Additional file 2 of DNA demethylation triggers cell free DNA release in colorectal cancer cells

Additional file 2: Table S1. Characteristics of CRC cell lines. (a-b) Annotation of the 240 CRC cell lines. For each cell line we report: (1) Cell line name; (2) Primary tumor site; (3) Source: established in our lab (from surgical samples or PDXs), obtained through a collaboration or purchased from an international cell line bank; (4) Supplier ID: detail about the cell line origin (the scientist with whom the collaboration was established or name of the international cell line bank); (5) Microsatellite status: microsatellite stable (MSS) or instable (MSI); (6) CIMP: Status for the CpG island methylator phenotype (CIMP-H, CIMP-L, CIMP3 and CIMP4); (7) CMS: consensus molecular subtypes (CMS1, CMS2, CMS3 or CMS4). Cell lines that couldn’t be confidently assigned to a single subtype (FDR>;5%) were labeled as NA (not available); (8) CRIS: colorectal cancer intrinsic subtypes (CRIS-A, CRIS-B, CRIS-C, CRIS-D or CRIS-E). Cell lines that couldn’t be confidently assigned to a single subtype (FDR>5%) were labeled as NA (not available); (9-13) APC, TP53, NRAS, KRAS, BRAF: mutational status for these genes, i.e., being wild-type (WT) or mutant (MUT) for each gene. The mutational status was determined based on the presence of somatic mutations that are associated with the alteration of protein sequences (missense SNVs, nonsense SNVs and indels); (14) (15) (16) Aneuploidy score, ploidy, aneuploidy score over ploidy calculated as described in the methods; (17) References: publications in which additional information about each cell line can be found. (c-d). STR (Short Tandem Repeats) profiles of the 88 CRC cell lines, used for the screening and validation dataset, considering 16 different loci.