GSM5017695: MM468_UNC_day33; Homo sapiens; RNA-Seq
For MDA-MB-468 cell line, for each single cell suspension (MM468_DMSO_day0-#1,MM468_5FU_day33-#1, MM468_5FU_day214-#1, MM468_5FU_day67-#2, MM468_5FU_day171-#2, MM468_5FU_day50-#3, MM468_5FU_day77-#3 and MM468_5FU_day202-#3), approximately 3,000 cells were loaded on a Chromium Single Cell Controller Instrument (Chromium Single Cell 3ʹv3, 10X Genomics, Ref: PN-1000075) according to the manufacturer's instructions. Samples and libraries were prepared according to the manufacturer's instructions.  For PDX model, before downstream analysis (scChIP-seq, scRNA-seq and bulk ChIP-seq), control and Capecitabine treated tumors were digested for 2 h at 37 °C with a cocktail of Collagenase I (Roche, Ref: 11088793001) and Hyaluronidase (Sigma-Aldrich, Ref: H3506). Cells were then individualized at 37°C using a cocktail of 0.25% Trypsin-Versen (Thermo Fisher Scientific, Ref: 15040-033), Dispase II (Sigma-Aldrich, Ref: D4693) and DNase I (Roche, Ref: 11284932001) as described previously53. Then, eBioscience red blood cell lysis buffer (Thermo Fisher Scientific, Ref: 00-4333-57) was added to the cell suspension to remove red blood cells. To increase the viability of the final cell suspension, dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec, Ref:130-090-101). Libraries were sequenced on a NovaSeq 6000 (Illumina) in PE8-8-91 with a coverage of 50,000 reads/cell.