Single cell RNA sequencing of colorectal cancer with diverse tissue dissociation protocols or fresh vs. frozen cell preparations.

To evaluate 3 different tissue dissociation protocols or fresh vs. frozen cell preparations, we performed single-cell RNA sequencing on cancer or distant normal tissue dissociates from 2 colorectal cancer patients. Total 18,409 cells from 10 sample preparations were analyzed (5 primary colorectal cancer and 5 matched normal mucosa). The results suggest highly consistent cellular proportions were recovered with different sample preparation methods. Ten batches of single cell RNA sequencing data were obtained from 2 patients, with 5 different sample preparations for primary colorectal cancer or matched normal mucosa respectively. For one patient, 3 different tissue dissociation protocols were applied for cancer and matched normal mucosa. For another freshly prepared or frozen-thawed cell stocks were tested for cancer and matched normal mucosa. After sequencing, we applied filtering criteria using nUMI, nGene and percent of mitochondrial genes to eliminate low-quality cells and 18,409 cells passed the filtering criteria. ****raw data files have not been provided due to patient privacy issues and will be available in EGA as controlled access****