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.

附加文件2：表S1。结直肠癌细胞系特征。（a-b）240株结直肠癌细胞系的注释信息。针对每一株细胞系，我们记录如下内容：（1）细胞系名称；（2）原发肿瘤部位；（3）来源：本实验室自建（来源于手术样本或患者来源异种移植瘤（Patient-Derived Xenografts, PDXs））、通过合作获取或从国际细胞系库购买；（4）供应商标识：细胞系来源的详细信息（合作对接的科研人员姓名，或国际细胞系库名称）；（5）微卫星状态：微卫星稳定（Microsatellite Stable, MSS）或微卫星不稳定（Microsatellite Instable, MSI）；（6）CIMP：CpG岛甲基化表型（CpG Island Methylator Phenotype, CIMP）状态，分为CIMP-H、CIMP-L、CIMP3及CIMP4；（7）共识分子亚型（Consensus Molecular Subtypes, CMS）：分为CMS1、CMS2、CMS3或CMS4。无法明确归为单一亚型（错误发现率（False Discovery Rate, FDR）>5%）的细胞系标记为NA（无有效数据）；（8）结直肠癌固有亚型（Colorectal Cancer Intrinsic Subtypes, CRIS）：分为CRIS-A、CRIS-B、CRIS-C、CRIS-D或CRIS-E。无法明确归为单一亚型（FDR>5%）的细胞系标记为NA（无有效数据）；（9-13）APC、TP53、NRAS、KRAS、BRAF基因的突变状态：即各基因的野生型（Wild Type, WT）或突变型（Mutant, MUT）。突变状态依据与蛋白质序列改变相关的体细胞突变（错义单核苷酸变异（Single Nucleotide Variants, SNVs）、无义单核苷酸变异及插入缺失（Insertions and Deletions, indels））的存在情况判定；（14）（15）（16）非整倍体评分、倍性、非整倍体评分与倍性的比值，计算方法详见方法部分；（17）参考文献：可获取各细胞系补充信息的相关文献。（c-d）针对用于筛选与验证数据集的88株结直肠癌细胞系，我们检测了16个不同基因座的短串联重复序列（Short Tandem Repeats, STR）分型结果。