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 28496,SRR26321412,SRX22029502,SRS19102283,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 1,R27,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R27,R27,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R27.fastq,fastq,23400.0,312.0,R27.fastq,0:75,A:7949;C:4612;G:4730;T:6100;N:9,75,,,,7949,4612,4730,6100,9,SRX22029502,SRS19102283,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.89642,,0.06772,,0.99827,,0.75,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28497,SRR26321413,SRX22029501,SRS19102284,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,1dpci 4,R22,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R22,R22,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R22.fastq,fastq,23400.0,312.0,R22.fastq,0:75,A:7470;C:4460;G:5063;T:6404;N:3,75,,,,7470,4460,5063,6404,3,SRX22029501,SRS19102284,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87073,,0.12167,,0.99801,,0.73157,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28498,SRR26321414,SRX22029500,SRS19102281,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,R21,R21,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R21,R21,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R21.fastq,fastq,23400.0,312.0,R21.fastq,0:75,A:7540;C:4349;G:4857;T:6646;N:8,75,,,,7540,4349,4857,6646,8,SRX22029500,SRS19102281,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.8839,,0.04494,,0.99768,,0.72769,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28499,SRR26321415,SRX22029499,SRS19102282,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,1dpci 2,R18,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R18,R18,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R18.fastq,fastq,23400.0,312.0,R18.fastq,0:75,A:7380;C:4430;G:5069;T:6518;N:3,75,,,,7380,4430,5069,6518,3,SRX22029499,SRS19102282,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87259,,0.11196,,0.99784,,0.69791,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28500,SRR26321416,SRX22029498,SRS19102280,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,1dpci 1,R17,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R17,R17,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R17.fastq,fastq,23400.0,312.0,R17.fastq,0:75,A:7322;C:4455;G:5111;T:6507;N:5,75,,,,7322,4455,5111,6507,5,SRX22029498,SRS19102280,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.90439,,0.12749,,0.99813,,0.71052,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28501,SRR26321417,SRX22029497,SRS19102279,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 5,R1,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R1,R1,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R1.fastq,fastq,23400.0,312.0,R1.fastq,0:75,A:7934;C:4560;G:4922;T:5980;N:4,75,,,,7934,4560,4922,5980,4,SRX22029497,SRS19102279,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87045,,0.10526,,0.99805,,0.71978,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28502,SRR26321418,SRX22029496,SRS19102277,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 4,R64,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R64,R64,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R64.fastq,fastq,23400.0,312.0,R64.fastq,0:75,A:7844;C:4626;G:4804;T:6126;N:0,75,,,,7844,4626,4804,6126,0,SRX22029496,SRS19102277,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.90119,,0.07509,,0.99839,,0.8,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28503,SRR26321419,SRX22029495,SRS19102278,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 3,R61,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R61,R61,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R61.fastq,fastq,23400.0,312.0,R61.fastq,0:75,A:7454;C:4556;G:4960;T:6425;N:5,75,,,,7454,4556,4960,6425,5,SRX22029495,SRS19102278,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.89098,,0.06015,,0.99813,,0.77102,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28504,SRR26321420,SRX22029494,SRS19102276,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,7dpci 4,30,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,30,30,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,30.fastq,fastq,23400.0,312.0,30.fastq,0:75,A:7732;C:4528;G:5150;T:5987;N:3,75,,,,7732,4528,5150,5987,3,SRX22029494,SRS19102276,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.88447,,0.13147,,0.99772,,0.71584,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28505,SRR26321421,SRX22029493,SRS19102275,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,R11,R11,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,R11,R11,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R11.fastq,fastq,23400.0,312.0,R11.fastq,0:75,A:7818;C:4507;G:5107;T:5956;N:12,75,,,,7818,4507,5107,5956,12,SRX22029493,SRS19102275,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.89345,,0.11475,,0.99847,,0.82258,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28506,SRR26321422,SRX22029492,SRS19102274,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,7dpci 2,31,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,31,31,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,31.fastq,fastq,23400.0,312.0,31.fastq,0:75,A:7470;C:4619;G:4802;T:6504;N:5,75,,,,7470,4619,4802,6504,5,SRX22029492,SRS19102274,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87699,,0.11111,,0.99829,,0.78918,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28507,SRR26321423,SRX22029491,SRS19102273,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,7dpci 1,R9,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,R9,R9,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R9.fastq,fastq,23400.0,312.0,R9.fastq,0:75,A:8130;C:4537;G:4809;T:5917;N:7,75,,,,8130,4537,4809,5917,7,SRX22029491,SRS19102273,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.83588,,0.05725,,0.99801,,0.68586,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28508,SRR26321424,SRX22029490,SRS19102272,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 4,R33,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R33,R33,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R33.fastq,fastq,23400.0,312.0,R33.fastq,0:75,A:7745;C:4421;G:4867;T:6360;N:7,75,,,,7745,4421,4867,6360,7,SRX22029490,SRS19102272,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87259,,0.07335,,0.99805,,0.71428,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28509,SRR26321425,SRX22029489,SRS19102271,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 3,R31,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R31,R31,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R31.fastq,fastq,23400.0,312.0,R31.fastq,0:75,A:7441;C:4483;G:5163;T:6313;N:0,75,,,,7441,4483,5163,6313,0,SRX22029489,SRS19102271,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.9,,0.05925,,0.9977,,0.68325,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28510,SRR26321426,SRX22029488,SRS19102270,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 2,R29,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R29,R29,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R29.fastq,fastq,23400.0,312.0,R29.fastq,0:75,A:7379;C:4698;G:5166;T:6156;N:1,75,,,,7379,4698,5166,6156,1,SRX22029488,SRS19102270,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.91016,,0.05859,,0.99797,,0.74528,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28511,SRR26321427,SRX22029487,SRS19102269,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 2,R62,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R62,R62,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R62.fastq,fastq,23400.0,312.0,R62.fastq,0:75,A:7383;C:4566;G:4713;T:6728;N:10,75,,,,7383,4566,4713,6728,10,SRX22029487,SRS19102269,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.91571,,0.05363,,0.99835,,0.77674,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 28512,SRR26321428,SRX22029486,SRS19102268,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,Replicate 1 for SHAM,SHAM 1,R63,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia: Melbourne|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R63,R63,ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R63.fastq,fastq,23400.0,312.0,R63.fastq,0:75,A:7516;C:4606;G:4765;T:6508;N:5,75,,,,7516,4606,4765,6508,5,SRX22029486,SRS19102268,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.90385,,0.0423,,0.99805,,0.72429,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System 35941,SRR33299145,SRX28544240,SRS24843420,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,WT4 ppat liver,,strain:ppat|isolate:RNA wt4|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA wt4,RNA wt4,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,WT4_ppat-liver_S28_R1_001.fastq.gz WT4_ppat-liver_S28_R2_001.fastq.gz,fastq fastq,12054556418.0,60504917.0,WT4 ppat liver S28 R1 001.fastq.gz,0:99.62 1:99.61,A:3156096964;C:2870076825;G:2908548000;T:3118003046;N:1831583,99,99,,,3156096964,2870076825,2908548000,3118003046,1831583,SRX28544240,SRS24843420,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Adult,Adult,Liver,Liver and Biliary System 35942,SRR33299146,SRX28544239,SRS24843419,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,WT3 ppat liver,,strain:ppat|isolate:RNA wt3|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA wt3,RNA wt3,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,WT3_ppat-liver_S27_R1_001.fastq.gz WT3_ppat-liver_S27_R2_001.fastq.gz,fastq fastq,13917840876.0,69735355.0,WT3 ppat liver S27 R1 001.fastq.gz,0:99.76 1:99.82,A:3668835621;C:3297107084;G:3353446119;T:3593656283;N:4795769,99,99,,,3668835621,3297107084,3353446119,3593656283,4795769,SRX28544239,SRS24843419,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Adult,Adult,Liver,Liver and Biliary System 35943,SRR33299147,SRX28544238,SRS24843418,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,WT2 ppat liver,,strain:ppat|isolate:RNA wt2|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA wt2,RNA wt2,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,WT2_ppat-liver_S26_R1_001.fastq.gz WT2_ppat-liver_S26_R2_001.fastq.gz,fastq fastq,13414385259.0,67138074.0,WT2 ppat liver S26 R1 001.fastq.gz,0:99.79 1:100.01,A:3544883230;C:3160905311;G:3259087045;T:3439671703;N:9837970,99,100,,,3544883230,3160905311,3259087045,3439671703,9837970,SRX28544238,SRS24843418,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Adult,Adult,Liver,Liver and Biliary System 35944,SRR33299148,SRX28544237,SRS24843417,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,WT1 ppat liver,,strain:ppat|isolate:RNA wt1|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA wt1,RNA wt1,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,WT1_ppat-liver_S25_R1_001.fastq.gz WT1_ppat-liver_S25_R2_001.fastq.gz,fastq fastq,10922184332.0,54765335.0,WT1 ppat liver S25 R1 001.fastq.gz,0:99.61 1:99.82,A:2868583271;C:2597837660;G:2681619273;T:2767298124;N:6846004,99,99,,,2868583271,2597837660,2681619273,2767298124,6846004,SRX28544237,SRS24843417,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Adult,Adult,Liver,Liver and Biliary System 35945,SRR33299149,SRX28544236,SRS24843416,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,Mut4 ppat liver,,strain:ppat|isolate:RNA mut4|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA mut4,RNA mut4,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,Mut4_ppat-liver_S36_R1_001.fastq.gz Mut4_ppat-liver_S36_R2_001.fastq.gz,fastq fastq,12530931476.0,62826169.0,Mut4 ppat liver S36 R1 001.fastq.gz,0:99.67 1:99.78,A:3324393503;C:2939109258;G:3014385499;T:3247670290;N:5372926,99,99,,,3324393503,2939109258,3014385499,3247670290,5372926,SRX28544236,SRS24843416,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Adult,Adult,Liver,Liver and Biliary System 35946,SRR33299150,SRX28544235,SRS24843415,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,Mut3 ppat liver,,strain:ppat|isolate:RNA mut3|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA mut3,RNA mut3,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,Mut3_ppat-liver_S35_R1_001.fastq.gz Mut3_ppat-liver_S35_R2_001.fastq.gz,fastq fastq,10720402854.0,53894468.0,Mut3 ppat liver S35 R1 001.fastq.gz,0:99.40 1:99.52,A:2864014346;C:2503521968;G:2584948225;T:2763732849;N:4185466,99,99,,,2864014346,2503521968,2584948225,2763732849,4185466,SRX28544235,SRS24843415,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Adult,Adult,Liver,Liver and Biliary System 35947,SRR33299151,SRX28544234,SRS24843414,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,Mut2 ppat liver,,strain:ppat|isolate:RNA mut2|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA mut2,RNA mut2,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,Mut2_ppat-liver_S34_R1_001.fastq.gz Mut2_ppat-liver_S34_R2_001.fastq.gz,fastq fastq,13658984938.0,68656301.0,Mut2 ppat liver S34 R1 001.fastq.gz,0:99.35 1:99.59,A:3634178483;C:3189694846;G:3300982525;T:3525339026;N:8790058,99,99,,,3634178483,3189694846,3300982525,3525339026,8790058,SRX28544234,SRS24843414,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Adult,Adult,Liver,Liver and Biliary System 35948,SRR33299152,SRX28544233,SRS24843413,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,Mut1 ppat liver,,strain:ppat|isolate:RNA mut1|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA mut1,RNA mut1,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,Mut1_ppat-liver_S33_R1_001.fastq.gz Mut1_ppat-liver_S33_R2_001.fastq.gz,fastq fastq,10934728288.0,54995591.0,Mut1 ppat liver S33 R1 001.fastq.gz,0:99.36 1:99.47,A:2909267644;C:2564520996;G:2638675283;T:2818803981;N:3460384,99,99,,,2909267644,2564520996,2638675283,2818803981,3460384,SRX28544233,SRS24843413,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Adult,Adult,Liver,Liver and Biliary System 35949,SRR33299154,SRX28544231,SRS24843411,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,Het4 ppat liver,,strain:ppat|isolate:RNA het4|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA het4,RNA het4,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,Het4_ppat-liver_S32_R1_001.fastq.gz Het4_ppat-liver_S32_R2_001.fastq.gz,fastq fastq,11933665535.0,59956025.0,Het4 ppat liver S32 R1 001.fastq.gz,0:99.47 1:99.57,A:3167338389;C:2796677179;G:2888967002;T:3076290728;N:4392237,99,99,,,3167338389,2796677179,2888967002,3076290728,4392237,SRX28544231,SRS24843411,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Adult,Adult,Liver,Liver and Biliary System 35950,SRR33299155,SRX28544230,SRS24843410,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,Het3 ppat liver,,strain:ppat|isolate:RNA het3|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA het3,RNA het3,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,Het3_ppat-liver_S31_R1_001.fastq.gz Het3_ppat-liver_S31_R2_001.fastq.gz,fastq fastq,8736836848.0,43909775.0,Het3 ppat liver S31 R1 001.fastq.gz,0:99.49 1:99.48,A:2316148154;C:2054859781;G:2098968973;T:2265744694;N:1115246,99,99,,,2316148154,2054859781,2098968973,2265744694,1115246,SRX28544230,SRS24843410,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Adult,Adult,Liver,Liver and Biliary System 35951,SRR33299156,SRX28544229,SRS24843409,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,Het2 ppat liver,,strain:ppat|isolate:RNA het2|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA het2,RNA het2,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,Het2_ppat-liver_S30_R1_001.fastq.gz Het2_ppat-liver_S30_R2_001.fastq.gz,fastq fastq,7931230506.0,39763891.0,Het2 ppat liver S30 R1 001.fastq.gz,0:99.72 1:99.74,A:2118901869;C:1861115765;G:1903240420;T:2046832152;N:1140300,99,99,,,2118901869,1861115765,1903240420,2046832152,1140300,SRX28544229,SRS24843409,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Adult,Adult,Liver,Liver and Biliary System 35952,SRR33299157,SRX28544228,SRS24843408,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,Het1 ppat liver,,strain:ppat|isolate:RNA het1|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA het1,RNA het1,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,Het1_ppat-liver_S29_R1_001.fastq.gz Het1_ppat-liver_S29_R2_001.fastq.gz,fastq fastq,8695997521.0,43696765.0,Het1 ppat liver S29 R1 001.fastq.gz,0:99.39 1:99.62,A:2300583830;C:2047586482;G:2114382364;T:2227671389;N:5773456,99,99,,,2300583830,2047586482,2114382364,2227671389,5773456,SRX28544228,SRS24843408,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Adult,Adult,Liver,Liver and Biliary System 35953,SRR33299171,SRX28544214,SRS24843394,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,WT pos 3,,strain:ppat|isolate:RNA wt pos 3|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA wt pos 3,RNA wt pos 3,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,WT-pos-3_S10_R1_001.fastq.gz WT-pos-3_S10_R2_001.fastq.gz,fastq fastq,15038194818.0,74446509.0,WT pos 3 S10 R1 001.fastq.gz,0:101 1:101,A:4616878123;C:2865206674;G:2927449871;T:4628427327;N:232823,101,101,,,4616878123,2865206674,2927449871,4628427327,232823,SRX28544214,SRS24843394,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Larval,Larval,Liver,Liver and Biliary System 35954,SRR33299172,SRX28544213,SRS24843393,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,WT pos 2,,strain:ppat|isolate:RNA wt pos 2|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA wt pos 2,RNA wt pos 2,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,WT-pos-2_S6_R1_001.fastq.gz WT-pos-2_S6_R2_001.fastq.gz,fastq fastq,12522438742.0,61992271.0,WT pos 2 S6 R1 001.fastq.gz,0:101 1:101,A:3774656054;C:2451528285;G:2501043573;T:3795016419;N:194411,101,101,,,3774656054,2451528285,2501043573,3795016419,194411,SRX28544213,SRS24843393,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Larval,Larval,Liver,Liver and Biliary System 35955,SRR33299173,SRX28544212,SRS24843392,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,WT pos 1,,strain:ppat|isolate:RNA wt pos 1|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA wt pos 1,RNA wt pos 1,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,WT-pos-1_S2_R1_001.fastq.gz WT-pos-1_S2_R2_001.fastq.gz,fastq fastq,13192760794.0,65310697.0,WT pos 1 S2 R1 001.fastq.gz,0:101 1:101,A:4175600031;C:2392141464;G:2448567492;T:4176248719;N:203088,101,101,,,4175600031,2392141464,2448567492,4176248719,203088,SRX28544212,SRS24843392,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Larval,Larval,Liver,Liver and Biliary System 35956,SRR33299174,SRX28544211,SRS24843391,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,WT neg 3,,strain:ppat|isolate:RNA wt neg 3|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA wt neg 3,RNA wt neg 3,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,WT-neg-3_S9_R1_001.fastq.gz WT-neg-3_S9_R2_001.fastq.gz,fastq fastq,14228466708.0,70437954.0,WT neg 3 S9 R1 001.fastq.gz,0:101 1:101,A:4251988096;C:2825656049;G:2882063617;T:4268538044;N:220902,101,101,,,4251988096,2825656049,2882063617,4268538044,220902,SRX28544211,SRS24843391,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Larval,Larval,Liver,Liver and Biliary System 35957,SRR33299176,SRX28544209,SRS24843389,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,WT neg 2,,strain:ppat|isolate:RNA wt neg 2|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA wt neg 2,RNA wt neg 2,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,WT-neg-2_S5_R1_001.fastq.gz WT-neg-2_S5_R2_001.fastq.gz,fastq fastq,29197644388.0,144542794.0,WT neg 2 S5 R1 001.fastq.gz,0:101 1:101,A:8825536643;C:5697075068;G:5851684325;T:8822896313;N:452039,101,101,,,8825536643,5697075068,5851684325,8822896313,452039,SRX28544209,SRS24843389,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Larval,Larval,Liver,Liver and Biliary System 35958,SRR33299177,SRX28544208,SRS24843388,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,WT neg 1,,strain:ppat|isolate:RNA wt neg 1|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA wt neg 1,RNA wt neg 1,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,WT-neg-1_S1_R1_001.fastq.gz WT-neg-1_S1_R2_001.fastq.gz,fastq fastq,24310317816.0,120348108.0,WT neg 1 S1 R1 001.fastq.gz,0:101 1:101,A:7529245228;C:4579294064;G:4681930604;T:7519470895;N:377025,101,101,,,7529245228,4579294064,4681930604,7519470895,377025,SRX28544208,SRS24843388,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Larval,Larval,Liver,Liver and Biliary System 35959,SRR33299178,SRX28544207,SRS24843387,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,Mut pos 3,,strain:ppat|isolate:RNA mut pos 3|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA mut pos 3,RNA mut pos 3,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,Mutant-pos-3_S12_R1_001.fastq.gz Mutant-pos-3_S12_R2_001.fastq.gz,fastq fastq,12331802050.0,61048525.0,Mutant pos 3 S12 R1 001.fastq.gz,0:101 1:101,A:3738975619;C:2387112788;G:2450941491;T:3754579907;N:192245,101,101,,,3738975619,2387112788,2450941491,3754579907,192245,SRX28544207,SRS24843387,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Larval,Larval,Liver,Liver and Biliary System 35960,SRR33299179,SRX28544206,SRS24843386,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,Mut pos 2,,strain:ppat|isolate:RNA mut pos 2|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA mut pos 2,RNA mut pos 2,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,Mutant-pos-2_S8_R1_001.fastq.gz Mutant-pos-2_S8_R2_001.fastq.gz,fastq fastq,14310451034.0,70843817.0,Mutant pos 2 S8 R1 001.fastq.gz,0:101 1:101,A:4323214668;C:2795555578;G:2854780783;T:4336680703;N:219302,101,101,,,4323214668,2795555578,2854780783,4336680703,219302,SRX28544206,SRS24843386,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Larval,Larval,Liver,Liver and Biliary System 35961,SRR33299180,SRX28544205,SRS24843385,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,Mut pos 1,,strain:ppat|isolate:RNA mut pos 1|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA mut pos 1,RNA mut pos 1,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,Mutant-pos-1_S4_R1_001.fastq.gz Mutant-pos-1_S4_R2_001.fastq.gz,fastq fastq,11742623802.0,58131801.0,Mutant pos 1 S4 R1 001.fastq.gz,0:101 1:101,A:3631609351;C:2213363935;G:2258388450;T:3639080712;N:181354,101,101,,,3631609351,2213363935,2258388450,3639080712,181354,SRX28544205,SRS24843385,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Larval,Larval,Liver,Liver and Biliary System 35962,SRR33299181,SRX28544204,SRS24843384,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,Mut neg 3,,strain:ppat|isolate:RNA mut neg 3|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA mut neg 3,RNA mut neg 3,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,Mutant-neg-3_S11_R1_001.fastq.gz Mutant-neg-3_S11_R2_001.fastq.gz,fastq fastq,24089537270.0,119255135.0,Mutant neg 3 S11 R1 001.fastq.gz,0:101 1:101,A:7187277815;C:4790199860;G:4897671441;T:7214028116;N:360038,101,101,,,7187277815,4790199860,4897671441,7214028116,360038,SRX28544204,SRS24843384,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Larval,Larval,Liver,Liver and Biliary System 35963,SRR33299182,SRX28544203,SRS24843383,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,Mut neg 2,,strain:ppat|isolate:RNA mut neg 2|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA mut neg 2,RNA mut neg 2,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,Mutant-neg-2_S7_R1_001.fastq.gz Mutant-neg-2_S7_R2_001.fastq.gz,fastq fastq,27776865470.0,137509235.0,Mutant neg 2 S7 R1 001.fastq.gz,0:101 1:101,A:8522694394;C:5302545250;G:5464259742;T:8486935677;N:430407,101,101,,,8522694394,5302545250,5464259742,8486935677,430407,SRX28544203,SRS24843383,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Larval,Larval,Liver,Liver and Biliary System 35964,SRR33299183,SRX28544202,SRS24843382,SRP580984,PRJNA1255065,A Novel Transgenic Reporter to Study Vertebrate Epigenetics,PRJNA1255065,Other,Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.,,,,,Mut neg 1,,strain:ppat|isolate:RNA mut neg 1|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of EpiTag Danio Rerio,RNA mut neg 1,RNA mut neg 1,Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP580984,,,Mutant-neg-1_S3_R1_001.fastq.gz Mutant-neg-1_S3_R2_001.fastq.gz,fastq fastq,12942402802.0,64071301.0,Mutant neg 1 S3 R1 001.fastq.gz,0:101 1:101,A:3952970077;C:2483104981;G:2560604982;T:3945521897;N:200865,101,101,,,3952970077,2483104981,2560604982,3945521897,200865,SRX28544202,SRS24843382,SRA2117853,NIH|NICHD,NIH,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2025-04-24,Larval,Larval,Liver,Liver and Biliary System 40352,SRR3098582,SRX1528549,SRS1246175,SRP068364,PRJNA308582,Transcriptional profiling through RNA seq of zebrafish larval liver post exposure to biliatresone a biliary toxin.,GSE76780,Transcriptome Analysis,We sequenced liver mRNA isolated from biliatresone treated zebrafish larvae and DMSO treated controls in order to elucidate the molecular pathways induced by biliatresone a biliary toxin that is responsible for outbreaks of biliary atresia in Australian liverstock. Overall design: Liver mRNA profiles of biliatresone treated zebrafish larvae and DMSO treated controls were generated by deep sequencing in duplicates.,,pubmed:27102575,,Biliatres1 2,GSM2037741,,source name:liver|tissue:liver|treatment:Biliatres1,Biliatres1 2,Hiseq control software HCS was used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zv9 whole genome using STAR. Python Htseq script was used to count the number of reads. Genome build: zv9 Supplementary files format and content: tab delimited text files include htseq count output.,liver,Zebrafish larvae were treated with biliatresone 0.5 ug/ml for four hours.,Livers were dissected directly in to the lysis buffer RLT and RNA was harvested using the standard Qiagen protocol RNeasy Mini Kit. 1 ug of total RNA was used for sequecning library construction and the libraries were prepared using the Truseq Stranded Ribo Zero Library Prep Kit.,,tissue:liver|treatment:Biliatres1,GSM2037741,GSM2037741: Biliatres1 2; Danio rerio; RNA Seq,GSM2037741,,1,Livers were dissected directly in to the lysis buffer RLT and RNA was harvested using the standard Qiagen protocol RNeasy Mini Kit. 1 ug of total RNA was used for sequecning library construction and the libraries were prepared using the Truseq Stranded Ribo Zero Library Prep Kit.,GEO Accession:GSM2037741,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP068364,,,Toxin_2-Pack_1.fq.gz Toxin_2-Pack_2.fq.gz,fastq fastq,11821468800.0,59107344.0,GSM2037741 r1,0:100 1:100,A:2991132983;C:2918961261;G:2932581309;T:2978195946;N:597301,100,100,,,2991132983,2918961261,2932581309,2978195946,597301,SRX1528549,SRS1246175,SRA333195,GEO,"Michael Pack, Medicine/DIgestive Diseases, University of Pennsylvania",2,0.84122,0.83891,0.11156,0.10952,0.76073,0.76049,0.61886,0.62136,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United States,2016-01-12,Larval,Larval,Liver,Liver and Biliary System 40353,SRR3098581,SRX1528548,SRS1246176,SRP068364,PRJNA308582,Transcriptional profiling through RNA seq of zebrafish larval liver post exposure to biliatresone a biliary toxin.,GSE76780,Transcriptome Analysis,We sequenced liver mRNA isolated from biliatresone treated zebrafish larvae and DMSO treated controls in order to elucidate the molecular pathways induced by biliatresone a biliary toxin that is responsible for outbreaks of biliary atresia in Australian liverstock. Overall design: Liver mRNA profiles of biliatresone treated zebrafish larvae and DMSO treated controls were generated by deep sequencing in duplicates.,,pubmed:27102575,,Biliatres1 1,GSM2037740,,source name:liver|tissue:liver|treatment:Biliatres1,Biliatres1 1,Hiseq control software HCS was used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zv9 whole genome using STAR. Python Htseq script was used to count the number of reads. Genome build: zv9 Supplementary files format and content: tab delimited text files include htseq count output.,liver,Zebrafish larvae were treated with biliatresone 0.5 ug/ml for four hours.,Livers were dissected directly in to the lysis buffer RLT and RNA was harvested using the standard Qiagen protocol RNeasy Mini Kit. 1 ug of total RNA was used for sequecning library construction and the libraries were prepared using the Truseq Stranded Ribo Zero Library Prep Kit.,,tissue:liver|treatment:Biliatres1,GSM2037740,GSM2037740: Biliatres1 1; Danio rerio; RNA Seq,GSM2037740,,1,Livers were dissected directly in to the lysis buffer RLT and RNA was harvested using the standard Qiagen protocol RNeasy Mini Kit. 1 ug of total RNA was used for sequecning library construction and the libraries were prepared using the Truseq Stranded Ribo Zero Library Prep Kit.,GEO Accession:GSM2037740,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP068364,,,Toxin_1-Pack_1.fq.gz Toxin_1-Pack_2.fq.gz,fastq fastq,11256964600.0,56284823.0,GSM2037740 r1,0:100 1:100,A:2904557741;C:2723715275;G:2731673206;T:2896488406;N:529972,100,100,,,2904557741,2723715275,2731673206,2896488406,529972,SRX1528548,SRS1246176,SRA333195,GEO,"Michael Pack, Medicine/DIgestive Diseases, University of Pennsylvania",2,0.88354,0.88079,0.10204,0.10016,0.76088,0.76142,0.61543,0.61859,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United States,2016-01-12,Larval,Larval,Liver,Liver and Biliary System 40354,SRR3098580,SRX1528547,SRS1246177,SRP068364,PRJNA308582,Transcriptional profiling through RNA seq of zebrafish larval liver post exposure to biliatresone a biliary toxin.,GSE76780,Transcriptome Analysis,We sequenced liver mRNA isolated from biliatresone treated zebrafish larvae and DMSO treated controls in order to elucidate the molecular pathways induced by biliatresone a biliary toxin that is responsible for outbreaks of biliary atresia in Australian liverstock. Overall design: Liver mRNA profiles of biliatresone treated zebrafish larvae and DMSO treated controls were generated by deep sequencing in duplicates.,,pubmed:27102575,,Control 2,GSM2037739,,source name:liver|tissue:liver|treatment:DMSO,Control 2,Hiseq control software HCS was used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zv9 whole genome using STAR. Python Htseq script was used to count the number of reads. Genome build: zv9 Supplementary files format and content: tab delimited text files include htseq count output.,liver,Zebrafish larvae were treated with biliatresone 0.5 ug/ml for four hours.,Livers were dissected directly in to the lysis buffer RLT and RNA was harvested using the standard Qiagen protocol RNeasy Mini Kit. 1 ug of total RNA was used for sequecning library construction and the libraries were prepared using the Truseq Stranded Ribo Zero Library Prep Kit.,,tissue:liver|treatment:DMSO,GSM2037739,GSM2037739: Control 2; Danio rerio; RNA Seq,GSM2037739,,1,Livers were dissected directly in to the lysis buffer RLT and RNA was harvested using the standard Qiagen protocol RNeasy Mini Kit. 1 ug of total RNA was used for sequecning library construction and the libraries were prepared using the Truseq Stranded Ribo Zero Library Prep Kit.,GEO Accession:GSM2037739,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP068364,,,Control_2-Pack_1.fq.gz Control_2-Pack_2.fq.gz,fastq fastq,11100792600.0,55503963.0,GSM2037739 r1,0:100 1:100,A:2815807606;C:2731691384;G:2743610074;T:2809211211;N:472325,100,100,,,2815807606,2731691384,2743610074,2809211211,472325,SRX1528547,SRS1246177,SRA333195,GEO,"Michael Pack, Medicine/DIgestive Diseases, University of Pennsylvania",2,0.85048,0.84831,0.10818,0.10631,0.76025,0.76041,0.6032,0.60884,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United States,2016-01-12,Larval,Larval,Liver,Liver and Biliary System 40355,SRR3098579,SRX1528546,SRS1246178,SRP068364,PRJNA308582,Transcriptional profiling through RNA seq of zebrafish larval liver post exposure to biliatresone a biliary toxin.,GSE76780,Transcriptome Analysis,We sequenced liver mRNA isolated from biliatresone treated zebrafish larvae and DMSO treated controls in order to elucidate the molecular pathways induced by biliatresone a biliary toxin that is responsible for outbreaks of biliary atresia in Australian liverstock. Overall design: Liver mRNA profiles of biliatresone treated zebrafish larvae and DMSO treated controls were generated by deep sequencing in duplicates.,,pubmed:27102575,,Control 1,GSM2037738,,source name:liver|tissue:liver|treatment:DMSO,Control 1,Hiseq control software HCS was used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zv9 whole genome using STAR. Python Htseq script was used to count the number of reads. Genome build: zv9 Supplementary files format and content: tab delimited text files include htseq count output.,liver,Zebrafish larvae were treated with biliatresone 0.5 ug/ml for four hours.,Livers were dissected directly in to the lysis buffer RLT and RNA was harvested using the standard Qiagen protocol RNeasy Mini Kit. 1 ug of total RNA was used for sequecning library construction and the libraries were prepared using the Truseq Stranded Ribo Zero Library Prep Kit.,,tissue:liver|treatment:DMSO,GSM2037738,GSM2037738: Control 1; Danio rerio; RNA Seq,GSM2037738,,1,Livers were dissected directly in to the lysis buffer RLT and RNA was harvested using the standard Qiagen protocol RNeasy Mini Kit. 1 ug of total RNA was used for sequecning library construction and the libraries were prepared using the Truseq Stranded Ribo Zero Library Prep Kit.,GEO Accession:GSM2037738,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP068364,,,Control_1-Pack_2.fq.gz Control_1-Pack_1.fq.gz,fastq fastq,11315242000.0,56576210.0,GSM2037738 r1,0:100 1:100,A:2768862811;C:2888735322;G:2893616488;T:2763590339;N:437040,100,100,,,2768862811,2888735322,2893616488,2763590339,437040,SRX1528546,SRS1246178,SRA333195,GEO,"Michael Pack, Medicine/DIgestive Diseases, University of Pennsylvania",2,0.7716,0.76823,0.09579,0.09326,0.78447,0.78472,0.62953,0.62992,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United States,2016-01-12,Larval,Larval,Liver,Liver and Biliary System 43766,SRR6072790,SRX3214264,SRS2539122,SRP118819,PRJNA412050,Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio,GSE104221,Other,The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.,,pubmed:29686887,,PCB126 LIVER4 RNA Seq,GSM2792790,,tissue:liver|treatment:PCB126|life history stage:Adult,PCB126 LIVER4 RNA Seq,Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.,liver,Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues.,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,,treatment:PCB126|life history stage:Adult,GSM2792790,GSM2792790: PCB126 LIVER4 RNA Seq; Danio rerio; RNA Seq,GSM2792790,,1,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,GEO Accession:GSM2792790,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP118819,,,PL4_S8_L001_R1_001.fastq.gz,fastq,2065199049.0,40494099.0,GSM2792790 r1,0:51 1:0,A:537667860;C:491492122;G:474752735;T:561265595;N:20737,51,0,,,537667860,491492122,474752735,561265595,20737,SRX3214264,SRS2539122,SRA612796,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.95491,,0.05029,,0.8566,,0.2706,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2017-09-25,Adult,Adult,Liver,Liver and Biliary System 43767,SRR6072789,SRX3214263,SRS2539121,SRP118819,PRJNA412050,Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio,GSE104221,Other,The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.,,pubmed:29686887,,PCB126 LIVER3 RNA Seq,GSM2792789,,tissue:liver|treatment:PCB126|life history stage:Adult,PCB126 LIVER3 RNA Seq,Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.,liver,Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues.,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,,treatment:PCB126|life history stage:Adult,GSM2792789,GSM2792789: PCB126 LIVER3 RNA Seq; Danio rerio; RNA Seq,GSM2792789,,1,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,GEO Accession:GSM2792789,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP118819,,,PL3_S7_L001_R1_001.fastq.gz,fastq,1517788764.0,29760564.0,GSM2792789 r1,0:51 1:0,A:406289885;C:352040945;G:336853453;T:422589608;N:14873,51,0,,,406289885,352040945,336853453,422589608,14873,SRX3214263,SRS2539121,SRA612796,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.93375,,0.06726,,0.79571,,0.40409,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2017-09-25,Adult,Adult,Liver,Liver and Biliary System 43768,SRR6072788,SRX3214262,SRS2539119,SRP118819,PRJNA412050,Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio,GSE104221,Other,The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.,,pubmed:29686887,,PCB126 LIVER2 RNA Seq,GSM2792788,,tissue:liver|treatment:PCB126|life history stage:Adult,PCB126 LIVER2 RNA Seq,Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.,liver,Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues.,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,,treatment:PCB126|life history stage:Adult,GSM2792788,GSM2792788: PCB126 LIVER2 RNA Seq; Danio rerio; RNA Seq,GSM2792788,,1,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,GEO Accession:GSM2792788,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP118819,,,PL2_S6_L001_R1_001.fastq.gz,fastq,1663827009.0,32624059.0,GSM2792788 r1,0:51 1:0,A:440971092;C:389436356;G:376385827;T:457016821;N:16913,51,0,,,440971092,389436356,376385827,457016821,16913,SRX3214262,SRS2539119,SRA612796,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.93754,,0.06276,,0.78577,,0.41784,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2017-09-25,Adult,Adult,Liver,Liver and Biliary System 43769,SRR6072787,SRX3214261,SRS2539118,SRP118819,PRJNA412050,Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio,GSE104221,Other,The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.,,pubmed:29686887,,PCB126 LIVER1 RNA Seq,GSM2792787,,tissue:liver|treatment:PCB126|life history stage:Adult,PCB126 LIVER1 RNA Seq,Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.,liver,Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues.,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,,treatment:PCB126|life history stage:Adult,GSM2792787,GSM2792787: PCB126 LIVER1 RNA Seq; Danio rerio; RNA Seq,GSM2792787,,1,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,GEO Accession:GSM2792787,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP118819,,,PL1_S5_L001_R1_001.fastq.gz,fastq,1478813391.0,28996341.0,GSM2792787 r1,0:51 1:0,A:386520452;C:351444640;G:339630756;T:401202492;N:15051,51,0,,,386520452,351444640,339630756,401202492,15051,SRX3214261,SRS2539118,SRA612796,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.93711,,0.05155,,0.82528,,0.38533,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2017-09-25,Adult,Adult,Liver,Liver and Biliary System 43770,SRR6072786,SRX3214260,SRS2539116,SRP118819,PRJNA412050,Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio,GSE104221,Other,The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.,,pubmed:29686887,,CONTROL LIVER4 RNA Seq,GSM2792786,,tissue:liver|treatment:DMSO|life history stage:Adult,CONTROL LIVER4 RNA Seq,Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.,liver,Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues.,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,,treatment:DMSO|life history stage:Adult,GSM2792786,GSM2792786: CONTROL LIVER4 RNA Seq; Danio rerio; RNA Seq,GSM2792786,,1,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,GEO Accession:GSM2792786,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP118819,,,CL4_S4_L001_R1_001.fastq.gz,fastq,1634157504.0,32042304.0,GSM2792786 r1,0:51 1:0,A:437707358;C:377414301;G:365716599;T:453302878;N:16368,51,0,,,437707358,377414301,365716599,453302878,16368,SRX3214260,SRS2539116,SRA612796,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.93072,,0.06837,,0.79886,,0.53212,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2017-09-25,Adult,Adult,Liver,Liver and Biliary System 43771,SRR6072785,SRX3214259,SRS2539117,SRP118819,PRJNA412050,Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio,GSE104221,Other,The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.,,pubmed:29686887,,CONTROL LIVER3 RNA Seq,GSM2792785,,tissue:liver|treatment:DMSO|life history stage:Adult,CONTROL LIVER3 RNA Seq,Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.,liver,Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues.,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,,treatment:DMSO|life history stage:Adult,GSM2792785,GSM2792785: CONTROL LIVER3 RNA Seq; Danio rerio; RNA Seq,GSM2792785,,1,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,GEO Accession:GSM2792785,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP118819,,,CL3_S3_L001_R1_001.fastq.gz,fastq,1571772366.0,30819066.0,GSM2792785 r1,0:51 1:0,A:415738375;C:368918710;G:354616717;T:432483203;N:15361,51,0,,,415738375,368918710,354616717,432483203,15361,SRX3214259,SRS2539117,SRA612796,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.93466,,0.06978,,0.79835,,0.54042,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2017-09-25,Adult,Adult,Liver,Liver and Biliary System 43772,SRR6072784,SRX3214258,SRS2539115,SRP118819,PRJNA412050,Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio,GSE104221,Other,The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.,,pubmed:29686887,,CONTROL LIVER2 RNA Seq,GSM2792784,,tissue:liver|treatment:DMSO|life history stage:Adult,CONTROL LIVER2 RNA Seq,Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.,liver,Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues.,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,,treatment:DMSO|life history stage:Adult,GSM2792784,GSM2792784: CONTROL LIVER2 RNA Seq; Danio rerio; RNA Seq,GSM2792784,,1,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,GEO Accession:GSM2792784,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP118819,,,CL2_S2_L001_R1_001.fastq.gz,fastq,1589259144.0,31161944.0,GSM2792784 r1,0:51 1:0,A:416206247;C:376814337;G:364565765;T:431656745;N:16050,51,0,,,416206247,376814337,364565765,431656745,16050,SRX3214258,SRS2539115,SRA612796,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.94952,,0.0459,,0.82595,,0.20166,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2017-09-25,Adult,Adult,Liver,Liver and Biliary System 43773,SRR6072783,SRX3214256,SRS2539114,SRP118819,PRJNA412050,Integrative analysis of transcriptional and DNA methylation changes associated with PCB126 exposure in adult zebrafish Danio rerio,GSE104221,Other,The aryl hydrocarbon receptor AHR is a ligand activated transcription factor well known for mediating the toxicity of environmental chemicals such as polychlorinated biphenyls PCBs and polyaromatic hydrocarbons PAHs. There is extensive knowledge on the range of target genes regulated by AHR ligands. However there is limited information on the effect of AHR ligands on DNA methylation. The objective of this study is to investigate genome wide changes in DNA methylation and gene expression patterns in response to PCB126 exposure. Adult zebrafish were exposed to 10 nM PCB126 for 24 hours waterborne exposure and were reared in clean water for xxx days before tissue sampling. DNA methylation and transcriptional changes in the liver and brain tissues were quantified by Reduced Representation Bisulfite Sequencing RRBS and RNAseq respectively. RRBS analysis revealed DNA hypomethylation in response to PCB exposure in both liver and brain tissues. We observed 482 and 476 differentially methylated regions DMRs in the liver and brain tissues respectively. Most of the DMRs are located more than 20 kilobases upstream of the transcriptional start sites. RNAseq results from the liver revealed differential expression of genes related to xenobiotic metabolism oxidative stress and carbohydrate metabolism in response to PCB exposure. In the brain PCB exposure altered the expression of genes involved in myelination and glutamate signaling. Our results suggest that there is very little correlation between DNA methylation and gene expression patterns among the differentially expressed genes DEGs. We are currently investigating the relationship between DMRs and DEGs. Overall design: Two different tissues Liver and brain from PCB126 and DMSO exposed zebrafish were analyzed for DNA methylation and gene expression using RRBS and RNAseq respectively. Four biological replicates per treatment were analyzed n=4 individual fish.,,pubmed:29686887,,CONTROL LIVER1 RNA Seq,GSM2792783,,tissue:liver|treatment:DMSO|life history stage:Adult,CONTROL LIVER1 RNA Seq,Enhanced RRBS data was processed by aligning the reads to the bisulfite converted genome using Bismark. CpG methylation calls were extracted from Bismark aligned bam files using MethylKit. Differential methylation analysis was carried out by SLIM method using methylKit RNAseq data was pre processed and aligned to the genome using STAR aligner and HTSeqcount was used to obtain mapped read counts Genome build: GRCz10 Supplementary files format and content: text files for RNAseq include mapped read counts; text files for ERRBS include CpG methylation calls.,liver,Adult zebrafish were exposed to either PCB126 or DMSO via waterborne exposure for xxx hours. post the exposure period fish were reared in clean water for 7 days before sampling the tissues.,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,,treatment:DMSO|life history stage:Adult,GSM2792783,GSM2792783: CONTROL LIVER1 RNA Seq; Danio rerio; RNA Seq,GSM2792783,,1,Total RNA and genomic DNA were isolated simultaneously using Zymo Research nucleic acid isolation kit. Enhanced RRBS library construction was done by double digesting genomic DNA with TaqaI and MspI. RNAseq library preparation was done using TruSeq illumina total RNA library prep kit.,GEO Accession:GSM2792783,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP118819,,,CL1_S1_L001_R1_001.fastq.gz,fastq,1654871715.0,32448465.0,GSM2792783 r1,0:51 1:0,A:437754996;C:387868090;G:371179005;T:458052604;N:17020,51,0,,,437754996,387868090,371179005,458052604,17020,SRX3214256,SRS2539114,SRA612796,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.92878,,0.0644,,0.79851,,0.53438,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2017-09-25,Adult,Adult,Liver,Liver and Biliary System 55199,SRR10153645,SRX6879060,SRS5414808,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,317E11,GSM4087880,,tissue:Liver|transgenic line:Tgfabp10a pt beta catenin|age:6 mpf at larval stg:No treatment|diagnosis:HCC,317E11,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Tgfabp10a pt beta catenin|age:6 mpf at larval stg:No treatment|diagnosis:HCC,GSM4087880,GSM4087880: 317E11; Danio rerio; RNA Seq,GSM4087880,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087880,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,15743X10_190116_A00421_0031_AHGYLMDSXX_S132_L004_R1_001.fastq.gz 15743X10_190116_A00421_0031_AHGYLMDSXX_S132_L004_R2_001.fastq.gz,fastq fastq,10867492650.0,35985075.0,GSM4087880 r1,0:151 1:151,A:2887410705;C:2554057138;G:2635696540;T:2790221641;N:106626,151,151,,,2887410705,2554057138,2635696540,2790221641,106626,SRX6879060,SRS5414808,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.95633,0.95841,0.03967,0.03882,0.76552,0.76508,0.54577,0.54524,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Adult,Adult,Liver,Liver and Biliary System 55200,SRR10153644,SRX6879059,SRS5414807,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,317E10,GSM4087879,,tissue:Liver|transgenic line:Tgfabp10a pt beta catenin|age:6 mpf at larval stg:No treatment|diagnosis:HCC,317E10,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Tgfabp10a pt beta catenin|age:6 mpf at larval stg:No treatment|diagnosis:HCC,GSM4087879,GSM4087879: 317E10; Danio rerio; RNA Seq,GSM4087879,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087879,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,15743X9_190116_A00421_0031_AHGYLMDSXX_S140_L004_R1_001.fastq.gz 15743X9_190116_A00421_0031_AHGYLMDSXX_S140_L004_R2_001.fastq.gz,fastq fastq,12407355014.0,41083957.0,GSM4087879 r1,0:151 1:151,A:3223341496;C:2995330964;G:3106514310;T:3082046779;N:121465,151,151,,,3223341496,2995330964,3106514310,3082046779,121465,SRX6879059,SRS5414807,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.96118,0.96245,0.04544,0.04421,0.76794,0.76818,0.53422,0.53557,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Adult,Adult,Liver,Liver and Biliary System 55201,SRR10153643,SRX6879058,SRS5414806,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,317E9,GSM4087878,,tissue:Liver|transgenic line:Tgfabp10a pt beta catenin|age:6 mpf at larval stg:No treatment|diagnosis:HCC,317E9,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Tgfabp10a pt beta catenin|age:6 mpf at larval stg:No treatment|diagnosis:HCC,GSM4087878,GSM4087878: 317E9; Danio rerio; RNA Seq,GSM4087878,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087878,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,15743X8_190116_A00421_0031_AHGYLMDSXX_S139_L004_R2_001.fastq.gz 15743X8_190116_A00421_0031_AHGYLMDSXX_S139_L004_R1_001.fastq.gz,fastq fastq,12506833814.0,41413357.0,GSM4087878 r1,0:151 1:151,A:3256498952;C:3005659489;G:3091306516;T:3153245982;N:122875,151,151,,,3256498952,3005659489,3091306516,3153245982,122875,SRX6879058,SRS5414806,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.93067,0.93234,0.05244,0.05164,0.79257,0.79322,0.53393,0.536,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Adult,Adult,Liver,Liver and Biliary System 55202,SRR10153642,SRX6879057,SRS5414805,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,317E6,GSM4087877,,tissue:Liver|transgenic line:Tgfabp10a pt beta catenin|age:6 mpf at larval stg:No treatment|diagnosis:HCC,317E6,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Tgfabp10a pt beta catenin|age:6 mpf at larval stg:No treatment|diagnosis:HCC,GSM4087877,GSM4087877: 317E6; Danio rerio; RNA Seq,GSM4087877,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087877,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,15743X7_190116_A00421_0031_AHGYLMDSXX_S138_L004_R1_001.fastq.gz 15743X7_190116_A00421_0031_AHGYLMDSXX_S138_L004_R2_001.fastq.gz,fastq fastq,13100368306.0,43378703.0,GSM4087877 r1,0:151 1:151,A:3411730545;C:3148933690;G:3219794660;T:3319781049;N:128362,151,151,,,3411730545,3148933690,3219794660,3319781049,128362,SRX6879057,SRS5414805,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.96451,0.96575,0.03471,0.03389,0.76583,0.76611,0.53899,0.54065,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Adult,Adult,Liver,Liver and Biliary System 55203,SRR10153641,SRX6879056,SRS5414804,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,317E5,GSM4087876,,tissue:Liver|transgenic line:Tgfabp10a pt beta catenin|age:6 mpf at larval stg:No treatment|diagnosis:HCC,317E5,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Tgfabp10a pt beta catenin|age:6 mpf at larval stg:No treatment|diagnosis:HCC,GSM4087876,GSM4087876: 317E5; Danio rerio; RNA Seq,GSM4087876,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087876,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,15743X6_190116_A00421_0031_AHGYLMDSXX_S137_L004_R1_001.fastq.gz 15743X6_190116_A00421_0031_AHGYLMDSXX_S137_L004_R2_001.fastq.gz,fastq fastq,12739600616.0,42184108.0,GSM4087876 r1,0:151 1:151,A:3314927478;C:3059256149;G:3141796417;T:3223495776;N:124796,151,151,,,3314927478,3059256149,3141796417,3223495776,124796,SRX6879056,SRS5414804,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.96091,0.963,0.03691,0.03616,0.76978,0.76976,0.52294,0.53428,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Adult,Adult,Liver,Liver and Biliary System 55204,SRR10153640,SRX6879055,SRS5414803,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,317C8,GSM4087875,,tissue:Liver|transgenic line:Wild Type|age:6 mpf at larval stg:No treatment|diagnosis:no HCC,317C8,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Wild Type|age:6 mpf at larval stg:No treatment|diagnosis:no HCC,GSM4087875,GSM4087875: 317C8; Danio rerio; RNA Seq,GSM4087875,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087875,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,15743X5_190116_A00421_0031_AHGYLMDSXX_S136_L004_R1_001.fastq.gz 15743X5_190116_A00421_0031_AHGYLMDSXX_S136_L004_R2_001.fastq.gz,fastq fastq,13478629044.0,44631222.0,GSM4087875 r1,0:151 1:151,A:3550728847;C:3189723236;G:3284554425;T:3453490478;N:132058,151,151,,,3550728847,3189723236,3284554425,3453490478,132058,SRX6879055,SRS5414803,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.95549,0.95786,0.0425,0.04094,0.81905,0.81949,0.55534,0.55036,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Adult,Adult,Liver,Liver and Biliary System 55205,SRR10153639,SRX6879054,SRS5414802,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,317C5,GSM4087874,,tissue:Liver|transgenic line:Wild Type|age:6 mpf at larval stg:No treatment|diagnosis:no HCC,317C5,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Wild Type|age:6 mpf at larval stg:No treatment|diagnosis:no HCC,GSM4087874,GSM4087874: 317C5; Danio rerio; RNA Seq,GSM4087874,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087874,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,15743X4_190116_A00421_0031_AHGYLMDSXX_S135_L004_R1_001.fastq.gz 15743X4_190116_A00421_0031_AHGYLMDSXX_S135_L004_R2_001.fastq.gz,fastq fastq,8833053644.0,29248522.0,GSM4087874 r1,0:151 1:151,A:2332531036;C:2082507857;G:2145030401;T:2272898348;N:86002,151,151,,,2332531036,2082507857,2145030401,2272898348,86002,SRX6879054,SRS5414802,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.9551,0.95675,0.03821,0.03703,0.8076,0.80773,0.52755,0.52774,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Adult,Adult,Liver,Liver and Biliary System 55206,SRR10153638,SRX6879053,SRS5414801,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,317C4,GSM4087873,,tissue:Liver|transgenic line:Wild Type|age:6 mpf at larval stg:No treatment|diagnosis:no HCC,317C4,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Wild Type|age:6 mpf at larval stg:No treatment|diagnosis:no HCC,GSM4087873,GSM4087873: 317C4; Danio rerio; RNA Seq,GSM4087873,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087873,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,15743X3_190116_A00421_0031_AHGYLMDSXX_S134_L004_R1_001.fastq.gz 15743X3_190116_A00421_0031_AHGYLMDSXX_S134_L004_R2_001.fastq.gz,fastq fastq,9551945316.0,31628958.0,GSM4087873 r1,0:151 1:151,A:2509027641;C:2264930498;G:2326337388;T:2451556539;N:93250,151,151,,,2509027641,2264930498,2326337388,2451556539,93250,SRX6879053,SRS5414801,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.95442,0.95572,0.03491,0.03446,0.82004,0.8213,0.5105,0.53479,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Adult,Adult,Liver,Liver and Biliary System 55207,SRR10153637,SRX6879052,SRS5414800,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,317C2,GSM4087872,,tissue:Liver|transgenic line:Wild Type|age:6 mpf at larval stg:No treatment|diagnosis:no HCC,317C2,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Wild Type|age:6 mpf at larval stg:No treatment|diagnosis:no HCC,GSM4087872,GSM4087872: 317C2; Danio rerio; RNA Seq,GSM4087872,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087872,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,15743X2_190116_A00421_0031_AHGYLMDSXX_S133_L004_R1_001.fastq.gz 15743X2_190116_A00421_0031_AHGYLMDSXX_S133_L004_R2_001.fastq.gz,fastq fastq,10920914034.0,36161967.0,GSM4087872 r1,0:151 1:151,A:2874727047;C:2582067274;G:2651510108;T:2812502625;N:106980,151,151,,,2874727047,2582067274,2651510108,2812502625,106980,SRX6879052,SRS5414800,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.95623,0.95884,0.04187,0.0408,0.81507,0.81566,0.57117,0.57296,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Adult,Adult,Liver,Liver and Biliary System 55208,SRR10153636,SRX6879051,SRS5414799,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,317C1,GSM4087871,,tissue:Liver|transgenic line:Wild Type|age:6 mpf at larval stg:No treatment|diagnosis:no HCC,317C1,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Wild Type|age:6 mpf at larval stg:No treatment|diagnosis:no HCC,GSM4087871,GSM4087871: 317C1; Danio rerio; RNA Seq,GSM4087871,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,15743X1_190116_A00421_0031_AHGYLMDSXX_S131_L004_R1_001.fastq.gz 15743X1_190116_A00421_0031_AHGYLMDSXX_S131_L004_R2_001.fastq.gz,fastq fastq,12844134292.0,42530246.0,GSM4087871 r1,0:151 1:151,A:3413728431;C:3010656807;G:3098858958;T:3320763824;N:126272,151,151,,,3413728431,3010656807,3098858958,3320763824,126272,SRX6879051,SRS5414799,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.95571,0.95824,0.04117,0.04043,0.81974,0.82039,0.5764,0.57228,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Adult,Adult,Liver,Liver and Biliary System 55209,SRR10153635,SRX6879050,SRS5414798,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,622,GSM4087870,,tissue:Liver|transgenic line:Tgfabp10a CreERT2|age:11 mpf at larval stg:0.1percent ethanol|diagnosis:no HCC,622,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Tgfabp10a CreERT2|age:11 mpf at larval stg:0.1percent ethanol|diagnosis:no HCC,GSM4087870,GSM4087870: 622; Danio rerio; RNA Seq,GSM4087870,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,16048X10_190607_A00421_0071_BHL22MDSXX_S21_L004_R1_001.fastq.gz 16048X10_190607_A00421_0071_BHL22MDSXX_S21_L004_R2_001.fastq.gz,fastq fastq,10097035082.0,33433891.0,GSM4087870 r1,0:151 1:151,A:2703497670;C:2359983079;G:2449399983;T:2583963895;N:190455,151,151,,,2703497670,2359983079,2449399983,2583963895,190455,SRX6879050,SRS5414798,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.95376,0.95451,0.04632,0.04565,0.81698,0.81838,0.57251,0.57069,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Adult,Adult,Liver,Liver and Biliary System 55210,SRR10153634,SRX6879049,SRS5414797,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,609,GSM4087869,,tissue:Liver|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC,609,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC,GSM4087869,GSM4087869: 609; Danio rerio; RNA Seq,GSM4087869,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,16048X9_190607_A00421_0071_BHL22MDSXX_S20_L004_R1_001.fastq.gz 16048X9_190607_A00421_0071_BHL22MDSXX_S20_L004_R2_001.fastq.gz,fastq fastq,9109094026.0,30162563.0,GSM4087869 r1,0:151 1:151,A:2407747194;C:2151727590;G:2238603631;T:2310854013;N:161598,151,151,,,2407747194,2151727590,2238603631,2310854013,161598,SRX6879049,SRS5414797,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.95438,0.95659,0.04172,0.04068,0.80267,0.80308,0.56788,0.56779,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Multi-stage,Multi-stage,Liver,Liver and Biliary System 55211,SRR10153633,SRX6879048,SRS5414796,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,624,GSM4087868,,tissue:Liver|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,624,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,GSM4087868,GSM4087868: 624; Danio rerio; RNA Seq,GSM4087868,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,16048X8_190607_A00421_0071_BHL22MDSXX_S19_L004_R1_001.fastq.gz 16048X8_190607_A00421_0071_BHL22MDSXX_S19_L004_R2_001.fastq.gz,fastq fastq,9818272170.0,32510835.0,GSM4087868 r1,0:151 1:151,A:2609919214;C:2318388621;G:2406490919;T:2483290917;N:182499,151,151,,,2609919214,2318388621,2406490919,2483290917,182499,SRX6879048,SRS5414796,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.95073,0.95151,0.04785,0.0469,0.80919,0.81055,0.54958,0.55772,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Multi-stage,Multi-stage,Liver,Liver and Biliary System 55212,SRR10153632,SRX6879047,SRS5414795,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,621,GSM4087867,,tissue:Liver|transgenic line:Tgfabp10a CreERT2|age:11 mpf at larval stg:0.1percent ethanol|diagnosis:no HCC,621,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Tgfabp10a CreERT2|age:11 mpf at larval stg:0.1percent ethanol|diagnosis:no HCC,GSM4087867,GSM4087867: 621; Danio rerio; RNA Seq,GSM4087867,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,16048X7_190607_A00421_0071_BHL22MDSXX_S18_L004_R1_001.fastq.gz 16048X7_190607_A00421_0071_BHL22MDSXX_S18_L004_R2_001.fastq.gz,fastq fastq,11748365646.0,38901873.0,GSM4087867 r1,0:151 1:151,A:3113993218;C:2779348539;G:2879824343;T:2974982583;N:216963,151,151,,,3113993218,2779348539,2879824343,2974982583,216963,SRX6879047,SRS5414795,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.95414,0.95586,0.04568,0.045,0.82406,0.82459,0.57313,0.5717,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Adult,Adult,Liver,Liver and Biliary System 55213,SRR10153631,SRX6879046,SRS5414794,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,625,GSM4087866,,tissue:Liver|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC,625,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC,GSM4087866,GSM4087866: 625; Danio rerio; RNA Seq,GSM4087866,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,16048X6_190607_A00421_0071_BHL22MDSXX_S17_L004_R2_001.fastq.gz 16048X6_190607_A00421_0071_BHL22MDSXX_S17_L004_R1_001.fastq.gz,fastq fastq,9650060284.0,31953842.0,GSM4087866 r1,0:151 1:151,A:2558021442;C:2277296580;G:2371770140;T:2442792643;N:179479,151,151,,,2558021442,2277296580,2371770140,2442792643,179479,SRX6879046,SRS5414794,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.95395,0.95537,0.0475,0.04582,0.79947,0.80046,0.53471,0.54384,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Multi-stage,Multi-stage,Liver,Liver and Biliary System 55214,SRR10153630,SRX6879045,SRS5414793,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,623,GSM4087865,,tissue:Liver|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,623,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,GSM4087865,GSM4087865: 623; Danio rerio; RNA Seq,GSM4087865,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087865,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,16048X5_190607_A00421_0071_BHL22MDSXX_S16_L004_R2_001.fastq.gz 16048X5_190607_A00421_0071_BHL22MDSXX_S16_L004_R1_001.fastq.gz,fastq fastq,11046705188.0,36578494.0,GSM4087865 r1,0:151 1:151,A:2912202858;C:2634649411;G:2724125067;T:2775523373;N:204479,151,151,,,2912202858,2634649411,2724125067,2775523373,204479,SRX6879045,SRS5414793,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.95836,0.95975,0.04299,0.04253,0.79433,0.795,0.55057,0.55465,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Multi-stage,Multi-stage,Liver,Liver and Biliary System 55215,SRR10153629,SRX6879044,SRS5414792,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,628,GSM4087864,,tissue:Liver|transgenic line:Tgfabp10a CreERT2|age:11 mpf at larval stg:0.1percent ethanol|diagnosis:no HCC,628,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Tgfabp10a CreERT2|age:11 mpf at larval stg:0.1percent ethanol|diagnosis:no HCC,GSM4087864,GSM4087864: 628; Danio rerio; RNA Seq,GSM4087864,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087864,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,16048X4_190607_A00421_0071_BHL22MDSXX_S15_L004_R1_001.fastq.gz 16048X4_190607_A00421_0071_BHL22MDSXX_S15_L004_R2_001.fastq.gz,fastq fastq,10869072714.0,35990307.0,GSM4087864 r1,0:151 1:151,A:2903873216;C:2545919454;G:2642728309;T:2776348820;N:202915,151,151,,,2903873216,2545919454,2642728309,2776348820,202915,SRX6879044,SRS5414792,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.95352,0.9553,0.04411,0.04352,0.79182,0.79275,0.5419,0.55314,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Adult,Adult,Liver,Liver and Biliary System 55216,SRR10153628,SRX6879043,SRS5414791,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,630,GSM4087863,,tissue:Liver|transgenic line:Tgfabp10a CreERT2|age:11 mpf at larval stg:0.1percent ethanol|diagnosis:no HCC,630,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Tgfabp10a CreERT2|age:11 mpf at larval stg:0.1percent ethanol|diagnosis:no HCC,GSM4087863,GSM4087863: 630; Danio rerio; RNA Seq,GSM4087863,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087863,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,16048X3_190607_A00421_0071_BHL22MDSXX_S1_L004_R1_001.fastq.gz 16048X3_190607_A00421_0071_BHL22MDSXX_S1_L004_R2_001.fastq.gz,fastq fastq,7918572880.0,26220440.0,GSM4087863 r1,0:151 1:151,A:2082991237;C:1875370870;G:1955583367;T:2004478821;N:148585,151,151,,,2082991237,1875370870,1955583367,2004478821,148585,SRX6879043,SRS5414791,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.85436,0.9553,0.04028,0.0454,0.81115,0.80428,0.54833,0.55156,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Adult,Adult,Liver,Liver and Biliary System 55217,SRR10153627,SRX6879042,SRS5414790,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,605,GSM4087862,,tissue:Liver|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,605,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,GSM4087862,GSM4087862: 605; Danio rerio; RNA Seq,GSM4087862,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087862,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,16048X2_190607_A00421_0071_BHL22MDSXX_S2_L004_R1_001.fastq.gz 16048X2_190607_A00421_0071_BHL22MDSXX_S2_L004_R2_001.fastq.gz,fastq fastq,9642566456.0,31929028.0,GSM4087862 r1,0:151 1:151,A:2562227409;C:2265732155;G:2354688485;T:2459736870;N:181537,151,151,,,2562227409,2265732155,2354688485,2459736870,181537,SRX6879042,SRS5414790,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.9525,0.95448,0.0459,0.04564,0.78173,0.78317,0.54755,0.54727,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Multi-stage,Multi-stage,Liver,Liver and Biliary System 55218,SRR10153626,SRX6879041,SRS5414789,SRP222804,PRJNA573071,Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC,GSE137787,Transcriptome Analysis,Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish compared to wildtype/nonHCC siblings.,parent bioproject:PRJNA573068,pubmed:31575545,,604,GSM4087861,,tissue:Liver|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,604,The Zebrafish GRCz11 FASTA and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.  Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.  Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.  Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.,Liver,Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer’s protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina’s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,Fish were raised following IACUC approved protocols in insititutional zebrafish facility.,transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf,GSM4087861,GSM4087861: 604; Danio rerio; RNA Seq,GSM4087861,,1,Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in 80C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50 Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050 Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control library preparation sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read 150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10,GEO Accession:GSM4087861,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP222804,,,16048X1_190607_A00421_0071_BHL22MDSXX_S3_L004_R1_001.fastq.gz 16048X1_190607_A00421_0071_BHL22MDSXX_S3_L004_R2_001.fastq.gz,fastq fastq,12056607986.0,39922543.0,GSM4087861 r1,0:151 1:151,A:3165745037;C:2870251386;G:2976751806;T:3043633552;N:226205,151,151,,,3165745037,2870251386,2976751806,3043633552,226205,SRX6879041,SRS5414789,SRA965568,GEO,"Pathology, University of California, San Francisco",2,0.95408,0.95527,0.04826,0.04735,0.79366,0.79425,0.52338,0.53718,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,bulk,bulk,,United States,2019-09-20,Multi-stage,Multi-stage,Liver,Liver and Biliary System 59319,SRR11856744,SRX8406857,SRS6719220,SRP264975,PRJNA635397,Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf,GSE151291,Transcriptome Analysis,Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx 175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions. Samples were obtained from 5 separate clutches. Samples were sequenced on NextSeq550 Illumina.,,,,5 dpf liver exposed to 350 mM Ethanol clutch 7,GSM4572124,,tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:20,5 dpf liver exposed to 350 mM Ethanol clutch 7,Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2 v2.1.0 with the parameters “–no novel junctions” and “–G” Accepted bam files were used for counting gene read numbers with HTSeq a 10 s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes,Liver,At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.,Larvae were anesthetized with tricane and 20 35 livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher 15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.,Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection embryos were divided into 30 mL plates 60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.,genotype:Tgfabp10a:ER tdTomato|pool:20|rna qbit concentrationng/ul:23.8,GSM4572124,GSM4572124: LIV 2ETOH 7; Danio rerio; RNA Seq,GSM4572124,,1,20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar,GEO Accession:GSM4572124,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP264975,,,LIV_2ETOH_7_S23_read2.fastq.gz LIV_2ETOH_7_S23_read1.fastq.gz,fastq fastq,6357898307.0,22104243.0,GSM4572124 r1,0:143.74 1:143.89,A:1712090294;C:1465925369;G:1489380825;T:1689427333;N:1074486,143,143,,,1712090294,1465925369,1489380825,1689427333,1074486,SRX8406857,SRS6719220,SRA1080364,GEO,"Biology, New York University Abu Dhabi",2,0.69131,0.71792,0.04808,0.0499,0.82477,0.83082,0.47278,0.49809,150,151,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,bulk,bulk,,United Arab Emirates,2020-05-27,Multi-stage,Multi-stage,Liver,Liver and Biliary System 59320,SRR11856743,SRX8406856,SRS6719219,SRP264975,PRJNA635397,Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf,GSE151291,Transcriptome Analysis,Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx 175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions. Samples were obtained from 5 separate clutches. Samples were sequenced on NextSeq550 Illumina.,,,,5 dpf liver exposed to 175mM Ethanol clutch 7,GSM4572123,,tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:20,5 dpf liver exposed to 175mM Ethanol clutch 7,Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2 v2.1.0 with the parameters “–no novel junctions” and “–G” Accepted bam files were used for counting gene read numbers with HTSeq a 10 s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes,Liver,At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.,Larvae were anesthetized with tricane and 20 35 livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher 15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.,Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection embryos were divided into 30 mL plates 60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.,genotype:Tgfabp10a:ER tdTomato|pool:20|rna qbit concentrationng/ul:15.7,GSM4572123,GSM4572123: LIV 1ETOH 7; Danio rerio; RNA Seq,GSM4572123,,1,20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar,GEO Accession:GSM4572123,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP264975,,,LIV_1ETOH_7_S22_read2.fastq.gz LIV_1ETOH_7_S22_read1.fastq.gz,fastq fastq,4305184103.0,15015974.0,GSM4572123 r1,0:143.31 1:143.40,A:1153593916;C:998854522;G:1012290687;T:1139809167;N:635811,143,143,,,1153593916,998854522,1012290687,1139809167,635811,SRX8406856,SRS6719219,SRA1080364,GEO,"Biology, New York University Abu Dhabi",2,0.9174,0.9191,0.06548,0.06503,0.8143,0.82148,0.54687,0.54095,151,151,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,bulk,bulk,,United Arab Emirates,2020-05-27,Multi-stage,Multi-stage,Liver,Liver and Biliary System 59321,SRR11856756,SRX8406855,SRS6719218,SRP264975,PRJNA635397,Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf,GSE151291,Transcriptome Analysis,Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx 175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions. Samples were obtained from 5 separate clutches. Samples were sequenced on NextSeq550 Illumina.,,,,5 dpf Untreated liver clutch 7,GSM4572122,,tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:20,5 dpf Untreated liver clutch 7,Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2 v2.1.0 with the parameters “–no novel junctions” and “–G” Accepted bam files were used for counting gene read numbers with HTSeq a 10 s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes,Liver,At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.,Larvae were anesthetized with tricane and 20 35 livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher 15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.,Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection embryos were divided into 30 mL plates 60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.,genotype:Tgfabp10a:ER tdTomato|pool:20|rna qbit concentrationng/ul:14.4,GSM4572122,GSM4572122: LIV UT 7; Danio rerio; RNA Seq,GSM4572122,,1,20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar,GEO Accession:GSM4572122,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP264975,,,LIV_UT_7_S21_read2.fastq.gz LIV_UT_7_S21_read1.fastq.gz,fastq fastq,4730299683.0,16394224.0,GSM4572122 r1,0:144.23 1:144.30,A:1269896715;C:1097260368;G:1106021062;T:1256450979;N:670559,144,144,,,1269896715,1097260368,1106021062,1256450979,670559,SRX8406855,SRS6719218,SRA1080364,GEO,"Biology, New York University Abu Dhabi",2,0.92607,0.92755,0.06001,0.05999,0.81613,0.82187,0.55335,0.53614,151,151,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,bulk,bulk,,United Arab Emirates,2020-05-27,Multi-stage,Multi-stage,Liver,Liver and Biliary System 59322,SRR11856755,SRX8406854,SRS6719217,SRP264975,PRJNA635397,Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf,GSE151291,Transcriptome Analysis,Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx 175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions. Samples were obtained from 5 separate clutches. Samples were sequenced on NextSeq550 Illumina.,,,,5 dpf liver exposed to 350 mM Ethanol clutch 5,GSM4572121,,tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:35,5 dpf liver exposed to 350 mM Ethanol clutch 5,Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2 v2.1.0 with the parameters “–no novel junctions” and “–G” Accepted bam files were used for counting gene read numbers with HTSeq a 10 s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes,Liver,At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.,Larvae were anesthetized with tricane and 20 35 livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher 15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.,Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection embryos were divided into 30 mL plates 60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.,genotype:Tgfabp10a:ER tdTomato|pool:35|rna qbit concentrationng/ul:32.6,GSM4572121,GSM4572121: LIV 2ETOH 5; Danio rerio; RNA Seq,GSM4572121,,1,20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar,GEO Accession:GSM4572121,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP264975,,,LIV_2ETOH_5_S20_read2.fastq.gz LIV_2ETOH_5_S20_read1.fastq.gz,fastq fastq,5199368627.0,17618880.0,GSM4572121 r1,0:147.54 1:147.56,A:1399517489;C:1172048358;G:1240786042;T:1386342191;N:674547,147,147,,,1399517489,1172048358,1240786042,1386342191,674547,SRX8406854,SRS6719217,SRA1080364,GEO,"Biology, New York University Abu Dhabi",2,0.91793,0.91561,0.14142,0.13588,0.80941,0.81889,0.47417,0.50399,151,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,bulk,bulk,,United Arab Emirates,2020-05-27,Multi-stage,Multi-stage,Liver,Liver and Biliary System 59323,SRR11856754,SRX8406853,SRS6719216,SRP264975,PRJNA635397,Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf,GSE151291,Transcriptome Analysis,Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx 175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions. Samples were obtained from 5 separate clutches. Samples were sequenced on NextSeq550 Illumina.,,,,5 dpf liver exposed to 175mM Ethanol clutch 5,GSM4572120,,tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:35,5 dpf liver exposed to 175mM Ethanol clutch 5,Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2 v2.1.0 with the parameters “–no novel junctions” and “–G” Accepted bam files were used for counting gene read numbers with HTSeq a 10 s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes,Liver,At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.,Larvae were anesthetized with tricane and 20 35 livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher 15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.,Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection embryos were divided into 30 mL plates 60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.,genotype:Tgfabp10a:ER tdTomato|pool:35|rna qbit concentrationng/ul:34.8,GSM4572120,GSM4572120: LIV 1ETOH 5; Danio rerio; RNA Seq,GSM4572120,,1,20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar,GEO Accession:GSM4572120,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP264975,,,LIV_1ETOH_5_S19_read2.fastq.gz LIV_1ETOH_5_S19_read1.fastq.gz,fastq fastq,4664825517.0,15773614.0,GSM4572120 r1,0:147.85 1:147.89,A:1254524905;C:1075035904;G:1088910190;T:1245664535;N:689983,147,147,,,1254524905,1075035904,1088910190,1245664535,689983,SRX8406853,SRS6719216,SRA1080364,GEO,"Biology, New York University Abu Dhabi",2,0.94346,0.94595,0.05958,0.05908,0.82183,0.83053,0.53444,0.52504,151,151,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,bulk,bulk,,United Arab Emirates,2020-05-27,Multi-stage,Multi-stage,Liver,Liver and Biliary System 59324,SRR11856753,SRX8406852,SRS6719215,SRP264975,PRJNA635397,Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf,GSE151291,Transcriptome Analysis,Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx 175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions. Samples were obtained from 5 separate clutches. Samples were sequenced on NextSeq550 Illumina.,,,,5 dpf Untreated liver clutch 5,GSM4572119,,tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:35,5 dpf Untreated liver clutch 5,Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2 v2.1.0 with the parameters “–no novel junctions” and “–G” Accepted bam files were used for counting gene read numbers with HTSeq a 10 s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes,Liver,At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.,Larvae were anesthetized with tricane and 20 35 livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher 15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.,Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection embryos were divided into 30 mL plates 60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.,genotype:Tgfabp10a:ER tdTomato|pool:35|rna qbit concentrationng/ul:31.2,GSM4572119,GSM4572119: LIV UT 5; Danio rerio; RNA Seq,GSM4572119,,1,20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar,GEO Accession:GSM4572119,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP264975,,,LIV_UT_5_S18_read2.fastq.gz LIV_UT_5_S18_read1.fastq.gz,fastq fastq,5809354899.0,19717109.0,GSM4572119 r1,0:147.29 1:147.35,A:1543780226;C:1359647607;G:1375859882;T:1529075527;N:991657,147,147,,,1543780226,1359647607,1375859882,1529075527,991657,SRX8406852,SRS6719215,SRA1080364,GEO,"Biology, New York University Abu Dhabi",2,0.94774,0.95056,0.05145,0.05139,0.82079,0.82735,0.52842,0.53743,151,151,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,bulk,bulk,,United Arab Emirates,2020-05-27,Multi-stage,Multi-stage,Liver,Liver and Biliary System 59325,SRR11856752,SRX8406851,SRS6719214,SRP264975,PRJNA635397,Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf,GSE151291,Transcriptome Analysis,Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx 175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions. Samples were obtained from 5 separate clutches. Samples were sequenced on NextSeq550 Illumina.,,,,5 dpf liver exposed to 350 mM Ethanol clutch 4,GSM4572118,,tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:25,5 dpf liver exposed to 350 mM Ethanol clutch 4,Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2 v2.1.0 with the parameters “–no novel junctions” and “–G” Accepted bam files were used for counting gene read numbers with HTSeq a 10 s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes,Liver,At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.,Larvae were anesthetized with tricane and 20 35 livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher 15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.,Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection embryos were divided into 30 mL plates 60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.,genotype:Tgfabp10a:ER tdTomato|pool:25|rna qbit concentrationng/ul:30,GSM4572118,GSM4572118: LIV 2ETOH 4; Danio rerio; RNA Seq,GSM4572118,,1,20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar,GEO Accession:GSM4572118,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP264975,,,LIV_2ETOH_4_S17_read2.fastq.gz LIV_2ETOH_4_S17_read1.fastq.gz,fastq fastq,8917001757.0,31312885.0,GSM4572118 r1,0:142.34 1:142.43,A:2376946463;C:2080235380;G:2109059237;T:2349386126;N:1374551,142,142,,,2376946463,2080235380,2109059237,2349386126,1374551,SRX8406851,SRS6719214,SRA1080364,GEO,"Biology, New York University Abu Dhabi",2,0.9451,0.9474,0.05499,0.05486,0.81201,0.81671,0.51433,0.49899,151,151,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,bulk,bulk,,United Arab Emirates,2020-05-27,Multi-stage,Multi-stage,Liver,Liver and Biliary System 59326,SRR11856751,SRX8406850,SRS6719213,SRP264975,PRJNA635397,Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf,GSE151291,Transcriptome Analysis,Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx 175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions. Samples were obtained from 5 separate clutches. Samples were sequenced on NextSeq550 Illumina.,,,,5 dpf liver exposed to 175mM Ethanol clutch 4,GSM4572117,,tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:25,5 dpf liver exposed to 175mM Ethanol clutch 4,Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2 v2.1.0 with the parameters “–no novel junctions” and “–G” Accepted bam files were used for counting gene read numbers with HTSeq a 10 s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes,Liver,At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.,At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.,Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection embryos were divided into 30 mL plates 60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.,genotype:Tgfabp10a:ER tdTomato|pool:25|rna qbit concentrationng/ul:25,GSM4572117,GSM4572117: LIV 1ETOH 4; Danio rerio; RNA Seq,GSM4572117,,1,20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar,GEO Accession:GSM4572117,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP264975,,,LIV_1ETOH_4_S16_read2.fastq.gz LIV_1ETOH_4_S16_read1.fastq.gz,fastq fastq,4433846645.0,15018858.0,GSM4572117 r1,0:147.60 1:147.62,A:1172428411;C:1023473648;G:1076620756;T:1160707870;N:615960,147,147,,,1172428411,1023473648,1076620756,1160707870,615960,SRX8406850,SRS6719213,SRA1080364,GEO,"Biology, New York University Abu Dhabi",2,0.94202,0.94639,0.05176,0.05178,0.8314,0.83907,0.52355,0.51763,143,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,bulk,bulk,,United Arab Emirates,2020-05-27,Multi-stage,Multi-stage,Liver,Liver and Biliary System 59327,SRR11856750,SRX8406849,SRS6719212,SRP264975,PRJNA635397,Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf,GSE151291,Transcriptome Analysis,Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx 175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions. Samples were obtained from 5 separate clutches. Samples were sequenced on NextSeq550 Illumina.,,,,5 dpf Untreated liver clutch 4,GSM4572116,,tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:25,5 dpf Untreated liver clutch 4,Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2 v2.1.0 with the parameters “–no novel junctions” and “–G” Accepted bam files were used for counting gene read numbers with HTSeq a 10 s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes,Liver,At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.,Larvae were anesthetized with tricane and 20 35 livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher 15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.,Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection embryos were divided into 30 mL plates 60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.,genotype:Tgfabp10a:ER tdTomato|pool:25|rna qbit concentrationng/ul:17.58,GSM4572116,GSM4572116: LIV UT 4; Danio rerio; RNA Seq,GSM4572116,,1,20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar,GEO Accession:GSM4572116,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP264975,,,LIV_UT_4_S15_read2.fastq.gz LIV_UT_4_S15_read1.fastq.gz,fastq fastq,6974105009.0,23629447.0,GSM4572116 r1,0:147.55 1:147.59,A:1890464005;C:1566267612;G:1641684624;T:1874721633;N:967135,147,147,,,1890464005,1566267612,1641684624,1874721633,967135,SRX8406849,SRS6719212,SRA1080364,GEO,"Biology, New York University Abu Dhabi",2,0.92362,0.92292,0.13719,0.13717,0.81152,0.82231,0.55749,0.56875,147,147,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,bulk,bulk,,United Arab Emirates,2020-05-27,Multi-stage,Multi-stage,Liver,Liver and Biliary System 59328,SRR11856749,SRX8406848,SRS6719211,SRP264975,PRJNA635397,Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf,GSE151291,Transcriptome Analysis,Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx 175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions. Samples were obtained from 5 separate clutches. Samples were sequenced on NextSeq550 Illumina.,,,,5 dpf liver exposed to 175mM Ethanol clutch 2,GSM4572115,,tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:20,5 dpf liver exposed to 175mM Ethanol clutch 2,Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2 v2.1.0 with the parameters “–no novel junctions” and “–G” Accepted bam files were used for counting gene read numbers with HTSeq a 10 s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes,Liver,At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.,Larvae were anesthetized with tricane and 20 35 livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher 15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.,Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection embryos were divided into 30 mL plates 60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.,genotype:Tgfabp10a:ER tdTomato|pool:20|rna qbit concentrationng/ul:18.1,GSM4572115,GSM4572115: LIV 1ETOH 2; Danio rerio; RNA Seq,GSM4572115,,1,20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar,GEO Accession:GSM4572115,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP264975,,,LIV_1ETOH_2_S13_read2.fastq.gz LIV_1ETOH_2_S13_read1.fastq.gz,fastq fastq,6052855736.0,21232534.0,GSM4572115 r1,0:142.48 1:142.60,A:1597569726;C:1423191233;G:1450513142;T:1580519025;N:1062610,142,142,,,1597569726,1423191233,1450513142,1580519025,1062610,SRX8406848,SRS6719211,SRA1080364,GEO,"Biology, New York University Abu Dhabi",2,0.94966,0.95254,0.04637,0.04576,0.82256,0.82826,0.50683,0.51378,151,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,bulk,bulk,,United Arab Emirates,2020-05-27,Multi-stage,Multi-stage,Liver,Liver and Biliary System 59329,SRR11856748,SRX8406847,SRS6719210,SRP264975,PRJNA635397,Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf,GSE151291,Transcriptome Analysis,Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx 175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions. Samples were obtained from 5 separate clutches. Samples were sequenced on NextSeq550 Illumina.,,,,5 dpf Untreated liver clutch 2,GSM4572114,,tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:20,5 dpf Untreated liver clutch 2,Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2 v2.1.0 with the parameters “–no novel junctions” and “–G” Accepted bam files were used for counting gene read numbers with HTSeq a 10 s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes,Liver,At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.,Larvae were anesthetized with tricane and 20 35 livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher 15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.,At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.,genotype:Tgfabp10a:ER tdTomato|pool:20|rna qbit concentrationng/ul:17.4,GSM4572114,GSM4572114: LIV UT 2; Danio rerio; RNA Seq,GSM4572114,,1,20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar,GEO Accession:GSM4572114,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP264975,,,LIV_UT_2_S12_read1.fastq.gz LIV_UT_2_S12_read2.fastq.gz,fastq fastq,5896961329.0,20821534.0,GSM4572114 r1,0:141.54 1:141.67,A:1594568853;C:1356093648;G:1372236539;T:1573104763;N:957526,141,141,,,1594568853,1356093648,1372236539,1573104763,957526,SRX8406847,SRS6719210,SRA1080364,GEO,"Biology, New York University Abu Dhabi",2,0.94954,0.95239,0.04824,0.0487,0.82363,0.83011,0.55109,0.56041,140,140,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,bulk,bulk,,United Arab Emirates,2020-05-27,Larval,Larval,Liver,Liver and Biliary System 59330,SRR11856747,SRX8406846,SRS6719209,SRP264975,PRJNA635397,Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf,GSE151291,Transcriptome Analysis,Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx 175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions. Samples were obtained from 5 separate clutches. Samples were sequenced on NextSeq550 Illumina.,,,,5 dpf liver exposed to 350 mM Ethanol clutch 1,GSM4572113,,tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:20,5 dpf liver exposed to 350 mM Ethanol clutch 1,Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2 v2.1.0 with the parameters “–no novel junctions” and “–G” Accepted bam files were used for counting gene read numbers with HTSeq a 10 s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes,Liver,At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.,Larvae were anesthetized with tricane and 20 35 livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher 15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.,Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection embryos were divided into 30 mL plates 60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.,genotype:Tgfabp10a:ER tdTomato|pool:20|rna qbit concentrationng/ul:16.4,GSM4572113,GSM4572113: LIV 2ETOH 1; Danio rerio; RNA Seq,GSM4572113,,1,20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar,GEO Accession:GSM4572113,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP264975,,,LIV_2ETOH_1_S11_read2.fastq.gz LIV_2ETOH_1_S11_read1.fastq.gz,fastq fastq,5019400938.0,17774097.0,GSM4572113 r1,0:141.13 1:141.27,A:1309017001;C:1200452411;G:1214953253;T:1294219330;N:758943,141,141,,,1309017001,1200452411,1214953253,1294219330,758943,SRX8406846,SRS6719209,SRA1080364,GEO,"Biology, New York University Abu Dhabi",2,0.95628,0.95923,0.05361,0.05331,0.80417,0.81117,0.45274,0.46681,131,131,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,bulk,bulk,,United Arab Emirates,2020-05-27,Multi-stage,Multi-stage,Liver,Liver and Biliary System 59331,SRR11856746,SRX8406845,SRS6719208,SRP264975,PRJNA635397,Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf,GSE151291,Transcriptome Analysis,Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx 175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions. Samples were obtained from 5 separate clutches. Samples were sequenced on NextSeq550 Illumina.,,,,5 dpf liver exposed to 175 mM Ethanol clutch 1,GSM4572112,,tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:20,5 dpf liver exposed to 175 mM Ethanol clutch 1,Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2 v2.1.0 with the parameters “–no novel junctions” and “–G” Accepted bam files were used for counting gene read numbers with HTSeq a 10 s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes,Liver,At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.,Larvae were anesthetized with tricane and 20 35 livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher 15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.,Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection embryos were divided into 30 mL plates 60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.,genotype:Tgfabp10a:ER tdTomato|pool:20|rna qbit concentrationng/ul:9.34,GSM4572112,GSM4572112: LIV 1ETOH 1; Danio rerio; RNA Seq,GSM4572112,,1,20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar,GEO Accession:GSM4572112,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP264975,,,LIV_1ETOH_1_S10_read2.fastq.gz LIV_1ETOH_1_S10_read1.fastq.gz,fastq fastq,5347733862.0,18832427.0,GSM4572112 r1,0:141.93 1:142.03,A:1419840934;C:1254883122;G:1270564370;T:1401639043;N:806393,141,142,,,1419840934,1254883122,1270564370,1401639043,806393,SRX8406845,SRS6719208,SRA1080364,GEO,"Biology, New York University Abu Dhabi",2,0.96009,0.96098,0.06164,0.06104,0.81785,0.82451,0.51603,0.52553,151,151,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,bulk,bulk,,United Arab Emirates,2020-05-27,Multi-stage,Multi-stage,Liver,Liver and Biliary System 59332,SRR11856745,SRX8406844,SRS6719207,SRP264975,PRJNA635397,Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf,GSE151291,Transcriptome Analysis,Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx 175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions. Samples were obtained from 5 separate clutches. Samples were sequenced on NextSeq550 Illumina.,,,,5 dpf Untreated liver clutch 1,GSM4572111,,tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:20,5 dpf Untreated liver clutch 1,Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2 v2.1.0 with the parameters “–no novel junctions” and “–G” Accepted bam files were used for counting gene read numbers with HTSeq a 10 s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes,Liver,At 96 hpf 4 days post the embryos were collected plates were treated with 1% and 2% Ethanol Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf 9 am the ethanol was washed out 3X and treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.,20 35 livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher 15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.,Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection embryos were divided into 30 mL plates 60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.,genotype:Tgfabp10a:ER tdTomato|pool:20|rna qbit concentrationng/ul:12.5,GSM4572111,GSM4572111: LIV UT 1; Danio rerio; RNA Seq,GSM4572111,,1,20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar,GEO Accession:GSM4572111,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP264975,,,LIV_UT_1_S9_read2.fastq.gz LIV_UT_1_S9_read1.fastq.gz,fastq fastq,4223733224.0,14914881.0,GSM4572111 r1,0:141.51 1:141.68,A:1130300439;C:980426283;G:997735889;T:1114572233;N:698380,141,141,,,1130300439,980426283,997735889,1114572233,698380,SRX8406844,SRS6719207,SRA1080364,GEO,"Biology, New York University Abu Dhabi",2,0.9553,0.95751,0.06169,0.06146,0.80943,0.81923,0.51998,0.50994,151,150,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,bulk,bulk,,United Arab Emirates,2020-05-27,Multi-stage,Multi-stage,Liver,Liver and Biliary System 61797,SRR13697048,SRX10086241,SRS8244029,SRP290950,PRJNA674050,RNA Seq of 120 hpf control sibling and mutant uhrf1 hi272 zebrafish livers,GSE160710,Transcriptome Analysis,"In this study we performed RNA seq on 5 dpf livers of uhrf1 hi272 mutants and phenotypically wild type siblings collected at 120 hpf. Overall design: ""To perform RNA seq on pools of uhrf1 hi272 mutant and sibling livers at 5 dpf we collected between 15 30 livers from 5 independent clutches of uhrf1 hi272 mutants and their phenotypically WT siblings which were sorted based on phenotype following immobilization using tricaine. We extracted total RNA from livers to generate libraries as per TRIzol protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2. Total RNA was DNAseI treated depleted for ribosomal RNA by using RiboZero and used for Illumina Library prep. RNA was analyzed on an Agilent 2100 Bioanalyzer. Illumina TruSeq RNA sample preparation version 2 protocol with Ribo Zero Gold. cDNA libraries were sequenced on the Illumina NextSeq500 platform to obtain 75 bp single end reads.",parent bioproject:PRJNA674302,pubmed:33854502,,120hpf uhrf1 hi272 mutant livers clutch 5 14 livers,GSM5077773,,source name:embryo livers|background:ABNYU|tissue:14 livers|developmental stage:120hpf|genotype:uhrf1 hi272 mutant|genotype:fabp10:CAAX EGFP transgenic liver,120hpf uhrf1 hi272 mutant livers clutch 5 14 livers,Illumina Casava software used for basecalling. Sequencing quality was assessed by using MultiQC v1.7 Trimmed read were mapped to GRCz10 whole genome using tophat2 with default parameters Alignment by HISTA2 with default parameters only paired reads are aligned and multiple alignments are kept Gene expression is counted in the exon of ensemble gene annotation TE quantification was taking the RepeatMasker annotation of danRer10 from UCSC table browser with HTseq in union mode Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V3.12 Genome build: GRCz10 Supplementary files format and content: csv files for raw reads count of genes and TEs,embryo livers,,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,,background:ABNYU|tissue:14 livers|developmental stage:120hpf|genotype:uhrf1 hi272 mutant|genotype:fabp10:CAAX EGFP transgenic liver,GSM5077773,GSM5077773: 120hpf uhrf1 hi272 mutant livers clutch 5 14 livers; Danio rerio; RNA Seq,GSM5077773,,1,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,GEO Accession:GSM5077773,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP290950,,,Liv5_Hi272_Mut_S21_read1.fastq.gz Liv5_Hi272_Mut_S21_read2.fastq.gz,fastq fastq,3001456956.0,10643687.0,GSM5077773 r1,0:140.67 1:141.33,A:864266108;C:644564956;G:687699500;T:804319968;N:606424,140,141,,,864266108,644564956,687699500,804319968,606424,SRX10086241,SRS8244029,SRA1153151,GEO,"Biology, New York University Abu Dhabi",2,0.69604,0.68063,0.16947,0.16547,0.79722,0.80606,0.54332,0.53758,139,139,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Arab Emirates,2021-02-12,Larval,Larval,Liver,Liver and Biliary System 61798,SRR13697047,SRX10086240,SRS8244028,SRP290950,PRJNA674050,RNA Seq of 120 hpf control sibling and mutant uhrf1 hi272 zebrafish livers,GSE160710,Transcriptome Analysis,"In this study we performed RNA seq on 5 dpf livers of uhrf1 hi272 mutants and phenotypically wild type siblings collected at 120 hpf. Overall design: ""To perform RNA seq on pools of uhrf1 hi272 mutant and sibling livers at 5 dpf we collected between 15 30 livers from 5 independent clutches of uhrf1 hi272 mutants and their phenotypically WT siblings which were sorted based on phenotype following immobilization using tricaine. We extracted total RNA from livers to generate libraries as per TRIzol protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2. Total RNA was DNAseI treated depleted for ribosomal RNA by using RiboZero and used for Illumina Library prep. RNA was analyzed on an Agilent 2100 Bioanalyzer. Illumina TruSeq RNA sample preparation version 2 protocol with Ribo Zero Gold. cDNA libraries were sequenced on the Illumina NextSeq500 platform to obtain 75 bp single end reads.",parent bioproject:PRJNA674302,pubmed:33854502,,120hpf uhrf1 hi272 sibling control livers clutch 5 15 livers,GSM5077772,,source name:embryo livers|background:ABNYU|tissue:15 livers|developmental stage:120hpf|genotype:uhrf1 hi272 sibling control|genotype:fabp10:CAAX EGFP transgenic liver,120hpf uhrf1 hi272 sibling control livers clutch 5 15 livers,Illumina Casava software used for basecalling. Sequencing quality was assessed by using MultiQC v1.7 Trimmed read were mapped to GRCz10 whole genome using tophat2 with default parameters Alignment by HISTA2 with default parameters only paired reads are aligned and multiple alignments are kept Gene expression is counted in the exon of ensemble gene annotation TE quantification was taking the RepeatMasker annotation of danRer10 from UCSC table browser with HTseq in union mode Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V3.12 Genome build: GRCz10 Supplementary files format and content: csv files for raw reads count of genes and TEs,embryo livers,,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,,background:ABNYU|tissue:15 livers|developmental stage:120hpf|genotype:uhrf1 hi272 sibling control|genotype:fabp10:CAAX EGFP transgenic liver,GSM5077772,GSM5077772: 120hpf uhrf1 hi272 sibling control livers clutch 5 15 livers; Danio rerio; RNA Seq,GSM5077772,,1,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,GEO Accession:GSM5077772,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP290950,,,Liv5_Hi272_Cont_S20_read1.fastq.gz Liv5_Hi272_Cont_S20_read2.fastq.gz,fastq fastq,3734309081.0,13148713.0,GSM5077772 r1,0:141.78 1:142.22,A:1010708383;C:862990780;G:872057106;T:987875074;N:677738,141,142,,,1010708383,862990780,872057106,987875074,677738,SRX10086240,SRS8244028,SRA1153151,GEO,"Biology, New York University Abu Dhabi",2,0.87372,0.87151,0.20099,0.20022,0.80908,0.81598,0.44856,0.54901,151,151,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Arab Emirates,2021-02-12,Larval,Larval,Liver,Liver and Biliary System 61799,SRR13697046,SRX10086239,SRS8244027,SRP290950,PRJNA674050,RNA Seq of 120 hpf control sibling and mutant uhrf1 hi272 zebrafish livers,GSE160710,Transcriptome Analysis,"In this study we performed RNA seq on 5 dpf livers of uhrf1 hi272 mutants and phenotypically wild type siblings collected at 120 hpf. Overall design: ""To perform RNA seq on pools of uhrf1 hi272 mutant and sibling livers at 5 dpf we collected between 15 30 livers from 5 independent clutches of uhrf1 hi272 mutants and their phenotypically WT siblings which were sorted based on phenotype following immobilization using tricaine. We extracted total RNA from livers to generate libraries as per TRIzol protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2. Total RNA was DNAseI treated depleted for ribosomal RNA by using RiboZero and used for Illumina Library prep. RNA was analyzed on an Agilent 2100 Bioanalyzer. Illumina TruSeq RNA sample preparation version 2 protocol with Ribo Zero Gold. cDNA libraries were sequenced on the Illumina NextSeq500 platform to obtain 75 bp single end reads.",parent bioproject:PRJNA674302,pubmed:33854502,,120hpf uhrf1 hi272 mutant livers clutch 4 17 livers,GSM5077771,,source name:embryo livers|background:ABNYU|tissue:17 livers|developmental stage:120hpf|genotype:uhrf1 hi272 mutant|genotype:fabp10:CAAX EGFP transgenic liver,120hpf uhrf1 hi272 mutant livers clutch 4 17 livers,Illumina Casava software used for basecalling. Sequencing quality was assessed by using MultiQC v1.7 Trimmed read were mapped to GRCz10 whole genome using tophat2 with default parameters Alignment by HISTA2 with default parameters only paired reads are aligned and multiple alignments are kept Gene expression is counted in the exon of ensemble gene annotation TE quantification was taking the RepeatMasker annotation of danRer10 from UCSC table browser with HTseq in union mode Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V3.12 Genome build: GRCz10 Supplementary files format and content: csv files for raw reads count of genes and TEs,embryo livers,,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,,background:ABNYU|tissue:17 livers|developmental stage:120hpf|genotype:uhrf1 hi272 mutant|genotype:fabp10:CAAX EGFP transgenic liver,GSM5077771,GSM5077771: 120hpf uhrf1 hi272 mutant livers clutch 4 17 livers; Danio rerio; RNA Seq,GSM5077771,,1,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,GEO Accession:GSM5077771,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP290950,,,Liv4_Hi272_Mut_S19_read1.fastq.gz Liv4_Hi272_Mut_S19_read2.fastq.gz,fastq fastq,3276151748.0,11617920.0,GSM5077771 r1,0:140.70 1:141.29,A:977455620;C:673145853;G:726449225;T:898362858;N:738192,140,141,,,977455620,673145853,726449225,898362858,738192,SRX10086239,SRS8244027,SRA1153151,GEO,"Biology, New York University Abu Dhabi",2,0.68912,0.67139,0.1657,0.16193,0.79764,0.80803,0.53779,0.53598,150,116,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Arab Emirates,2021-02-12,Larval,Larval,Liver,Liver and Biliary System 61800,SRR13697045,SRX10086238,SRS8244026,SRP290950,PRJNA674050,RNA Seq of 120 hpf control sibling and mutant uhrf1 hi272 zebrafish livers,GSE160710,Transcriptome Analysis,"In this study we performed RNA seq on 5 dpf livers of uhrf1 hi272 mutants and phenotypically wild type siblings collected at 120 hpf. Overall design: ""To perform RNA seq on pools of uhrf1 hi272 mutant and sibling livers at 5 dpf we collected between 15 30 livers from 5 independent clutches of uhrf1 hi272 mutants and their phenotypically WT siblings which were sorted based on phenotype following immobilization using tricaine. We extracted total RNA from livers to generate libraries as per TRIzol protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2. Total RNA was DNAseI treated depleted for ribosomal RNA by using RiboZero and used for Illumina Library prep. RNA was analyzed on an Agilent 2100 Bioanalyzer. Illumina TruSeq RNA sample preparation version 2 protocol with Ribo Zero Gold. cDNA libraries were sequenced on the Illumina NextSeq500 platform to obtain 75 bp single end reads.",parent bioproject:PRJNA674302,pubmed:33854502,,120hpf uhrf1 hi272 sibling control livers clutch 4 15 livers,GSM5077770,,source name:embryo livers|background:ABNYU|tissue:15 livers|developmental stage:120hpf|genotype:uhrf1 hi272 sibling control|genotype:fabp10:CAAX EGFP transgenic liver,120hpf uhrf1 hi272 sibling control livers clutch 4 15 livers,Illumina Casava software used for basecalling. Sequencing quality was assessed by using MultiQC v1.7 Trimmed read were mapped to GRCz10 whole genome using tophat2 with default parameters Alignment by HISTA2 with default parameters only paired reads are aligned and multiple alignments are kept Gene expression is counted in the exon of ensemble gene annotation TE quantification was taking the RepeatMasker annotation of danRer10 from UCSC table browser with HTseq in union mode Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V3.12 Genome build: GRCz10 Supplementary files format and content: csv files for raw reads count of genes and TEs,embryo livers,,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,,background:ABNYU|tissue:15 livers|developmental stage:120hpf|genotype:uhrf1 hi272 sibling control|genotype:fabp10:CAAX EGFP transgenic liver,GSM5077770,GSM5077770: 120hpf uhrf1 hi272 sibling control livers clutch 4 15 livers; Danio rerio; RNA Seq,GSM5077770,,1,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,GEO Accession:GSM5077770,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP290950,,,Liv4_Hi272_Cont_S18_read1.fastq.gz Liv4_Hi272_Cont_S18_read2.fastq.gz,fastq fastq,4150092990.0,14452288.0,GSM5077770 r1,0:143.40 1:143.76,A:1133667805;C:947360423;G:959413467;T:1108872991;N:778304,143,143,,,1133667805,947360423,959413467,1108872991,778304,SRX10086238,SRS8244026,SRA1153151,GEO,"Biology, New York University Abu Dhabi",2,0.8869,0.88472,0.19855,0.19906,0.80403,0.81103,0.53957,0.54379,151,151,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Arab Emirates,2021-02-12,Larval,Larval,Liver,Liver and Biliary System 61801,SRR13697044,SRX10086237,SRS8244025,SRP290950,PRJNA674050,RNA Seq of 120 hpf control sibling and mutant uhrf1 hi272 zebrafish livers,GSE160710,Transcriptome Analysis,"In this study we performed RNA seq on 5 dpf livers of uhrf1 hi272 mutants and phenotypically wild type siblings collected at 120 hpf. Overall design: ""To perform RNA seq on pools of uhrf1 hi272 mutant and sibling livers at 5 dpf we collected between 15 30 livers from 5 independent clutches of uhrf1 hi272 mutants and their phenotypically WT siblings which were sorted based on phenotype following immobilization using tricaine. We extracted total RNA from livers to generate libraries as per TRIzol protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2. Total RNA was DNAseI treated depleted for ribosomal RNA by using RiboZero and used for Illumina Library prep. RNA was analyzed on an Agilent 2100 Bioanalyzer. Illumina TruSeq RNA sample preparation version 2 protocol with Ribo Zero Gold. cDNA libraries were sequenced on the Illumina NextSeq500 platform to obtain 75 bp single end reads.",parent bioproject:PRJNA674302,pubmed:33854502,,120hpf uhrf1 hi272 mutant livers clutch 3 20 livers,GSM5077769,,source name:embryo livers|background:ABNYU|tissue:20 livers|developmental stage:120hpf|genotype:uhrf1 hi272 mutant|genotype:fabp10:CAAX EGFP transgenic liver,120hpf uhrf1 hi272 mutant livers clutch 3 20 livers,Illumina Casava software used for basecalling. Sequencing quality was assessed by using MultiQC v1.7 Trimmed read were mapped to GRCz10 whole genome using tophat2 with default parameters Alignment by HISTA2 with default parameters only paired reads are aligned and multiple alignments are kept Gene expression is counted in the exon of ensemble gene annotation TE quantification was taking the RepeatMasker annotation of danRer10 from UCSC table browser with HTseq in union mode Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V3.12 Genome build: GRCz10 Supplementary files format and content: csv files for raw reads count of genes and TEs,embryo livers,,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,,background:ABNYU|tissue:20 livers|developmental stage:120hpf|genotype:uhrf1 hi272 mutant|genotype:fabp10:CAAX EGFP transgenic liver,GSM5077769,GSM5077769: 120hpf uhrf1 hi272 mutant livers clutch 3 20 livers; Danio rerio; RNA Seq,GSM5077769,,1,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,GEO Accession:GSM5077769,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP290950,,,Liv3_Hi272_Mut_S17_read1.fastq.gz Liv3_Hi272_Mut_S17_read2.fastq.gz,fastq fastq,3702889415.0,12922948.0,GSM5077769 r1,0:143.09 1:143.45,A:1009880299;C:851478850;G:857751462;T:983102909;N:675895,143,143,,,1009880299,851478850,857751462,983102909,675895,SRX10086237,SRS8244025,SRA1153151,GEO,"Biology, New York University Abu Dhabi",2,0.88804,0.89108,0.20284,0.20421,0.76268,0.77078,0.45927,0.55145,151,150,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Arab Emirates,2021-02-12,Larval,Larval,Liver,Liver and Biliary System 61802,SRR13697043,SRX10086236,SRS8244024,SRP290950,PRJNA674050,RNA Seq of 120 hpf control sibling and mutant uhrf1 hi272 zebrafish livers,GSE160710,Transcriptome Analysis,"In this study we performed RNA seq on 5 dpf livers of uhrf1 hi272 mutants and phenotypically wild type siblings collected at 120 hpf. Overall design: ""To perform RNA seq on pools of uhrf1 hi272 mutant and sibling livers at 5 dpf we collected between 15 30 livers from 5 independent clutches of uhrf1 hi272 mutants and their phenotypically WT siblings which were sorted based on phenotype following immobilization using tricaine. We extracted total RNA from livers to generate libraries as per TRIzol protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2. Total RNA was DNAseI treated depleted for ribosomal RNA by using RiboZero and used for Illumina Library prep. RNA was analyzed on an Agilent 2100 Bioanalyzer. Illumina TruSeq RNA sample preparation version 2 protocol with Ribo Zero Gold. cDNA libraries were sequenced on the Illumina NextSeq500 platform to obtain 75 bp single end reads.",parent bioproject:PRJNA674302,pubmed:33854502,,120hpf uhrf1 hi272 sibling control livers clutch 3 15 livers,GSM5077768,,source name:embryo livers|background:ABNYU|tissue:15 livers|developmental stage:120hpf|genotype:uhrf1 hi272 sibling control|genotype:fabp10:CAAX EGFP transgenic liver,120hpf uhrf1 hi272 sibling control livers clutch 3 15 livers,Illumina Casava software used for basecalling. Sequencing quality was assessed by using MultiQC v1.7 Trimmed read were mapped to GRCz10 whole genome using tophat2 with default parameters Alignment by HISTA2 with default parameters only paired reads are aligned and multiple alignments are kept Gene expression is counted in the exon of ensemble gene annotation TE quantification was taking the RepeatMasker annotation of danRer10 from UCSC table browser with HTseq in union mode Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V3.12 Genome build: GRCz10 Supplementary files format and content: csv files for raw reads count of genes and TEs,embryo livers,,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,,background:ABNYU|tissue:15 livers|developmental stage:120hpf|genotype:uhrf1 hi272 sibling control|genotype:fabp10:CAAX EGFP transgenic liver,GSM5077768,GSM5077768: 120hpf uhrf1 hi272 sibling control livers clutch 3 15 livers; Danio rerio; RNA Seq,GSM5077768,,1,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,GEO Accession:GSM5077768,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP290950,,,Liv3_Hi272_Cont_S16_read1.fastq.gz Liv3_Hi272_Cont_S16_read2.fastq.gz,fastq fastq,4268554487.0,14785222.0,GSM5077768 r1,0:144.19 1:144.52,A:1141012338;C:998019786;G:1007986995;T:1120710703;N:824665,144,144,,,1141012338,998019786,1007986995,1120710703,824665,SRX10086236,SRS8244024,SRA1153151,GEO,"Biology, New York University Abu Dhabi",2,0.88149,0.88048,0.18716,0.18617,0.81655,0.82382,0.56321,0.56447,151,151,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Arab Emirates,2021-02-12,Larval,Larval,Liver,Liver and Biliary System 61803,SRR13697042,SRX10086235,SRS8244023,SRP290950,PRJNA674050,RNA Seq of 120 hpf control sibling and mutant uhrf1 hi272 zebrafish livers,GSE160710,Transcriptome Analysis,"In this study we performed RNA seq on 5 dpf livers of uhrf1 hi272 mutants and phenotypically wild type siblings collected at 120 hpf. Overall design: ""To perform RNA seq on pools of uhrf1 hi272 mutant and sibling livers at 5 dpf we collected between 15 30 livers from 5 independent clutches of uhrf1 hi272 mutants and their phenotypically WT siblings which were sorted based on phenotype following immobilization using tricaine. We extracted total RNA from livers to generate libraries as per TRIzol protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2. Total RNA was DNAseI treated depleted for ribosomal RNA by using RiboZero and used for Illumina Library prep. RNA was analyzed on an Agilent 2100 Bioanalyzer. Illumina TruSeq RNA sample preparation version 2 protocol with Ribo Zero Gold. cDNA libraries were sequenced on the Illumina NextSeq500 platform to obtain 75 bp single end reads.",parent bioproject:PRJNA674302,pubmed:33854502,,120hpf uhrf1 hi272 mutant livers clutch 2 25 livers,GSM5077767,,source name:embryo livers|background:ABNYU|tissue:25 livers|developmental stage:120hpf|genotype:uhrf1 hi272 mutant|genotype:fabp10:CAAX EGFP transgenic liver,120hpf uhrf1 hi272 mutant livers clutch 2 25 livers,Illumina Casava software used for basecalling. Sequencing quality was assessed by using MultiQC v1.7 Trimmed read were mapped to GRCz10 whole genome using tophat2 with default parameters Alignment by HISTA2 with default parameters only paired reads are aligned and multiple alignments are kept Gene expression is counted in the exon of ensemble gene annotation TE quantification was taking the RepeatMasker annotation of danRer10 from UCSC table browser with HTseq in union mode Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V3.12 Genome build: GRCz10 Supplementary files format and content: csv files for raw reads count of genes and TEs,embryo livers,,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,,background:ABNYU|tissue:25 livers|developmental stage:120hpf|genotype:uhrf1 hi272 mutant|genotype:fabp10:CAAX EGFP transgenic liver,GSM5077767,GSM5077767: 120hpf uhrf1 hi272 mutant livers clutch 2 25 livers; Danio rerio; RNA Seq,GSM5077767,,1,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,GEO Accession:GSM5077767,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP290950,,,Liv2_Hi272_Mut_S15_read1.fastq.gz Liv2_Hi272_Mut_S15_read2.fastq.gz,fastq fastq,4597310328.0,15948140.0,GSM5077767 r1,0:143.86 1:144.41,A:1281515349;C:1027622166;G:1039158272;T:1248185853;N:828688,143,144,,,1281515349,1027622166,1039158272,1248185853,828688,SRX10086235,SRS8244023,SRA1153151,GEO,"Biology, New York University Abu Dhabi",2,0.88418,0.88398,0.20254,0.20226,0.77177,0.7893,0.54539,0.5437,151,151,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Arab Emirates,2021-02-12,Larval,Larval,Liver,Liver and Biliary System 61804,SRR13697041,SRX10086234,SRS8244022,SRP290950,PRJNA674050,RNA Seq of 120 hpf control sibling and mutant uhrf1 hi272 zebrafish livers,GSE160710,Transcriptome Analysis,"In this study we performed RNA seq on 5 dpf livers of uhrf1 hi272 mutants and phenotypically wild type siblings collected at 120 hpf. Overall design: ""To perform RNA seq on pools of uhrf1 hi272 mutant and sibling livers at 5 dpf we collected between 15 30 livers from 5 independent clutches of uhrf1 hi272 mutants and their phenotypically WT siblings which were sorted based on phenotype following immobilization using tricaine. We extracted total RNA from livers to generate libraries as per TRIzol protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2. Total RNA was DNAseI treated depleted for ribosomal RNA by using RiboZero and used for Illumina Library prep. RNA was analyzed on an Agilent 2100 Bioanalyzer. Illumina TruSeq RNA sample preparation version 2 protocol with Ribo Zero Gold. cDNA libraries were sequenced on the Illumina NextSeq500 platform to obtain 75 bp single end reads.",parent bioproject:PRJNA674302,pubmed:33854502,,120hpf uhrf1 hi272 sibling control livers clutch 2 15 livers,GSM5077766,,source name:embryo livers|background:ABNYU|tissue:15 livers|developmental stage:120hpf|genotype:uhrf1 hi272 sibling control|genotype:fabp10:CAAX EGFP transgenic liver,120hpf uhrf1 hi272 sibling control livers clutch 2 15 livers,Illumina Casava software used for basecalling. Sequencing quality was assessed by using MultiQC v1.7 Trimmed read were mapped to GRCz10 whole genome using tophat2 with default parameters Alignment by HISTA2 with default parameters only paired reads are aligned and multiple alignments are kept Gene expression is counted in the exon of ensemble gene annotation TE quantification was taking the RepeatMasker annotation of danRer10 from UCSC table browser with HTseq in union mode Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V3.12 Genome build: GRCz10 Supplementary files format and content: csv files for raw reads count of genes and TEs,embryo livers,,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,,background:ABNYU|tissue:15 livers|developmental stage:120hpf|genotype:uhrf1 hi272 sibling control|genotype:fabp10:CAAX EGFP transgenic liver,GSM5077766,GSM5077766: 120hpf uhrf1 hi272 sibling control livers clutch 2 15 livers; Danio rerio; RNA Seq,GSM5077766,,1,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,GEO Accession:GSM5077766,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP290950,,,Liv2_Hi272_Cont_S13_read1.fastq.gz Liv2_Hi272_Cont_S13_read2.fastq.gz,fastq fastq,4251128659.0,14886682.0,GSM5077766 r1,0:142.59 1:142.97,A:1189485827;C:942762954;G:979088501;T:1138917097;N:874280,142,142,,,1189485827,942762954,979088501,1138917097,874280,SRX10086234,SRS8244022,SRA1153151,GEO,"Biology, New York University Abu Dhabi",2,0.81696,0.80258,0.1714,0.16858,0.78926,0.7973,0.54286,0.54297,151,151,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Arab Emirates,2021-02-12,Larval,Larval,Liver,Liver and Biliary System 61805,SRR13697040,SRX10086233,SRS8244021,SRP290950,PRJNA674050,RNA Seq of 120 hpf control sibling and mutant uhrf1 hi272 zebrafish livers,GSE160710,Transcriptome Analysis,"In this study we performed RNA seq on 5 dpf livers of uhrf1 hi272 mutants and phenotypically wild type siblings collected at 120 hpf. Overall design: ""To perform RNA seq on pools of uhrf1 hi272 mutant and sibling livers at 5 dpf we collected between 15 30 livers from 5 independent clutches of uhrf1 hi272 mutants and their phenotypically WT siblings which were sorted based on phenotype following immobilization using tricaine. We extracted total RNA from livers to generate libraries as per TRIzol protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2. Total RNA was DNAseI treated depleted for ribosomal RNA by using RiboZero and used for Illumina Library prep. RNA was analyzed on an Agilent 2100 Bioanalyzer. Illumina TruSeq RNA sample preparation version 2 protocol with Ribo Zero Gold. cDNA libraries were sequenced on the Illumina NextSeq500 platform to obtain 75 bp single end reads.",parent bioproject:PRJNA674302,pubmed:33854502,,120hpf uhrf1 hi272 mutant livers clutch 1 22 livers,GSM5077765,,source name:embryo livers|background:ABNYU|tissue:22 livers|developmental stage:120hpf|genotype:uhrf1 hi272 mutant|genotype:fabp10:CAAX EGFP transgenic liver,120hpf uhrf1 hi272 mutant livers clutch 1 22 livers,Illumina Casava software used for basecalling. Sequencing quality was assessed by using MultiQC v1.7 Trimmed read were mapped to GRCz10 whole genome using tophat2 with default parameters Alignment by HISTA2 with default parameters only paired reads are aligned and multiple alignments are kept Gene expression is counted in the exon of ensemble gene annotation TE quantification was taking the RepeatMasker annotation of danRer10 from UCSC table browser with HTseq in union mode Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V3.12 Genome build: GRCz10 Supplementary files format and content: csv files for raw reads count of genes and TEs,embryo livers,,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,,background:ABNYU|tissue:22 livers|developmental stage:120hpf|genotype:uhrf1 hi272 mutant|genotype:fabp10:CAAX EGFP transgenic liver,GSM5077765,GSM5077765: 120hpf uhrf1 hi272 mutant livers clutch 1 22 livers; Danio rerio; RNA Seq,GSM5077765,,1,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,GEO Accession:GSM5077765,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP290950,,,Liv1_Hi272_Mut_S14_read1.fastq.gz Liv1_Hi272_Mut_S14_read2.fastq.gz,fastq fastq,3949222292.0,13997773.0,GSM5077765 r1,0:140.79 1:141.34,A:1045521928;C:936306390;G:944175682;T:1022498070;N:720222,140,141,,,1045521928,936306390,944175682,1022498070,720222,SRX10086233,SRS8244021,SRA1153151,GEO,"Biology, New York University Abu Dhabi",2,0.88992,0.89254,0.18597,0.18591,0.82256,0.83132,0.46333,0.55432,113,113,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Arab Emirates,2021-02-12,Larval,Larval,Liver,Liver and Biliary System 61806,SRR13697039,SRX10086232,SRS8244020,SRP290950,PRJNA674050,RNA Seq of 120 hpf control sibling and mutant uhrf1 hi272 zebrafish livers,GSE160710,Transcriptome Analysis,"In this study we performed RNA seq on 5 dpf livers of uhrf1 hi272 mutants and phenotypically wild type siblings collected at 120 hpf. Overall design: ""To perform RNA seq on pools of uhrf1 hi272 mutant and sibling livers at 5 dpf we collected between 15 30 livers from 5 independent clutches of uhrf1 hi272 mutants and their phenotypically WT siblings which were sorted based on phenotype following immobilization using tricaine. We extracted total RNA from livers to generate libraries as per TRIzol protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2. Total RNA was DNAseI treated depleted for ribosomal RNA by using RiboZero and used for Illumina Library prep. RNA was analyzed on an Agilent 2100 Bioanalyzer. Illumina TruSeq RNA sample preparation version 2 protocol with Ribo Zero Gold. cDNA libraries were sequenced on the Illumina NextSeq500 platform to obtain 75 bp single end reads.",parent bioproject:PRJNA674302,pubmed:33854502,,120hpf uhrf1 hi272 sibling control livers clutch 1 15 livers,GSM5077764,,source name:embryo livers|background:ABNYU|tissue:15 livers|developmental stage:120hpf|genotype:uhrf1 hi272 sibling control|genotype:fabp10:CAAX EGFP transgenic liver,120hpf uhrf1 hi272 sibling control livers clutch 1 15 livers,Illumina Casava software used for basecalling. Sequencing quality was assessed by using MultiQC v1.7 Trimmed read were mapped to GRCz10 whole genome using tophat2 with default parameters Alignment by HISTA2 with default parameters only paired reads are aligned and multiple alignments are kept Gene expression is counted in the exon of ensemble gene annotation TE quantification was taking the RepeatMasker annotation of danRer10 from UCSC table browser with HTseq in union mode Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V3.12 Genome build: GRCz10 Supplementary files format and content: csv files for raw reads count of genes and TEs,embryo livers,,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,,background:ABNYU|tissue:15 livers|developmental stage:120hpf|genotype:uhrf1 hi272 sibling control|genotype:fabp10:CAAX EGFP transgenic liver,GSM5077764,GSM5077764: 120hpf uhrf1 hi272 sibling control livers clutch 1 15 livers; Danio rerio; RNA Seq,GSM5077764,,1,14 25 livers from 5 dpf 120 hpf zebrafish embryos were dissected pooled per library preparation. RNA extraction was carried out following stadard triZOL protocol https://www.thermofisher.com/ae/en/home/references/protocols/nucleic acid purification and analysis/mrna protocols/trizol plus rna purification kit.html#prot2.,GEO Accession:GSM5077764,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP290950,,,Liv1_Hi272_Cont_S12_read1.fastq.gz Liv1_Hi272_Cont_S12_read2.fastq.gz,fastq fastq,4337753855.0,15383844.0,GSM5077764 r1,0:140.72 1:141.24,A:1148991433;C:1024314911;G:1038408589;T:1125174452;N:864470,140,141,,,1148991433,1024314911,1038408589,1125174452,864470,SRX10086232,SRS8244020,SRA1153151,GEO,"Biology, New York University Abu Dhabi",2,0.86837,0.86761,0.20248,0.20193,0.81527,0.82359,0.45034,0.55409,151,151,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,ribozero,bulk,bulk,bulk,,United Arab Emirates,2021-02-12,Larval,Larval,Liver,Liver and Biliary System 68202,SRR17658919,SRX13826963,SRS11706208,SRP355728,PRJNA798522,Bulk RNA Seq Reveals Toxicity effects of Zinc in the liver of zebra fish,PRJNA798522,Other,Our results showed environment related zinc contamination could change zebrafish nature behaviors and exhibit heterogeneous toxicity,,,,CLF duplication 3,Ctrl3 liver female 3,,strain:AB|dev stage:adult12|sex:female|tissue:liver12|BioSampleModel:Model organism or animal,,,,,,,,,CLF duplication 3,Ctrl3 liver female 3,Ctrl3 liver female 3,Ctrl3 liver female 3,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP355728,,,CLF3_1.fq.gz CLF3_2.fq.gz,fastq fastq,6712722900.0,22375743.0,CLF3 1.fq.gz,0:150 1:150,A:1783792403;C:1575082041;G:1585315564;T:1767759802;N:773090,150,150,,,1783792403,1575082041,1585315564,1767759802,773090,SRX13826963,SRS11706208,SRA1358625,Chinese Academy of Fishery Sciences|Freshwater Fisheries Research Center,Chinese Academy of Fishery Sciences,2,0.9662,0.96595,0.01762,0.01789,0.8887,0.88828,0.15778,0.15829,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2022-01-19,Adult,Adult,Liver,Liver and Biliary System 68203,SRR17658920,SRX13826962,SRS11706207,SRP355728,PRJNA798522,Bulk RNA Seq Reveals Toxicity effects of Zinc in the liver of zebra fish,PRJNA798522,Other,Our results showed environment related zinc contamination could change zebrafish nature behaviors and exhibit heterogeneous toxicity,,,,Z1LF duplication 1,Zincone1 liver female 1,,strain:AB|dev stage:adult13|sex:female|tissue:liver13|BioSampleModel:Model organism or animal,,,,,,,,,Z1LF duplication 1,Zincone1 liver female 1,Zincone1 liver female 1,Zincone1 liver female 1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP355728,,,Z1LF1_2.fq.gz Z1LF1_1.fq.gz,fastq fastq,6782491200.0,22608304.0,Z1LF1 1.fq.gz,0:150 1:150,A:1789405575;C:1606823947;G:1605287980;T:1780124329;N:849369,150,150,,,1789405575,1606823947,1605287980,1780124329,849369,SRX13826962,SRS11706207,SRA1358625,Chinese Academy of Fishery Sciences|Freshwater Fisheries Research Center,Chinese Academy of Fishery Sciences,2,0.96811,0.9688,0.02477,0.02493,0.88345,0.88316,0.13943,0.13875,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2022-01-19,Adult,Adult,Liver,Liver and Biliary System 68204,SRR17658921,SRX13826961,SRS11706206,SRP355728,PRJNA798522,Bulk RNA Seq Reveals Toxicity effects of Zinc in the liver of zebra fish,PRJNA798522,Other,Our results showed environment related zinc contamination could change zebrafish nature behaviors and exhibit heterogeneous toxicity,,,,Z1LF duplication 2,Zincone2 liver female 2,,strain:AB|dev stage:adult14|sex:female|tissue:liver14|BioSampleModel:Model organism or animal,,,,,,,,,Z1LF duplication 2,Zincone2 liver female 2,Zincone2 liver female 2,Zincone2 liver female 2,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP355728,,,Z1LF2_1.fq.gz Z1LF2_2.fq.gz,fastq fastq,6742673100.0,22475577.0,Z1LF2 1.fq.gz,0:150 1:150,A:1792296919;C:1582977645;G:1582194285;T:1784406986;N:797265,150,150,,,1792296919,1582977645,1582194285,1784406986,797265,SRX13826961,SRS11706206,SRA1358625,Chinese Academy of Fishery Sciences|Freshwater Fisheries Research Center,Chinese Academy of Fishery Sciences,2,0.96512,0.96401,0.02268,0.02287,0.8784,0.87868,0.1342,0.13433,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,bulk,bulk,,China,2022-01-19,Adult,Adult,Liver,Liver and Biliary System