design: RNAseq of colorectal cancer cell lines (LS1034/HCT116) cultured with iPSC-derived intestinal stroma, separated by EpCAM expression (MACS). Monocultures of each cell line and co-cultures with LS1034 or HCT116 with stroma.
library_construction_protocol: Cells were washed with PBS 1x and then dissociated with TrypLE Select. Cells were labelled with anti-EpCAM magnetic beads and separated using a MACS column into EpCAM+ and EpCAM- populations. Cells were lysed with the lysis buffer (see extraction kit details) RNA was extracted using GenElute™ Mammalian Total RNA Miniprep Kit following manufacturer's instructions (Cat no. RTN70 - Sigma Aldrich) PolyA enrichment of mRNA, RT first-strand cDNA library with ligation of sequencing adapters