{"database": "metadata", "table": "run_metadata", "rows": [[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 \u00df catenin. \u00df catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the \u00df catenin protein  leading to nuclear and/or cytoplasmic localization of \u00df catenin and downstream activation of Wnt target genes. In patient HCC samples  \u00df 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 \u00df catenin activation are not well understood. To define mechanisms of \u00df catenin driven HCC initiation  we generated a Cre lox system that enabled switching on activated \u00df 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 \u00df catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/\u00df catenin signaling heterogeneity later in hepatocarcinogenesis  we performed RNA seq analysis of zebrafish \u00df catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that \u201cCancer\u201d and \u201cLiver Tumor\u201d 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 \u00df 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 \u00df 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", null, "630", "GSM4087863", null, "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.\u00a0 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.\u00a0 Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.\u00a0 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\uf0b0C 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\u2019s 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\u2019s 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", null, "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\uf0b0C 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", null, "SRP222804", null, null, "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, null, null, 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", null, "United States", "2019-09-20", "Adult", "Adult", "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": ["55216"], "units": {}, "query_ms": 10.130973998457193}