SPINK1-COL18A1 Crosstalk Shapes Epigenome and Drives Cancer Stemness in Pancreatic Ductal Adenocarcinoma
Bulk RNA seq and bulk ATAC seq of SPINK1 knockout (sgSPINK1) compared to control (sgCtrl) in PANC-1 cell line to study the effect of SPINK1 on the transcriptome and chromatin accessibility of PDAC cells.Bulk RNA sequencing and analysis: Total RNA was extracted from sgCtrl and sgSPINK1 PANC-1 cells using RNeasy Mini Kit (Qiagen, Cat no. 74104) and DNAse treatment (Qiagen, Cat no. 79254) according to the manufacturer protocol. Library preparation and sequencing were performed at Yale Center for Genome Analysis (YCGA), Yale University.Bulk ATAC sequencing and analysis: Sample processing and sequencing were performed by Active Motif Inc. (Carlsbad, CA, USA). A total of 100,000 cells per sample were cryopreserved in a medium containing 50 percent FBS, 40 percent growth medium, and 10 percent DMSO and sent to Active Motif for ATAC-sequencing.