run_metadata: 55196

This data as json

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
55196	SRR10153191	SRX6878621	SRS5414403	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 ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß 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 ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß 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 ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” 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 ß 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 ß 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		NoHCC [Single cell]	GSM4087821		tissue:Liver\|transgenic line:Tgfabp10a flox beta catenin\|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC	NoHCC [Single cell]	10x Genomics’ 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 ‘cellranger mkref’ but shared the common Danio rerio genome reference build GRCz11 with annotations from Ensembl release 94. The Ensembl gene annotations were filtered with ‘cellranger mkgtf’ for gene biotypes matching ‘protein coding’ ‘lincRNA’ and ‘antisense’ tags. All samples had additional transgenic sequence/annotations added. Each sample was processed with ‘cellranger count’ pipeline with their respective transgenic genome build with parameter ‘ expect cells=3000’ In attempt to recover those perhaps lower quality GEM partitions the raw gene barcode matrices from ‘cellranger count’ located in ‘outs/raw gene bc matrices’ 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’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C 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’ 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°C for 45 min followed by 85°C 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 flox beta catenin\|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC	GSM4087821	GSM4087821: NoHCC [Single cell]; Danio rerio; RNA Seq	GSM4087821		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C 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°C for 45 min followed by 85°C 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:GSM4087821	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP222786			15547X4_S11_L007_R2_001.fastq.gz 15547X4_S11_L007_R1_001.fastq.gz	fastq fastq	16861988178.0	133825303.0	GSM4087821 r1	0:26 1:100	A:4788108995;C:3905645218;G:3694064311;T:4468647482;N:5522172	26	100			4788108995	3905645218	3694064311	4468647482	5522172	SRX6878621	SRS5414403	SRA965504	GEO	Pathology, University of California, San Francisco	2	0.00236	0.93017	0.0008	0.04645	0.99626	0.89043	0.52233	0.64352	26	100	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2019-09-20	Multi-stage	Multi-stage	Liver	Liver and Biliary System