title: GSM7848113: WCM668_C1D1_EP7-11_cfDNA; Homo sapiens; Bisulfite-Seq
library_construction_protocol: Plasma was separated from whole blood with a standard double spin protocol and stored at -80°C. The input plasma volume ranged between 1mL and 2mL depending on the cohort.  For cfDNA extraction of samples processed in Trento, plasma was thawed at RT and immediately processed with the QIAamp Circulating Nucleic Acid Kit (QIAGEN) according to the manufacturer's protocol. The extracted cfDNA was eluted in 30 µL Tris HCl 10mM pH8 and quantified with Qubit dsDNA High Sensitivity Assay (Invitrogen); the quality was assessed using the Bioanalyzer High Sensitivity DNA Kit (Agilent). For samples processed at Weill Cornell Medicine (WCM, DFCI, and Alisertib trial) cfDNA was extracted from plasma using the NeoGeneStar Cell-Free DNA Purification kit per manufacturer'