For Chromium 10X single cell RNA sequencing, I know >70% viability is recommended for cells; however, has anyone used or seen datasets using cells with lower viabilities? How low? Can data be successfully filtered to remove the large percentages of dead cells by looking at gene number, UMI number, and percentages of mitochondrial genes?
For single cell sequencing on the Chromium 10X platform and others poor quality cells often stand out. If you are checking for viability (with DAPI and flow) it would be worth gating them out. But from my experience damaged cells with little mRNA can be filtered easily. Strictly for RNAseq viability is not key rather that you are picking up the mRNA signature. So rapid processing and keeping your cells cool is important. Additionally you want to ensure you have a good single cell suspension as the other abnormal cell types that may be difficult to filter out are doublets/multiplets though again they usually do stick out in any pre-analysis QC.
- Badges
- Science topic
- Similar topics
- Engineering
- Materials Engineering
- Powders