Comparison of gene expression in CSCs (tumorspheres) vs non-CSCs (2D adherent condition) from A13A PDAC cell line [ATAC-seq]

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest and most metastatic cancers in human. PDACs respond poorly to therapies, partly due to cancer stem cells (CSCs) that self-renew, survive chemotherapies, metastasise and replenish the tumor. Factors secreted by tumor cells mediate autocrine/paracrine crosstalk with surrounding cells contributing to the stem cell niche but are still insufficiently characterised. Here we used quantitative SILAC proteomics to identify secreted factors enriched in CSC secretome compared to non-CSCs. Our data uncovered factors that mediate the crosstalk between CSCs and non-CSCs as well as genes mediating the gene expression circuitries regulating CSC proliferation. To investigate the differences of chromatin accessibility between PDAC CSCs (A13A_P_Ctrl samples) and non-CSCs (A13A_Adh_Ctrl samples) in A13A PDAC cell line. We grew CSCs (A13A_P_Ctrl samples) in 3D condition in suspension as tumor spheres for 7 days from single cell suspension, and non-CSCs (A13A_Adh_Ctrl samples) in 2D condition on petri dishes until 80% confluency before collecting samples for total RNA isolation in triplicates.