{"database": "metadata", "table": "run_metadata", "rows": [[72454, "SRR22557575", "SRX18521036", "SRS15989660", "SRP411740", "PRJNA909412", "Molecular characterisation of a mutant kras driven zebrafish model of hepatocellular carcinoma", "GSE220282", "Transcriptome Analysis", "We used doxycycline dox treatment to generate a larval model of hepatocellular carcinoma HCC22. In this model  we induced the expression of a single EGFP krasG12V transgene  denoted TOkrasG12VT/+ in developing livers by treating with doxycycline between 2 dpf 7 dpf dpf. This led to the accumulation of a constitutively active  EGFP tagged  potently oncogenic form of Kras specifically in hepatocytes  causing hepatocyte hyperplasia and a substantial increase in total liver volume. We used RNA sequencing to analyse the gene expression patterns of hepatocytes expressing the krasG12V transgene compared to wildtype WT livers expressing no transgene. We detected more than 6000 significantly upregulated genes in dox treated TOkrasG12VT/+ livers compared WT livers  and a further 6000+ genes were significantly downregulated. Of the upregulated genes  many were significantly enriched in KEGG pathways associated with highly proliferative cancers  including DNA replication  cell cycle and DNA damage repair. Geneset enrichment analysis identified a positive correlation between the differential gene expression data from the dox treated TOkrasG12VT/+ versus WT livers and the differential gene expression data for the HCC LIHC and healthy liver subsets available from The Cancer Genome Atlas. We also found a positive correlation between the DEGs from the dox treated TOkrasG12VT/+ versus WT livers and a small HCC expression signature based on four patient samples carrying KRAS G12 or KRAS G13 mutations. These observations build on previous reports that dox treated TOkrasG12VT/+ zebrafish provide an authentic model of human HCC. Overall design: Paired end RNA sequencing data was generated for 8 samples of zebrafish liver. Of these samples  3 are wild type WT and 5 are kras mutants. Differential analyses were performed  identifying differentially expressed genes between the kras mutant and wild type groups. Please note  all WT and 2 of the mutant samples are sequenced over 2 runs.", null, "pubmed:36648336", null, "Kras mutant  3", "GSM6797834", null, "source name:Liver|tissue:Liver|cell type:hepatocytes|genotype:kras mutant|treatment:Doxycycline 20mg/L from 2 dpf 7 dpf dpf", "Kras mutant  3", "The\u00a0base calling and quality scoring were determined using Real Time Analysis on board software v2.4.6 Reads were aligned to the zebrafish genome by Rsubread version 2.10.5 Fragment read pair counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function Genes were identified using Ensembl annotation to the GRCz11 genome  version 101 Assembly: GRCz11 Supplementary files format and content: tab delimited text files wre written from the R prompt; columns represent Ensembl Gene ID  total gene length total base count of all exons and the number of fragments mapping to that gene", "Liver", "Treatment group received oxycycline 20mg/L from 2 dpf 7 dpf dpf", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", "E3 medium comprising 5mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSO4", "tissue:Liver|cell type:hepatocytes|genotype:kras mutant|treatment:Doxycycline 20mg/L from 2 dpf 7 dpf dpf", "GSM6797834", "GSM6797834: Kras mutant  3; Danio rerio; RNA Seq", "GSM6797834 r1", "GSM6797834", "1", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP411740", null, null, "WT-K-3b_S6_R1.fastq.gz WT-K-3b_S6_R2.fastq.gz", "fastq fastq", 126178415.0, 782575.0, "GSM6797834 r2", "0:80.62 1:80.61", "A:33725497;C:29453850;G:29082084;T:33561572;N:355412", 80, 80, null, null, 33725497, 29453850, 29082084, 33561572, 355412, "SRX18521036", "SRS15989660", "SRA1554907", "Walter and Eliza Hall Institute of Medical Research", "Walter and Eliza Hall Institute of Medical Research", 2, 0.89216, 0.8883, 0.13334, 0.12896, 0.74734, 0.74854, 0.596, 0.60101, 81, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Australia", "2022-12-06", "Multi-stage", "Multi-stage", "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": ["72454"], "units": {}, "query_ms": 14.568883998435922}