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Baseline CHC transcriptomes

RNA sequencing of Baseline CHC-noHCC and CHC-HCC samples. Snap frozen biopsies were crushed in liquid nitrogen. Total RNA was extracted using RNA MiniPrep Plus kit (Zymo Research) according to the manufacturer’s instructions. RNA sequencing of baseline CHC samples was done in paired-end mode on an Illumina HiSeq 2500 with 101 cycles. RNA-Seq was performed at the Department of Biosystems Science and Engineering ETH Zurich, D-BSSE in Basel.

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

1 Dataset

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000001591	We conducted a nested case–control study within a prospective liver biopsy biobank at the University Hospital Basel. Patients with chronic hepatitis C (CHC) who developed hepatocellular carcinoma (HCC) during follow-up (index cases, CHC-HCC) were identified and 1:2 propensity score-matched to CHC controls without HCC (controls, CHC-nonHCC). Matching included clinical, demographic, and virological risk factors for HCC. Liver biopsies were analyzed using RNA and whole-exome sequencing.	Illumina HiSeq 2500 Illumina NovaSeq 6000	139