{"database": "metadata", "table": "run_metadata", "rows": [[53175, "SRR9708005", "SRX6465919", "SRS5126684", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week HBx Srcp53  DIO sample 2", "GSM3954323", null, "source name:8week HBx Srcp53  Overfed|strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Overfed", "8week HBx Srcp53  DIO sample 2", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week HBx Srcp53  Overfed", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl 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 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Overfed", "GSM3954323", "GSM3954323: 8week HBx Srcp53  DIO sample 2; Danio rerio; RNA Seq", "GSM3954323", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl 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 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954323", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "TriDIO11_1.fq.gz TriDIO11_2.fq.gz", "fastq fastq", 4249297200.0, 14164324.0, "GSM3954323 r1", "0:150 1:150", "A:1118373146;C:1004287869;G:1022623288;T:1103209208;N:803689", 150, 150, null, null, 1118373146, 1004287869, 1022623288, 1103209208, 803689, "SRX6465919", "SRS5126684", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.93432, 0.93585, 0.02504, 0.0252, 0.84147, 0.84404, 0.40759, 0.40621, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["53175"], "units": {}, "query_ms": 9.643603996664751}