Extraction of Genomic DNA and RNA from Tissue Biopsies
Genomic DNA and total RNA from biopsies from the discovery cohort were extracted using the ZR‐Duet DNA and RNA MiniPrep Plus Kit (Zymo Research, Freiburg im Breisgau, Germany) following the manufacturer’s instructions. Prior to extraction, biopsies were crushed in liquid nitrogen to facilitate lysis. Extracted DNA was quantified using the Qubit Fluorometer (Invitrogen, Waltham, MA, USA) [17 (link)]. DNA from peripheral blood leucocytes (‘buffy coat’) was extracted using the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. For the validation cohort, DNA was extracted using the ChargeSwitch Genomic DNA Mini Tissue Kit (Invitrogen) following the manufacturer’s instructions [8 (link)].
Gallon J., Coto‐Llerena M., Ercan C., Bianco G., Paradiso V., Nuciforo S., Taha‐Melitz S., Meier M., Boldanova T., Pérez‐del‐Pulgar S., Rodríguez‐Tajes S., von Flüe M., Soysal S.D., Kollmar O., Llovet J.M., Villanueva A., Terracciano L.M., Heim M.H., Ng C.K, & Piscuoglio S. (2021). Epigenetic priming in chronic liver disease impacts the transcriptional and genetic landscapes of hepatocellular carcinoma. Molecular Oncology, 16(3), 665-682.
Corresponding Organization : SIB Swiss Institute of Bioinformatics
Other organizations :
Consorci Institut D'Investigacions Biomediques August Pi I Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Hospital Clínic de Barcelona, Universitat de Barcelona, Icahn School of Medicine at Mount Sinai, Humanitas University, Istituti di Ricovero e Cura a Carattere Scientifico
Extraction method for genomic DNA and total RNA from biopsies (ZR‐Duet DNA and RNA MiniPrep Plus Kit)
Extraction method for DNA from peripheral blood leucocytes (DNeasy Blood and Tissue Kit)
Extraction method for DNA in the validation cohort (ChargeSwitch Genomic DNA Mini Tissue Kit)
dependent variables
Extracted genomic DNA quantity (measured using Qubit Fluorometer)
control variables
Crushing of biopsies in liquid nitrogen prior to extraction
Manufacturer's instructions followed for all extraction kits
Annotations
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