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Basel Liver Biopsy Biobank

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Markus Heim
markus.heim@unibas.ch

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This DAC controls 6 datasets

Dataset ID	Description	Technology	Samples
EGAD50000000060	We aimed to identify somatic mutations and transcriptional differences that could explain the resistance to Doxorubicin. This dataset includes RNA-Seq of HCC biopsies and Organoids and WES of Organoids.	Illumina HiSeq 2500 Illumina NovaSeq 6000 unspecified	52
EGAD50000002291	A total of 16 patients with primary liver cancer, who first underwent diagnostic biopsy and then surgical resection shortly afterwards (median 27 days) were included. Tumor and non-tumor biopsy and resection tissue were analyzed by RNA sequencing. Total RNA from frozen tumor- and non-tumor tissue from biopsy and resection specimens was extracted using the ZR-Duet DNA and RNA MiniPrep Plus kit (Zymo Research) according to the manufacturer’s instructions. Prior to extraction, frozen tissues were crushed in liquid nitrogen to facilitate lysis. Extracted RNA was quantified using the Qubit Fluorometer (Thermo Fisher Scientific). 200 ng total RNA was used for RNAseq library prep with the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) according to the manufacturer’s specifications. Paired-End sequencing was performed on a Novaseq 6000 (Illumina) with 51 cycles at the Genomics Facility Basel according to the manufacturer’s guidelines.	Illumina NovaSeq 6000	60
EGAD50000002957	Dataset consists of tumors and matched non-tumor livers from 22 patients with multifocal hepatocellular carcinoma. Tissues were obtained from at least two distinct tumor nodules undergoing liver biopsies. Note: refer to the supplementary table of the manuscript for patient IDs and further clinical data.	Illumina HiSeq 2500	121
EGAD50000002958	Dataset consists of tumors and matched non-tumor livers from 22 patients with multifocal hepatocellular carcinoma. Tissues were obtained from at least two distinct tumor nodules undergoing liver biopsies. Note: refer to the supplementary table of the manuscript for patient IDs and further clinical data.	Illumina HiSeq 2500	95
EGAD50000003150	WES analysis of Hepatocellular Carcinoma Organoids (HCCOs), and their single cell derived outgrowths. We asses variants and Copy Number Variations after single cell bottle-necks.	Illumina NovaSeq X	30
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