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Cellular plasticity drives regeneration of heterogeneity in hepatocellular carcinoma organoids

Using patient-derived HCC organoids (HCCOs), we investigated the cellular basis of heterogeneity in HCC.We performed single-cell outgrowth assays and scRNAseq of sublines and the original parental HCCO.

Type: RNASeq
Archive: European Genome-phenome Archive (EGA)

1 Dataset

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Dataset ID	Description	Technology	Samples
EGAD50000003151	FASTQ files were processed using the TrailmakerTM pipeline module (v1.5.0, Parse Biosciences). Unfiltered count matrices were uploaded to Trailmaker, and background was removed by setting a minimum transcripts per cell threshold on a per sample basis (threshold range: 998 to 1799). Dead or dying cells were removed by filtering barcodes with high mitochondrial content on a per sample basis (threshold range: 12.62% to 21.1%). Outliers in the distribution of number of genes vs number of transcripts were removed by fitting a spline regression model (p-values between 0.000003 and 0.000264). Cells with a high probability of being doublets were filtered out using the scDblFinder method on a per sample basis (threshold range: 0.72763 to 0.80853). Read counts were normalized by log1p. Output files are normalized counts.	Illumina NovaSeq 6000	8