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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
53190 SRR9707990 SRX6465904 SRS5126670 SRP215269 PRJNA555341 Obesity synergizes with HBx Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq] GSE134495 Transcriptome Analysis Previous studies have identified liver cancer associated to NASH diabetes obesity and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover the results showed metabolism and genetic information processing including the pathways of fatty acid metabolism steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type HBxp53 Srcp53 and HBx Srcp53 zebrafish in normal overfed and high fat diet. RNA was prepared from liver and analyzed by RNAseq. parent bioproject:PRJNA555327 pubmed:31795276   8week WT NOR sample 1 GSM3954308   source name:8week WT Normal diet|strain/background:AB|genotype/variation:WT|tissue:Liver|diet:Normal diet 8week WT NOR sample 1 Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters mm dta x 1 2 S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package. 8week WT Normal diet The three mpf of four types of fish were fed using three different feeding methods: normal diet overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily and high fat diet fish food one spoon about 0.22g three times daily. For 8 weeks the zebrafishes were sacrificed and liver specimens were collected. Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The AB zebrafish strain Danio rerio Tgfabp10a:src p53 Tgfabp10a:HBx p53 and Tgfabp10a:HBx src p53 were used and growth for 8 weeks. strain/background:AB|genotype/variation:WT|tissue:Liver|diet:Normal diet GSM3954308 GSM3954308: 8week WT NOR sample 1; Danio rerio; RNA Seq GSM3954308   1 Total RNA was isolated by NucleoSpin® RNA kit MACHEREY NAGEL US following the manufacturer manual and RNA samples was eluted in 40 μl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H and DNA Polymerase I and RNase H respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next the adaptor ligated cDNA were treated with 3 μl USER Enzyme before PCR. Then the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. GEO Accession:GSM3954308 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP215269     WT_NOR2_1.fq.gz WT_NOR2_2.fq.gz fastq fastq 4215976200.0 14053254.0 GSM3954308 r1 0:150 1:150 A:1099428840;C:1005939535;G:1020758972;T:1089047539;N:801314 150 150     1099428840 1005939535 1020758972 1089047539 801314 SRX6465904 SRS5126670 SRA922815 GEO National Chiao Tung University 2 0.92522 0.92502 0.02531 0.02547 0.87113 0.8734 0.28382 0.28497 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming nebnext bulk unknown unknown   Taiwan 2019-07-18 Juvenile Juvenile Liver Liver and Biliary System