MOESM1 of Regional methylome profiling reveals dynamic epigenetic heterogeneity and convergent hypomethylation of stem cell quiescence-associated genes in breast cancer following neoadjuvant chemotherapy

Yumei Luo, Juan Huang, Yi Tang, Xitu Luo, Lingxia Ge, Xiujie Sheng, Xiaofang Sun, Yaoyong Chen, Detu Zhu
2019 Figshare  
Additional file 1: Table S1. Clinical Characteristics of Selected Breast Cancer Patients. Table S2. Primers and probes used in ddPCR MethyLight assays. Figure S1. Unsupervised clustering of top 1% most variable probes of all the 870 TCGA-BRCA 450K samples. Figure S2. Unsupervised clustering of top 1% most variable probes of all the 870 TCGA-BRCA 450K samples with PR/ER/HER2 annotations. Figure S3. Unsupervised clustering of top 1% most variable probes of all the 870 TCGA-BRCA 450K samples with
more » ... 450K samples with TNM annotations. Figure S4. Histopathological analysis of selected breast cancer patients. Figure S5. Sampling procedures. (A) Breast cancer patients were selected who underwent core needle biopsy sampling, followed by CET neoadjuvant chemotherapy regimens, and finally surgical removal of the breast tumors. Each patient derived 3-4 core needle biopsy specimens prior to NAC, and each post-NAC tumor tissue was spatially dissected into 6-7 sectors; (B) Breast cancer patients were selected whose breast tumors were surgically removed without neoadjuvant chemotherapy treatment. Each tumor tissue was spatially dissected into 6 sectors. Figure S6. Unsupervised clustering of top 1% most variable probes of samples from 5 patients without chemotherapy separately. Figure S7. Unsupervised clustering of 450K array probes mapped to known genes associated to chemotherapy resistant: ABCB1, DUSP4, ETS1, FOXC1, GSTP1, PTEN and TGM2. Figure S8. Unsupervised clustering of MeTIL signature probes of all the samples. Figure S9. DM genes in KEGG cAMP signaling pathway in the 3 NAC-treated patients. Red color indicates hypermethylated genes; blue color indicates hypomethylated genes. Figure S10. DM genes in KEGG Pathways in Cancer in the 3 NAC-treated patients. Red color indicates hypermethylated genes; blue color indicates hypomethylated genes. Figure S11. Establishment of multiplexed Methylight ddPCR. (A) Locations of CpGs in the MethyLight primers and probes and the amplicons for methylated loci of interest, and the C-LESS-C1 assay that amplifies [...]
doi:10.6084/m9.figshare.7693004 fatcat:6oyuieve2jeeperpxg3zjwfoxe