{"database": "metadata", "table": "run_metadata", "rows": [[55197, "SRR10153190", "SRX6878620", "SRS5414402", "SRP222786", "PRJNA573063", "Single cell transcriptomic analysis of two models of zebrafish beta catenin driven HCC", "GSE137784", "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 three 6mpf liver samples from three different transgenic lines with/without xxx hydroxytamoxifen TAM treatment.", "parent bioproject:PRJNA573068", "pubmed:31575545", null, "HCCCreLox [Single cell]", "GSM4087820", null, "tissue:Liver|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "HCCCreLox [Single cell]", "10x Genomics\u2019 Cell Ranger software v2.2.0 executed primary data analysis for each sample. Pipeline 'cellranger mkfastq' generated R1 26 bp and R2 100 bp  FASTQ files. Custom transgenic genomic reference was built with \u2018cellranger mkref\u2019  but shared the common Danio rerio genome reference build GRCz11 with annotations from Ensembl release 94. The Ensembl gene annotations were filtered with \u2018cellranger mkgtf\u2019 for gene biotypes matching \u2018protein coding\u2019  \u2018lincRNA\u2019 and \u2018antisense\u2019 tags. All samples had additional transgenic sequence/annotations added. Each sample was processed with \u2018cellranger count\u2019 pipeline with their respective transgenic genome build with parameter \u2018  expect cells=3000\u2019 In attempt to recover those perhaps lower quality GEM partitions  the raw gene barcode matrices from \u2018cellranger count\u2019 located in \u2018outs/raw gene bc matrices\u2019 was processed with the EmptyDrops algorithm R package DropletUtils v1.2.2 to discriminate cells from background GEM partitions at a false discovery rate FDR of 1% Lun ATL et al.  2019. GEM partitions with 500 UMI counts or less were considered to be devoid of viable cells  while those with at least 10 000 UMI counts were automatically considered to be cells. Cell based QC metrics were calculated with R package scater v1.10.1 using the calculateQCMetrics function McCarthy DJ et al.  2017. Principal component analysis PCA on the cell based QC metrics combined with a multivariate outlier method flagged cells with outlying values in QC metrics as suspect P. Filzmoser et al.  2008. Cells with extremely low UMI counts  extremely low gene counts or extremely high percentage of expression attributed to mitochondrial genes were also flagged as low quality. Extremeness in any of these three measures was determined by 3 median absolute deviations from the median with the scater::isOutlier function applied to each sample individually. Additionally  cells were required to have greater than 800 UMIs and less than 20% of total expression attributed to mitochondrial transcripts. Those cells suspected of being low quality were removed from downstream analysis. Genome build: GRCz11 Supplementary files format and content: MTX", "Liver", "Larvae for Samples 2 and 3 were treated with 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 remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank\u2019s Buffered Saline Solution HBSS without xxx red  with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter  and the filtrate was centrifuged at 1200 RPM  4\uf0b0C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin.  The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific.  The Chromium Single Cell Gene Expression Solution with 3\u2019 chemistry  version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction.  Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs  the micro droplets.  Within individual GEMs  cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53\u00b0C for 45 min followed by 85\u00b0C for 5 min.  Subsequent A tailing  end repair  adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Sequencing", "Fish were raised following IACUC approved protocols in insititutional zebrafish facility.", "transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "GSM4087820", "GSM4087820: HCCCreLox [Single cell]; Danio rerio; RNA Seq", "GSM4087820", 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 remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank's Buffered Saline Solution HBSS without xxx red  with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter  and the filtrate was centrifuged at 1200 RPM  4\uf0b0C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin.  The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific.  The Chromium Single Cell Gene Expression Solution with three prime chemistry  version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction.  Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs  the micro droplets.  Within individual GEMs  cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53\u00b0C for 45 min followed by 85\u00b0C for 5 min.  Subsequent A tailing  end repair  adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Sequencing", "GEO Accession:GSM4087820", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP222786", null, null, "15547X2_S9_L006_R1_001.fastq.gz 15547X2_S9_L006_R2_001.fastq.gz", "fastq fastq", 16758654318.0, 133005193.0, "GSM4087820 r1", "0:26 1:100", "A:4758015356;C:3904784528;G:3787834220;T:4302283542;N:5736672", 26, 100, null, null, 4758015356, 3904784528, 3787834220, 4302283542, 5736672, "SRX6878620", "SRS5414402", "SRA965504", "GEO", "Pathology, University of California, San Francisco", 2, 0.00291, 0.94432, 0.00084, 0.04281, 0.99539, 0.88203, 0.48041, 0.60684, 26, 100, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-09-20", "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": ["55197"], "units": {}, "query_ms": 13.401215999692795}