source name:Alcohol exposed Female Liver 2|strain:short fin 'AB' strain|condition:Alcohol exposed|Sex:female|tissue:Liver ALFL rep2 Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues Alcohol exposed Female Liver 2 For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects. Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank. strain:short fin 'AB' strain|condition:Alcohol exposed|Sex:Female|tissue:Liver GSM4259034 GSM4259034: ALFL rep2; Danio rerio; RNA Seq GSM4259034   1 Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. GEO Accession:GSM4259034 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP241164     ALFL2_R1.fastq.gz ALFL2_R2.fastq.gz fastq fastq 8678803800.0 43394019.0 GSM4259034 r1 0:100 1:100 A:2254928688;C:2084380554;G:2076784437;T:2258809206;N:3900915 100 100     2254928688 2084380554 2076784437 2258809206 3900915 SRX7538237 SRS5976901 SRA1023469 GEO CSIR Centre for Cellular and Molecular biology 2 0.9695 0.96915 0.03085 0.03134 0.80908 0.8127 0.29284 0.31107 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   India 2020-01-10 Juvenile Juvenile Liver Liver and Biliary System
56072 56072 SRR10868213 SRX7538236 SRS5976900 SRP241164 PRJNA600413 Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome GSE143416 Transcriptome Analysis Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male with…   pubmed:33163595   ALFL rep1 GSM4259033   source name:Alcohol exposed Female Liver 1|strain:short fin 'AB' strain|condition:Alcohol exposed|Sex:female|tissue:Liver ALFL rep1 Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues Alcohol exposed Female Liver 1 For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects. Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank. strain:short fin 'AB' strain|condition:Alcohol exposed|Sex:Female|tissue:Liver GSM4259033 GSM4259033: ALFL rep1; Danio rerio; RNA Seq GSM4259033   1 Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. GEO Accession:GSM4259033 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP241164     ALFL1_R2.fastq.gz ALFL1_R1.fastq.gz fastq fastq 9562583000.0 47812915.0 GSM4259033 r1 0:100 1:100 A:2511938021;C:2281314685;G:2285416160;T:2479465786;N:4448348 100 100     2511938021 2281314685 2285416160 2479465786 4448348 SRX7538236 SRS5976900 SRA1023469 GEO CSIR Centre for Cellular and Molecular biology 2 0.96678 0.96014 0.03186 0.03232 0.81205 0.81832 0.31507 0.30599 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   India 2020-01-10 Juvenile Juvenile Liver Liver and Biliary System
56073 56073 SRR10868212 SRX7538235 SRS5976899 SRP241164 PRJNA600413 Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome GSE143416 Transcriptome Analysis Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male with…   pubmed:33163595   ALML rep2 GSM4259032   source name:Alcohol exposed Male Liver 2|strain:short fin 'AB' strain|condition:Alcohol exposed|Sex:male|tissue:Liver ALML rep2 Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues Alcohol exposed Male Liver 2 For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects. Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank. strain:short fin 'AB' strain|condition:Alcohol exposed|Sex:Male|tissue:Liver GSM4259032 GSM4259032: ALML rep2; Danio rerio; RNA Seq GSM4259032   1 Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. GEO Accession:GSM4259032 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP241164     ALML2_R2.fastq.gz ALML2_R1.fastq.gz fastq fastq 5920856200.0 29604281.0 GSM4259032 r1 0:100 1:100 A:1560024572;C:1398117012;G:1390600317;T:1568986226;N:3128073 100 100     1560024572 1398117012 1390600317 1568986226 3128073 SRX7538235 SRS5976899 SRA1023469 GEO CSIR Centre for Cellular and Molecular biology 2 0.94976 0.94841 0.05469 0.05628 0.79415 0.79864 0.55278 0.54546 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   India 2020-01-10 Juvenile Juvenile Liver Liver and Biliary System
56074 56074 SRR10868211 SRX7538234 SRS5976898 SRP241164 PRJNA600413 Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome GSE143416 Transcriptome Analysis Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male with…   pubmed:33163595   ALML rep1 GSM4259031   source name:Alcohol exposed Male Liver 1|strain:short fin 'AB' strain|condition:Alcohol exposed|Sex:male|tissue:Liver ALML rep1 Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues Alcohol exposed Male Liver 1 For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects. Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank. strain:short fin 'AB' strain|condition:Alcohol exposed|Sex:Male|tissue:Liver GSM4259031 GSM4259031: ALML rep1; Danio rerio; RNA Seq GSM4259031   1 Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. GEO Accession:GSM4259031 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP241164     ALML1_R1.fastq.gz ALML1_R2.fastq.gz fastq fastq 6004949000.0 30024745.0 GSM4259031 r1 0:100 1:100 A:1546230434;C:1462161154;G:1452941715;T:1540051007;N:3564690 100 100     1546230434 1462161154 1452941715 1540051007 3564690 SRX7538234 SRS5976898 SRA1023469 GEO CSIR Centre for Cellular and Molecular biology 2 0.95167 0.95003 0.04572 0.04615 0.79746 0.80018 0.48729 0.48752 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   India 2020-01-10 Juvenile Juvenile Liver Liver and Biliary System
56075 56075 SRR10868210 SRX7538233 SRS5976897 SRP241164 PRJNA600413 Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome GSE143416 Transcriptome Analysis Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male with…   pubmed:33163595   CTFL rep2 GSM4259030   source name:Control Female Liver 2|strain:short fin 'AB' strain|condition:Control|Sex:female|tissue:Liver CTFL rep2 Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues Control Female Liver 2 For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects. Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank. strain:short fin 'AB' strain|condition:Control|Sex:Female|tissue:Liver GSM4259030 GSM4259030: CTFL rep2; Danio rerio; RNA Seq GSM4259030   1 Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. GEO Accession:GSM4259030 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP241164     CTFL2_R1.fastq.gz CTFL2_R2.fastq.gz fastq fastq 8204545000.0 41022725.0 GSM4259030 r1 0:100 1:100 A:2141255352;C:1960063343;G:1940272991;T:2159263280;N:3690034 100 100     2141255352 1960063343 1940272991 2159263280 3690034 SRX7538233 SRS5976897 SRA1023469 GEO CSIR Centre for Cellular and Molecular biology 2 0.96794 0.96592 0.03373 0.03363 0.83051 0.83372 0.26497 0.27281 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   India 2020-01-10 Juvenile Juvenile Liver Liver and Biliary System
56076 56076 SRR10868209 SRX7538232 SRS5976896 SRP241164 PRJNA600413 Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome GSE143416 Transcriptome Analysis Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male with…   pubmed:33163595   CTFL rep1 GSM4259029   source name:Control Female Liver 1|strain:short fin 'AB' strain|condition:Control|Sex:female|tissue:Liver CTFL rep1 Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues Control Female Liver 1 For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects. Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank. strain:short fin 'AB' strain|condition:Control|Sex:Female|tissue:Liver GSM4259029 GSM4259029: CTFL rep1; Danio rerio; RNA Seq GSM4259029   1 Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. GEO Accession:GSM4259029 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP241164     CTFL1_R1.fastq.gz CTFL1_R2.fastq.gz fastq fastq 7090165000.0 35450825.0 GSM4259029 r1 0:100 1:100 A:1885143566;C:1658541874;G:1661861079;T:1881339038;N:3279443 100 100     1885143566 1658541874 1661861079 1881339038 3279443 SRX7538232 SRS5976896 SRA1023469 GEO CSIR Centre for Cellular and Molecular biology 2 0.95522 0.95538 0.03516 0.03563 0.81556 0.81734 0.32249 0.3228 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   India 2020-01-10 Juvenile Juvenile Liver Liver and Biliary System
56077 56077 SRR10868208 SRX7538231 SRS5976895 SRP241164 PRJNA600413 Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome GSE143416 Transcriptome Analysis Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male with…   pubmed:33163595   CTML rep2 GSM4259028   source name:Control Male Liver 2|strain:short fin 'AB' strain|condition:Control|Sex:male|tissue:Liver CTML rep2 Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues Control Male Liver 2 For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects. Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank. strain:short fin 'AB' strain|condition:Control|Sex:Male|tissue:Liver GSM4259028 GSM4259028: CTML rep2; Danio rerio; RNA Seq GSM4259028   1 Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. GEO Accession:GSM4259028 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP241164     CTML2_R1.fastq.gz CTML2_R2.fastq.gz fastq fastq 9796791200.0 48983956.0 GSM4259028 r1 0:100 1:100 A:2721758622;C:2238538476;G:2213513091;T:2622439538;N:541473 100 100     2721758622 2238538476 2213513091 2622439538 541473 SRX7538231 SRS5976895 SRA1023469 GEO CSIR Centre for Cellular and Molecular biology 2 0.9236 0.92195 0.07857 0.07792 0.79095 0.79431 0.55394 0.55633 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   India 2020-01-10 Juvenile Juvenile Liver Liver and Biliary System
56078 56078 SRR10868207 SRX7538230 SRS5976894 SRP241164 PRJNA600413 Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome GSE143416 Transcriptome Analysis Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure – one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio shortfin 'AB' strain of both sexes i.e Male control Female control Male alcohol exposed Female alcohol exposed Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control three replicates of female control two replicates of Male alcohol exposed two replicates of Female alcohol exposed three replicates of Male with…   pubmed:33163595   CTML rep1 GSM4259027   source name:Control Male Liver 1|strain:short fin 'AB' strain|condition:Control|Sex:male|tissue:Liver CTML rep1 Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR runThreadN 16 runMode alignReads readFilesCommand zcat outSAMstrandField intronMotif outSAMtype BAM SortedByCoordinate quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters rsem calculate expression bam no bam output p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues Control Male Liver 1 For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C water salinity of 3 g of sea salt per liter and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations both partners control only male alcohol exposed only female alcohol exposed and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding we kept male and female fish in the same breeding tank a night before the breeding. The next morning breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects. Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer’s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty naïve wild type short fin ‘AB’strainD. rerio60 males 60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus each group was composed of 30 fish exclusively either male or female maintained in a 20 L water tank. strain:short fin 'AB' strain|condition:Control|Sex:Male|tissue:Liver GSM4259027 GSM4259027: CTML rep1; Danio rerio; RNA Seq GSM4259027   1 Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200 μl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at 80 °C. Total RNA was prepared using NucleoSpin® RNA kit Macherey Nagel REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis respectively. All RNA samples were stored at 80 °C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions. GEO Accession:GSM4259027 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP241164     CTML1_R1.fastq.gz CTML1_R2.fastq.gz fastq fastq 8984067200.0 44920336.0 GSM4259027 r1 0:100 1:100 A:2427722499;C:2092739125;G:2070318707;T:2392809051;N:477818 100 100     2427722499 2092739125 2070318707 2392809051 477818 SRX7538230 SRS5976894 SRA1023469 GEO CSIR Centre for Cellular and Molecular biology 2 0.92804 0.92566 0.06599 0.06574 0.80728 0.80791 0.53925 0.53265 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   India 2020-01-10 Juvenile Juvenile Liver Liver and Biliary System
65887 65887 SRR15667963 SRX11964789 SRS9973857 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train overfeed 6 GSM5549117   source name:liver|tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL liver train overfeed 6 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL GSM5549117 GSM5549117: liver train overfeed 6; Danio rerio; RNA Seq GSM5549117   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549117 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L24B_1.fq.gz L24B_2.fq.gz fastq fastq 4893222400.0 48932224.0 GSM5549117 r1 0:100 1:100 A:1299363606;C:1127714226;G:1149448002;T:1316696566;N:0 100 100     1299363606 1127714226 1149448002 1316696566 0 SRX11964789 SRS9973857 SRA1285419 GEO ZMF, University Heidelberg 1 0.94811   0.06102   0.81306   0.58353   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65888 65888 SRR15667962 SRX11964788 SRS9973856 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train overfeed 5 GSM5549116   source name:liver|tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL liver train overfeed 5 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL GSM5549116 GSM5549116: liver train overfeed 5; Danio rerio; RNA Seq GSM5549116   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549116 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L23B_1.fq.gz L23B_2.fq.gz fastq fastq 4864315800.0 48643158.0 GSM5549116 r1 0:100 1:100 A:1269157216;C:1139579077;G:1173873653;T:1281705854;N:0 100 100     1269157216 1139579077 1173873653 1281705854 0 SRX11964788 SRS9973856 SRA1285419 GEO ZMF, University Heidelberg 1 0.94747   0.0487   0.81779   0.56304   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65889 65889 SRR15667961 SRX11964787 SRS9973855 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train overfeed 4 GSM5549115   source name:liver|tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL liver train overfeed 4 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL GSM5549115 GSM5549115: liver train overfeed 4; Danio rerio; RNA Seq GSM5549115   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549115 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L22B_1.fq.gz L22B_2.fq.gz fastq fastq 4861767400.0 48617674.0 GSM5549115 r1 0:100 1:100 A:1272156595;C:1138672054;G:1163686667;T:1287252084;N:0 100 100     1272156595 1138672054 1163686667 1287252084 0 SRX11964787 SRS9973855 SRA1285419 GEO ZMF, University Heidelberg 1 0.95316   0.0514   0.82008   0.50642   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65890 65890 SRR15667960 SRX11964786 SRS9973854 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train overfeed 3 GSM5549114   source name:liver|tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL liver train overfeed 3 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL GSM5549114 GSM5549114: liver train overfeed 3; Danio rerio; RNA Seq GSM5549114   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549114 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L21B_1.fq.gz L21B_2.fq.gz fastq fastq 4830571800.0 48305718.0 GSM5549114 r1 0:100 1:100 A:1279428022;C:1123545637;G:1144703564;T:1282894577;N:0 100 100     1279428022 1123545637 1144703564 1282894577 0 SRX11964786 SRS9973854 SRA1285419 GEO ZMF, University Heidelberg 1 0.95734   0.02001   0.8868   0.12725   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65891 65891 SRR15667959 SRX11964785 SRS9973853 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train overfeed 2 GSM5549113   source name:liver|tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL liver train overfeed 2 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL GSM5549113 GSM5549113: liver train overfeed 2; Danio rerio; RNA Seq GSM5549113   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549113 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L20B_1.fq.gz L20B_2.fq.gz fastq fastq 4798900200.0 47989002.0 GSM5549113 r1 0:100 1:100 A:1264903507;C:1122454994;G:1142785530;T:1268756169;N:0 100 100     1264903507 1122454994 1142785530 1268756169 0 SRX11964785 SRS9973853 SRA1285419 GEO ZMF, University Heidelberg 1 0.95953   0.02579   0.87251   0.20039   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65892 65892 SRR15667958 SRX11964784 SRS9973852 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train overfeed 1 GSM5549112   source name:liver|tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL liver train overfeed 1 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL GSM5549112 GSM5549112: liver train overfeed 1; Danio rerio; RNA Seq GSM5549112   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549112 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L19B_1.fq.gz L19B_2.fq.gz fastq fastq 4834397800.0 48343978.0 GSM5549112 r1 0:100 1:100 A:1279393804;C:1125815329;G:1148443590;T:1280745077;N:0 100 100     1279393804 1125815329 1148443590 1280745077 0 SRX11964784 SRS9973852 SRA1285419 GEO ZMF, University Heidelberg 1 0.95933   0.02008   0.89483   0.14592   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65893 65893 SRR15667957 SRX11964783 SRS9973851 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train ctrl 6 GSM5549111   source name:liver|tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL liver train ctrl 6 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL GSM5549111 GSM5549111: liver train ctrl 6; Danio rerio; RNA Seq GSM5549111   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549111 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L18B_1.fq.gz L18B_2.fq.gz fastq fastq 4821948400.0 48219484.0 GSM5549111 r1 0:100 1:100 A:1291565962;C:1101325255;G:1121237816;T:1307819367;N:0 100 100     1291565962 1101325255 1121237816 1307819367 0 SRX11964783 SRS9973851 SRA1285419 GEO ZMF, University Heidelberg 1 0.94729   0.06306   0.81207   0.58228   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65894 65894 SRR15667956 SRX11964782 SRS9973850 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train ctrl 5 GSM5549110   source name:liver|tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL liver train ctrl 5 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL GSM5549110 GSM5549110: liver train ctrl 5; Danio rerio; RNA Seq GSM5549110   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549110 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L17B_1.fq.gz L17B_2.fq.gz fastq fastq 4803628200.0 48036282.0 GSM5549110 r1 0:100 1:100 A:1284799467;C:1098135007;G:1120469212;T:1300224514;N:0 100 100     1284799467 1098135007 1120469212 1300224514 0 SRX11964782 SRS9973850 SRA1285419 GEO ZMF, University Heidelberg 1 0.9496   0.0625   0.81456   0.59107   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65895 65895 SRR15667955 SRX11964781 SRS9973849 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train ctrl 4 GSM5549109   source name:liver|tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL liver train ctrl 4 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL GSM5549109 GSM5549109: liver train ctrl 4; Danio rerio; RNA Seq GSM5549109   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549109 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L16B_1.fq.gz L16B_2.fq.gz fastq fastq 4810847400.0 48108474.0 GSM5549109 r1 0:100 1:100 A:1282522728;C:1105003262;G:1127602301;T:1295719109;N:0 100 100     1282522728 1105003262 1127602301 1295719109 0 SRX11964781 SRS9973849 SRA1285419 GEO ZMF, University Heidelberg 1 0.94654   0.05935   0.81525   0.55406   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65896 65896 SRR15667954 SRX11964780 SRS9973848 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train ctrl 3 GSM5549108   source name:liver|tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL liver train ctrl 3 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL GSM5549108 GSM5549108: liver train ctrl 3; Danio rerio; RNA Seq GSM5549108   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549108 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L15B_1.fq.gz L15B_2.fq.gz fastq fastq 4985037400.0 49850374.0 GSM5549108 r1 0:100 1:100 A:1350433123;C:1126555415;G:1149552334;T:1358496528;N:0 100 100     1350433123 1126555415 1149552334 1358496528 0 SRX11964780 SRS9973848 SRA1285419 GEO ZMF, University Heidelberg 1 0.94223   0.05241   0.81753   0.38734   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65897 65897 SRR15667953 SRX11964779 SRS9973847 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train ctrl 2 GSM5549107   source name:liver|tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL liver train ctrl 2 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL GSM5549107 GSM5549107: liver train ctrl 2; Danio rerio; RNA Seq GSM5549107   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549107 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L14B_1.fq.gz L14B_2.fq.gz fastq fastq 4804454800.0 48044548.0 GSM5549107 r1 0:100 1:100 A:1265573746;C:1124189778;G:1148662079;T:1266029197;N:0 100 100     1265573746 1124189778 1148662079 1266029197 0 SRX11964779 SRS9973847 SRA1285419 GEO ZMF, University Heidelberg 1 0.95891   0.02268   0.88392   0.17772   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65898 65898 SRR15667952 SRX11964778 SRS9973846 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver train ctrl 1 GSM5549106   source name:liver|tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL liver train ctrl 1 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL GSM5549106 GSM5549106: liver train ctrl 1; Danio rerio; RNA Seq GSM5549106   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549106 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L13B_1.fq.gz L13B_2.fq.gz fastq fastq 4822830200.0 48228302.0 GSM5549106 r1 0:100 1:100 A:1276481281;C:1123835516;G:1144873235;T:1277640168;N:0 100 100     1276481281 1123835516 1144873235 1277640168 0 SRX11964778 SRS9973846 SRA1285419 GEO ZMF, University Heidelberg 1 0.96141   0.0197   0.89388   0.1349   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65899 65899 SRR15667951 SRX11964777 SRS9973845 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl overfeed 6 GSM5549105   source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL liver ctrl overfeed 6 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL GSM5549105 GSM5549105: liver ctrl overfeed 6; Danio rerio; RNA Seq GSM5549105   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549105 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L9B_1.fq.gz L9B_2.fq.gz fastq fastq 4818164600.0 48181646.0 GSM5549105 r1 0:100 1:100 A:1279585168;C:1117941633;G:1137085086;T:1283552713;N:0 100 100     1279585168 1117941633 1137085086 1283552713 0 SRX11964777 SRS9973845 SRA1285419 GEO ZMF, University Heidelberg 1 0.95794   0.0217   0.8772   0.13327   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65900 65900 SRR15667950 SRX11964776 SRS9973844 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl overfeed 5 GSM5549104   source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL liver ctrl overfeed 5 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL GSM5549104 GSM5549104: liver ctrl overfeed 5; Danio rerio; RNA Seq GSM5549104   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549104 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L8B_1.fq.gz L8B_2.fq.gz fastq fastq 4815366200.0 48153662.0 GSM5549104 r1 0:100 1:100 A:1274920749;C:1122213902;G:1140211257;T:1278020292;N:0 100 100     1274920749 1122213902 1140211257 1278020292 0 SRX11964776 SRS9973844 SRA1285419 GEO ZMF, University Heidelberg 1 0.95864   0.02123   0.88805   0.13863   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65901 65901 SRR15667949 SRX11964775 SRS9973843 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl overfeed 4 GSM5549103   source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL liver ctrl overfeed 4 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL GSM5549103 GSM5549103: liver ctrl overfeed 4; Danio rerio; RNA Seq GSM5549103   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549103 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L7B_1.fq.gz L7B_2.fq.gz fastq fastq 4806451200.0 48064512.0 GSM5549103 r1 0:100 1:100 A:1272428504;C:1119437887;G:1139899400;T:1274685409;N:0 100 100     1272428504 1119437887 1139899400 1274685409 0 SRX11964775 SRS9973843 SRA1285419 GEO ZMF, University Heidelberg 1 0.9605   0.02337   0.87625   0.17173   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65902 65902 SRR15667948 SRX11964774 SRS9973842 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl overfeed 3 GSM5549102   source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL liver ctrl overfeed 3 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL GSM5549102 GSM5549102: liver ctrl overfeed 3; Danio rerio; RNA Seq GSM5549102   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549102 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L12B_1.fq.gz L12B_2.fq.gz fastq fastq 4808986200.0 48089862.0 GSM5549102 r1 0:100 1:100 A:1282711930;C:1106482446;G:1126540026;T:1293251798;N:0 100 100     1282711930 1106482446 1126540026 1293251798 0 SRX11964774 SRS9973842 SRA1285419 GEO ZMF, University Heidelberg 1 0.95163   0.05783   0.80872   0.56282   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65903 65903 SRR15667947 SRX11964773 SRS9973841 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl overfeed 2 GSM5549101   source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL liver ctrl overfeed 2 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL GSM5549101 GSM5549101: liver ctrl overfeed 2; Danio rerio; RNA Seq GSM5549101   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549101 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L11B_1.fq.gz L11B_2.fq.gz fastq fastq 4813626000.0 48136260.0 GSM5549101 r1 0:100 1:100 A:1280868095;C:1108012462;G:1126540954;T:1298204489;N:0 100 100     1280868095 1108012462 1126540954 1298204489 0 SRX11964773 SRS9973841 SRA1285419 GEO ZMF, University Heidelberg 1 0.94831   0.05349   0.81513   0.57243   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65904 65904 SRR15667946 SRX11964772 SRS9973840 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl overfeed 1 GSM5549100   source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL liver ctrl overfeed 1 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL GSM5549100 GSM5549100: liver ctrl overfeed 1; Danio rerio; RNA Seq GSM5549100   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549100 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L10B_1.fq.gz L10B_2.fq.gz fastq fastq 4810219200.0 48102192.0 GSM5549100 r1 0:100 1:100 A:1291986049;C:1097301072;G:1114733041;T:1306199038;N:0 100 100     1291986049 1097301072 1114733041 1306199038 0 SRX11964772 SRS9973840 SRA1285419 GEO ZMF, University Heidelberg 1 0.9477   0.06719   0.80762   0.56967   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65905 65905 SRR15667945 SRX11964771 SRS9973839 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl ctrl 6 GSM5549099   source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL liver ctrl ctrl 6 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL GSM5549099 GSM5549099: liver ctrl ctrl 6; Danio rerio; RNA Seq GSM5549099   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549099 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L6B_1.fq.gz L6B_2.fq.gz fastq fastq 4800718000.0 48007180.0 GSM5549099 r1 0:100 1:100 A:1258342638;C:1122320482;G:1144931913;T:1275122967;N:0 100 100     1258342638 1122320482 1144931913 1275122967 0 SRX11964771 SRS9973839 SRA1285419 GEO ZMF, University Heidelberg 1 0.953   0.05324   0.81257   0.58562   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65906 65906 SRR15667944 SRX11964770 SRS9973838 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl ctrl 5 GSM5549098   source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL liver ctrl ctrl 5 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL GSM5549098 GSM5549098: liver ctrl ctrl 5; Danio rerio; RNA Seq GSM5549098   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549098 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L5B_1.fq.gz L5B_2.fq.gz fastq fastq 4806088800.0 48060888.0 GSM5549098 r1 0:100 1:100 A:1271888694;C:1114093824;G:1133421540;T:1286684742;N:0 100 100     1271888694 1114093824 1133421540 1286684742 0 SRX11964770 SRS9973838 SRA1285419 GEO ZMF, University Heidelberg 1 0.95001   0.05792   0.807   0.56126   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65907 65907 SRR15667943 SRX11964769 SRS9973837 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl ctrl 4 GSM5549097   source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL liver ctrl ctrl 4 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL GSM5549097 GSM5549097: liver ctrl ctrl 4; Danio rerio; RNA Seq GSM5549097   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549097 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L4B_1.fq.gz L4B_2.fq.gz fastq fastq 4793658200.0 47936582.0 GSM5549097 r1 0:100 1:100 A:1278328591;C:1101882376;G:1120230481;T:1293216752;N:0 100 100     1278328591 1101882376 1120230481 1293216752 0 SRX11964769 SRS9973837 SRA1285419 GEO ZMF, University Heidelberg 1 0.94635   0.06821   0.77814   0.57203   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65908 65908 SRR15667942 SRX11964768 SRS9973836 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl ctrl 3 GSM5549096   source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL liver ctrl ctrl 3 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL GSM5549096 GSM5549096: liver ctrl ctrl 3; Danio rerio; RNA Seq GSM5549096   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549096 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L3B_1.fq.gz L3B_2.fq.gz fastq fastq 4826663000.0 48266630.0 GSM5549096 r1 0:100 1:100 A:1279595092;C:1123953174;G:1141367365;T:1281747369;N:0 100 100     1279595092 1123953174 1141367365 1281747369 0 SRX11964768 SRS9973836 SRA1285419 GEO ZMF, University Heidelberg 1 0.9594   0.02127   0.88463   0.12493   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65909 65909 SRR15667941 SRX11964767 SRS9973835 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl ctrl 2 GSM5549095   source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL liver ctrl ctrl 2 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL GSM5549095 GSM5549095: liver ctrl ctrl 2; Danio rerio; RNA Seq GSM5549095   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549095 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L2B_1.fq.gz L2B_2.fq.gz fastq fastq 4825604600.0 48256046.0 GSM5549095 r1 0:100 1:100 A:1280321186;C:1120511740;G:1138899889;T:1285871785;N:0 100 100     1280321186 1120511740 1138899889 1285871785 0 SRX11964767 SRS9973835 SRA1285419 GEO ZMF, University Heidelberg 1 0.95896   0.0192   0.88899   0.11515   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
65910 65910 SRR15667940 SRX11964766 SRS9973834 SRP334698 PRJNA758884 Metabolic and transcriptional adaptations improve physical performance of zebrafish GSE183023 Transcriptome Analysis Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2 and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately the effects of training and overfeeding on blood glucose muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain including 6 control fish 6 overfed fish 6 trained fish 6 trained and overfed fish   pubmed:34679716   liver ctrl ctrl 1 GSM5549094   source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL liver ctrl ctrl 1 trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. liver Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total. Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols Zebrafish of the ABTL strain were reared and maintained at 28 °C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank. tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL GSM5549094 GSM5549094: liver ctrl ctrl 1; Danio rerio; RNA Seq GSM5549094   1 Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy® Mini Kit from QIAGEN Hilden Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols GEO Accession:GSM5549094 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED BGISEQ BGISEQ-500   SRP334698     L1B_1.fq.gz L1B_2.fq.gz fastq fastq 4829756800.0 48297568.0 GSM5549094 r1 0:100 1:100 A:1282017434;C:1119791375;G:1138880812;T:1289067179;N:0 100 100     1282017434 1119791375 1138880812 1289067179 0 SRX11964766 SRS9973834 SRA1285419 GEO ZMF, University Heidelberg 1 0.95838   0.03146   0.8479   0.28451   100   B   usable mapping rate bgi bgi unknown cdna_unspecified unknown bulk unknown unknown   Germany 2021-08-30 Juvenile Juvenile Liver Liver and Biliary System
71670 71670 SRR21930613 SRX17915137 SRS15430839 SRP403013 PRJNA891244 Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model GSE215899 Transcriptome Analysis Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin and their non transgenic siblings.   pubmed:36768797   Aminus6 GSM6645224   source name:Liver|tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf Aminus6 The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92 curated to remove contigs unknown and alternate chromsomes using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: ‘ align star paired all’ and used the combined fasta file and gtf file as input for the ‘ fastaRef’ and ‘ gtfFile’ parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests Z+ was tested against the 3 other groups as well as p > 0.05 between the A and Z groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample Liver   Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols. Zebrafish were maintained at 28°C on a 14 h light/10 h dark cycle tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf GSM6645224 GSM6645224: Aminus6; Danio rerio; RNA Seq GSM6645224 r1 GSM6645224 1 Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP403013     Aminus6_S24_R1_001.fastq.gz Aminus6_S24_R2_001.fastq.gz fastq fastq 6999317053.0 46500434.0 GSM6645224 r1 0:75.15 1:75.37 A:1800440367;C:1667972609;G:1696169122;T:1822834920;N:11900035 75 75     1800440367 1667972609 1696169122 1822834920 11900035 SRX17915137 SRS15430839 SRA1521803 Monash Bioinformatics Platform, Monash Bioinformatics Platform Monash Bioinformatics Platform, Monash Bioinformatics Platform 2 0.97713 0.97834 0.05347 0.05209 0.77285 0.77516 0.5586 0.56518 76 76 B B biological fallback assumption illumina nextseq unknown poly_a trueseq bulk unknown unknown   Australia 2022-10-17 Juvenile Juvenile Liver Liver and Biliary System
71671 71671 SRR21930614 SRX17915136 SRS15430838 SRP403013 PRJNA891244 Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model GSE215899 Transcriptome Analysis Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin and their non transgenic siblings.   pubmed:36768797   Aminus5 GSM6645223   source name:Liver|tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf Aminus5 The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92 curated to remove contigs unknown and alternate chromsomes using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: ‘ align star paired all’ and used the combined fasta file and gtf file as input for the ‘ fastaRef’ and ‘ gtfFile’ parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests Z+ was tested against the 3 other groups as well as p > 0.05 between the A and Z groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample Liver   Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols. Zebrafish were maintained at 28°C on a 14 h light/10 h dark cycle tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf GSM6645223 GSM6645223: Aminus5; Danio rerio; RNA Seq GSM6645223 r1 GSM6645223 1 Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP403013     Aminus5_S23_R1_001.fastq.gz Aminus5_S23_R2_001.fastq.gz fastq fastq 6882375184.0 45764657.0 GSM6645223 r1 0:75.05 1:75.33 A:1748753730;C:1653160606;G:1699833991;T:1766084534;N:14542323 75 75     1748753730 1653160606 1699833991 1766084534 14542323 SRX17915136 SRS15430838 SRA1521803 Monash Bioinformatics Platform, Monash Bioinformatics Platform Monash Bioinformatics Platform, Monash Bioinformatics Platform 2 0.97955 0.9807 0.04149 0.04021 0.81251 0.81499 0.56267 0.56974 76 76 B B biological fallback assumption illumina nextseq unknown poly_a trueseq bulk unknown unknown   Australia 2022-10-17 Juvenile Juvenile Liver Liver and Biliary System
71672 71672 SRR21930615 SRX17915135 SRS15430837 SRP403013 PRJNA891244 Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model GSE215899 Transcriptome Analysis Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin and their non transgenic siblings.   pubmed:36768797   Aminus4 GSM6645222   source name:Liver|tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf Aminus4 The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92 curated to remove contigs unknown and alternate chromsomes using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: ‘ align star paired all’ and used the combined fasta file and gtf file as input for the ‘ fastaRef’ and ‘ gtfFile’ parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests Z+ was tested against the 3 other groups as well as p > 0.05 between the A and Z groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample Liver   Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols. Zebrafish were maintained at 28°C on a 14 h light/10 h dark cycle tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf GSM6645222 GSM6645222: Aminus4; Danio rerio; RNA Seq GSM6645222 r1 GSM6645222 1 Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP403013     Aminus4_S22_R1_001.fastq.gz Aminus4_S22_R2_001.fastq.gz fastq fastq 6224741592.0 41292003.0 GSM6645222 r1 0:75.33 1:75.42 A:1571265090;C:1516463036;G:1536688036;T:1593637495;N:6687935 75 75     1571265090 1516463036 1536688036 1593637495 6687935 SRX17915135 SRS15430837 SRA1521803 Monash Bioinformatics Platform, Monash Bioinformatics Platform Monash Bioinformatics Platform, Monash Bioinformatics Platform 2 0.97898 0.98108 0.03911 0.03771 0.81653 0.81947 0.56503 0.50775 76 76 B B biological fallback assumption illumina nextseq unknown poly_a trueseq bulk unknown unknown   Australia 2022-10-17 Juvenile Juvenile Liver Liver and Biliary System
71673 71673 SRR21930616 SRX17915134 SRS15430836 SRP403013 PRJNA891244 Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model GSE215899 Transcriptome Analysis Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin and their non transgenic siblings.   pubmed:36768797   Aminus3 GSM6645221   source name:Liver|tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf Aminus3 The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92 curated to remove contigs unknown and alternate chromsomes using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: ‘ align star paired all’ and used the combined fasta file and gtf file as input for the ‘ fastaRef’ and ‘ gtfFile’ parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests Z+ was tested against the 3 other groups as well as p > 0.05 between the A and Z groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample Liver   Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols. Zebrafish were maintained at 28°C on a 14 h light/10 h dark cycle tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf GSM6645221 GSM6645221: Aminus3; Danio rerio; RNA Seq GSM6645221 r1 GSM6645221 1 Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP403013     Aminus3_S21_R1_001.fastq.gz Aminus3_S21_R2_001.fastq.gz fastq fastq 6894036879.0 45787003.0 GSM6645221 r1 0:75.18 1:75.39 A:1733625309;C:1688222190;G:1692381570;T:1767645633;N:12162177 75 75     1733625309 1688222190 1692381570 1767645633 12162177 SRX17915134 SRS15430836 SRA1521803 Monash Bioinformatics Platform, Monash Bioinformatics Platform Monash Bioinformatics Platform, Monash Bioinformatics Platform 2 0.97919 0.98055 0.04869 0.04724 0.80647 0.80866 0.57236 0.55519 76 76 B B biological fallback assumption illumina nextseq unknown poly_a trueseq bulk unknown unknown   Australia 2022-10-17 Juvenile Juvenile Liver Liver and Biliary System
71674 71674 SRR21930617 SRX17915133 SRS15430835 SRP403013 PRJNA891244 Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model GSE215899 Transcriptome Analysis Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin and their non transgenic siblings.   pubmed:36768797   Aminus2 GSM6645220   source name:Liver|tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf Aminus2 The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92 curated to remove contigs unknown and alternate chromsomes using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: ‘ align star paired all’ and used the combined fasta file and gtf file as input for the ‘ fastaRef’ and ‘ gtfFile’ parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests Z+ was tested against the 3 other groups as well as p > 0.05 between the A and Z groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample Liver   Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols. Zebrafish were maintained at 28°C on a 14 h light/10 h dark cycle tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf GSM6645220 GSM6645220: Aminus2; Danio rerio; RNA Seq GSM6645220 r1 GSM6645220 1 Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP403013     Aminus2_S20_R1_001.fastq.gz Aminus2_S20_R2_001.fastq.gz fastq fastq 6328688976.0 42049798.0 GSM6645220 r1 0:75.16 1:75.34 A:1583871529;C:1558452442;G:1563731549;T:1612985194;N:9648262 75 75     1583871529 1558452442 1563731549 1612985194 9648262 SRX17915133 SRS15430835 SRA1521803 Monash Bioinformatics Platform, Monash Bioinformatics Platform Monash Bioinformatics Platform, Monash Bioinformatics Platform 2 0.98159 0.98224 0.04493 0.04338 0.80748 0.81117 0.54259 0.53675 76 75 B B biological fallback assumption illumina nextseq unknown poly_a trueseq bulk unknown unknown   Australia 2022-10-17 Juvenile Juvenile Liver Liver and Biliary System
71675 71675 SRR21930618 SRX17915132 SRS15430834 SRP403013 PRJNA891244 Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model GSE215899 Transcriptome Analysis Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin and their non transgenic siblings.   pubmed:36768797   Aminus1 GSM6645219   source name:Liver|tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf Aminus1 The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92 curated to remove contigs unknown and alternate chromsomes using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: ‘ align star paired all’ and used the combined fasta file and gtf file as input for the ‘ fastaRef’ and ‘ gtfFile’ parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests Z+ was tested against the 3 other groups as well as p > 0.05 between the A and Z groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample Liver   Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols. Zebrafish were maintained at 28°C on a 14 h light/10 h dark cycle tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf GSM6645219 GSM6645219: Aminus1; Danio rerio; RNA Seq GSM6645219 r1 GSM6645219 1 Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP403013     Aminus1_S19_R1_001.fastq.gz Aminus1_S19_R2_001.fastq.gz fastq fastq 7762770945.0 51727376.0 GSM6645219 r1 0:74.75 1:75.32 A:1894174587;C:1946921294;G:1972242071;T:1919829619;N:29603374 74 75     1894174587 1946921294 1972242071 1919829619 29603374 SRX17915132 SRS15430834 SRA1521803 Monash Bioinformatics Platform, Monash Bioinformatics Platform Monash Bioinformatics Platform, Monash Bioinformatics Platform 2 0.9826 0.98415 0.06315 0.0603 0.824 0.8257 0.56313 0.56424 73 76 B B biological fallback assumption illumina nextseq unknown poly_a trueseq bulk unknown unknown   Australia 2022-10-17 Juvenile Juvenile Liver Liver and Biliary System
71676 71676 SRR21930619 SRX17915131 SRS15430833 SRP403013 PRJNA891244 Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model GSE215899 Transcriptome Analysis Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin and their non transgenic siblings.   pubmed:36768797   Aplus6 GSM6645218   source name:Liver|tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf Aplus6 The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92 curated to remove contigs unknown and alternate chromsomes using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: ‘ align star paired all’ and used the combined fasta file and gtf file as input for the ‘ fastaRef’ and ‘ gtfFile’ parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests Z+ was tested against the 3 other groups as well as p > 0.05 between the A and Z groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample Liver   Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols. Zebrafish were maintained at 28°C on a 14 h light/10 h dark cycle tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf GSM6645218 GSM6645218: Aplus6; Danio rerio; RNA Seq GSM6645218 r1 GSM6645218 1 Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP403013     Aplus6_S18_R1_001.fastq.gz Aplus6_S18_R2_001.fastq.gz fastq fastq 6587924798.0 43792481.0 GSM6645218 r1 0:75.09 1:75.35 A:1653688853;C:1603968356;G:1644621250;T:1672657500;N:12988839 75 75     1653688853 1603968356 1644621250 1672657500 12988839 SRX17915131 SRS15430833 SRA1521803 Monash Bioinformatics Platform, Monash Bioinformatics Platform Monash Bioinformatics Platform, Monash Bioinformatics Platform 2 0.97388 0.97651 0.04971 0.04851 0.82057 0.82513 0.57851 0.58339 76 76 B B biological fallback assumption illumina nextseq unknown poly_a trueseq bulk unknown unknown   Australia 2022-10-17 Juvenile Juvenile Liver Liver and Biliary System
71677 71677 SRR21930620 SRX17915130 SRS15430832 SRP403013 PRJNA891244 Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model GSE215899 Transcriptome Analysis Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin and their non transgenic siblings.   pubmed:36768797   Aplus5 GSM6645217   source name:Liver|tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf Aplus5 The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92 curated to remove contigs unknown and alternate chromsomes using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: ‘ align star paired all’ and used the combined fasta file and gtf file as input for the ‘ fastaRef’ and ‘ gtfFile’ parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests Z+ was tested against the 3 other groups as well as p > 0.05 between the A and Z groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample Liver   Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols. Zebrafish were maintained at 28°C on a 14 h light/10 h dark cycle tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf GSM6645217 GSM6645217: Aplus5; Danio rerio; RNA Seq GSM6645217 r1 GSM6645217 1 Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP403013     Aplus5_S17_R1_001.fastq.gz Aplus5_S17_R2_001.fastq.gz fastq fastq 7309309046.0 48586335.0 GSM6645217 r1 0:75.09 1:75.35 A:1775647597;C:1845303690;G:1876798549;T:1796722054;N:14837156 75 75     1775647597 1845303690 1876798549 1796722054 14837156 SRX17915130 SRS15430832 SRA1521803 Monash Bioinformatics Platform, Monash Bioinformatics Platform Monash Bioinformatics Platform, Monash Bioinformatics Platform 2 0.97946 0.98073 0.08026 0.07732 0.82298 0.8244 0.57059 0.57796 76 75 B B biological fallback assumption illumina nextseq unknown poly_a trueseq bulk unknown unknown   Australia 2022-10-17 Juvenile Juvenile Liver Liver and Biliary System
71678 71678 SRR21930621 SRX17915129 SRS15430831 SRP403013 PRJNA891244 Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model GSE215899 Transcriptome Analysis Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin and their non transgenic siblings.   pubmed:36768797   Aplus4 GSM6645216   source name:Liver|tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf Aplus4 The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92 curated to remove contigs unknown and alternate chromsomes using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: ‘ align star paired all’ and used the combined fasta file and gtf file as input for the ‘ fastaRef’ and ‘ gtfFile’ parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests Z+ was tested against the 3 other groups as well as p > 0.05 between the A and Z groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample Liver   Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols. Zebrafish were maintained at 28°C on a 14 h light/10 h dark cycle tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf GSM6645216 GSM6645216: Aplus4; Danio rerio; RNA Seq GSM6645216 r1 GSM6645216 1 Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP403013     Aplus4_S16_R1_001.fastq.gz Aplus4_S16_R2_001.fastq.gz fastq fastq 6589984047.0 44071744.0 GSM6645216 r1 0:74.26 1:75.27 A:1660708324;C:1563178084;G:1662308339;T:1661946771;N:41842529 74 75     1660708324 1563178084 1662308339 1661946771 41842529 SRX17915129 SRS15430831 SRA1521803 Monash Bioinformatics Platform, Monash Bioinformatics Platform Monash Bioinformatics Platform, Monash Bioinformatics Platform 2 0.97415 0.97416 0.04422 0.04323 0.81639 0.82075 0.5854 0.58865 75 75 B B biological fallback assumption illumina nextseq unknown poly_a trueseq bulk unknown unknown   Australia 2022-10-17 Juvenile Juvenile Liver Liver and Biliary System
71679 71679 SRR21930622 SRX17915128 SRS15430830 SRP403013 PRJNA891244 Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model GSE215899 Transcriptome Analysis Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin and their non transgenic siblings.   pubmed:36768797   Aplus3 GSM6645215   source name:Liver|tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf Aplus3 The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92 curated to remove contigs unknown and alternate chromsomes using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: ‘ align star paired all’ and used the combined fasta file and gtf file as input for the ‘ fastaRef’ and ‘ gtfFile’ parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests Z+ was tested against the 3 other groups as well as p > 0.05 between the A and Z groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample Liver   Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols. Zebrafish were maintained at 28°C on a 14 h light/10 h dark cycle tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf GSM6645215 GSM6645215: Aplus3; Danio rerio; RNA Seq GSM6645215 r1 GSM6645215 1 Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP403013     Aplus3_S15_R1_001.fastq.gz Aplus3_S15_R2_001.fastq.gz fastq fastq 6881303008.0 45881629.0 GSM6645215 r1 0:74.67 1:75.31 A:1705776092;C:1687176683;G:1744678234;T:1714771420;N:28900579 74 75     1705776092 1687176683 1744678234 1714771420 28900579 SRX17915128 SRS15430830 SRA1521803 Monash Bioinformatics Platform, Monash Bioinformatics Platform Monash Bioinformatics Platform, Monash Bioinformatics Platform 2 0.97636 0.97803 0.04693 0.04579 0.82106 0.82313 0.57573 0.57226 74 76 B B biological fallback assumption illumina nextseq unknown poly_a trueseq bulk unknown unknown   Australia 2022-10-17 Juvenile Juvenile Liver Liver and Biliary System
71680 71680 SRR21930623 SRX17915127 SRS15430829 SRP403013 PRJNA891244 Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model GSE215899 Transcriptome Analysis Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin and their non transgenic siblings.   pubmed:36768797   Aplus2 GSM6645214   source name:Liver|tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf Aplus2 The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92 curated to remove contigs unknown and alternate chromsomes using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: ‘ align star paired all’ and used the combined fasta file and gtf file as input for the ‘ fastaRef’ and ‘ gtfFile’ parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests Z+ was tested against the 3 other groups as well as p > 0.05 between the A and Z groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample Liver   Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols. Zebrafish were maintained at 28°C on a 14 h light/10 h dark cycle tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf GSM6645214 GSM6645214: Aplus2; Danio rerio; RNA Seq GSM6645214 r1 GSM6645214 1 Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP403013     Aplus2_S14_R1_001.fastq.gz Aplus2_S14_R2_001.fastq.gz fastq fastq 6485624173.0 43138712.0 GSM6645214 r1 0:75.02 1:75.32 A:1640295930;C:1579957383;G:1589952337;T:1661697493;N:13721030 75 75     1640295930 1579957383 1589952337 1661697493 13721030 SRX17915127 SRS15430829 SRA1521803 Monash Bioinformatics Platform, Monash Bioinformatics Platform Monash Bioinformatics Platform, Monash Bioinformatics Platform 2 0.97327 0.97467 0.03267 0.03179 0.74434 0.74675 0.49993 0.51727 76 76 B B biological fallback assumption illumina nextseq unknown poly_a trueseq bulk unknown unknown   Australia 2022-10-17 Juvenile Juvenile Liver Liver and Biliary System
71681 71681 SRR21930624 SRX17915126 SRS15430828 SRP403013 PRJNA891244 Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model GSE215899 Transcriptome Analysis Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin and their non transgenic siblings.   pubmed:36768797   Aplus1 GSM6645213   source name:Liver|tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf Aplus1 The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92 curated to remove contigs unknown and alternate chromsomes using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: ‘ align star paired all’ and used the combined fasta file and gtf file as input for the ‘ fastaRef’ and ‘ gtfFile’ parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests Z+ was tested against the 3 other groups as well as p > 0.05 between the A and Z groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample Liver   Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols. Zebrafish were maintained at 28°C on a 14 h light/10 h dark cycle tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf GSM6645213 GSM6645213: Aplus1; Danio rerio; RNA Seq GSM6645213 r1 GSM6645213 1 Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP403013     Aplus1_S13_R1_001.fastq.gz Aplus1_S13_R2_001.fastq.gz fastq fastq 6817630277.0 45605717.0 GSM6645213 r1 0:74.17 1:75.32 A:1674389239;C:1667008346;G:1749740407;T:1678172490;N:48319795 74 75     1674389239 1667008346 1749740407 1678172490 48319795 SRX17915126 SRS15430828 SRA1521803 Monash Bioinformatics Platform, Monash Bioinformatics Platform Monash Bioinformatics Platform, Monash Bioinformatics Platform 2 0.97585 0.97763 0.04067 0.03939 0.79943 0.80235 0.54802 0.55959 74 76 B B biological fallback assumption illumina nextseq unknown poly_a trueseq bulk unknown unknown   Australia 2022-10-17 Juvenile Juvenile Liver Liver and Biliary System
71682 71682 SRR21930625 SRX17915125 SRS15430827 SRP403013 PRJNA891244 Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model GSE215899 Transcriptome Analysis Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin and their non transgenic siblings.   pubmed:36768797   Zminus6 GSM6645212   source name:Liver|tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf Zminus6 The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92 curated to remove contigs unknown and alternate chromsomes using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: ‘ align star paired all’ and used the combined fasta file and gtf file as input for the ‘ fastaRef’ and ‘ gtfFile’ parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests Z+ was tested against the 3 other groups as well as p > 0.05 between the A and Z groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample Liver   Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols. Zebrafish were maintained at 28°C on a 14 h light/10 h dark cycle tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf GSM6645212 GSM6645212: Zminus6; Danio rerio; RNA Seq GSM6645212 r1 GSM6645212 1 Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP403013     Zminus6_S12_R1_001.fastq.gz Zminus6_S12_R2_001.fastq.gz fastq fastq 7741229236.0 51641892.0 GSM6645212 r1 0:74.56 1:75.34 A:1947072330;C:1874720729;G:1913091115;T:1968158284;N:38186778 74 75     1947072330 1874720729 1913091115 1968158284 38186778 SRX17915125 SRS15430827 SRA1521803 Monash Bioinformatics Platform, Monash Bioinformatics Platform Monash Bioinformatics Platform, Monash Bioinformatics Platform 2 0.98122 0.98292 0.04442 0.04278 0.80436 0.80655 0.56155 0.58034 76 75 B B biological fallback assumption illumina nextseq unknown poly_a trueseq bulk unknown unknown   Australia 2022-10-17 Juvenile Juvenile Liver Liver and Biliary System
71683 71683 SRR21930626 SRX17915124 SRS15430826 SRP403013 PRJNA891244 Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model GSE215899 Transcriptome Analysis Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin and their non transgenic siblings.   pubmed:36768797   Zminus5 GSM6645211   source name:Liver|tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf Zminus5 The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92 curated to remove contigs unknown and alternate chromsomes using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: ‘ align star paired all’ and used the combined fasta file and gtf file as input for the ‘ fastaRef’ and ‘ gtfFile’ parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests Z+ was tested against the 3 other groups as well as p > 0.05 between the A and Z groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample Liver   Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols. Zebrafish were maintained at 28°C on a 14 h light/10 h dark cycle tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf GSM6645211 GSM6645211: Zminus5; Danio rerio; RNA Seq GSM6645211 r1 GSM6645211 1 Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP403013     Zminus5_S11_R1_001.fastq.gz Zminus5_S11_R2_001.fastq.gz fastq fastq 7001244905.0 46579742.0 GSM6645211 r1 0:74.99 1:75.32 A:1764508171;C:1705392619;G:1719391191;T:1794863129;N:17089795 74 75     1764508171 1705392619 1719391191 1794863129 17089795 SRX17915124 SRS15430826 SRA1521803 Monash Bioinformatics Platform, Monash Bioinformatics Platform Monash Bioinformatics Platform, Monash Bioinformatics Platform 2 0.97841 0.97975 0.04435 0.04344 0.80523 0.80704 0.56559 0.55911 76 76 B B biological fallback assumption illumina nextseq unknown poly_a trueseq bulk unknown unknown   Australia 2022-10-17 Juvenile Juvenile Liver Liver and Biliary System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;