Technical Note - Removal of Dead Cells from Single Cell Suspensions Improves Performance for 10x Genomics® Single Cell Applications

This Technical Note discusses the impact of non-viable cells in single cell suspensions on single cell genomics data quality. 10x Genomics' Single Cell Protocols require suspensions of viable, single cells as input. The removal of dead cells and other contaminants from single cell suspensions is critical to obtaining high quality data. Depending on the sample type and sample preparation method, the fraction of dead cells in a single cell suspension can vary significantly. Dead cells easily lyse, resulting in the release of ambient RNA. This cell-free RNA can contribute to the background noise of the assay and will compromise the quality of single cell data. In this Technical Note we compare datasets generated from single cell suspensions containing varying amounts of non-viable cells to highlight the importance of removing dead cells from single cell suspensions prior to use with the Single Cell 3’ v2 Protocol.

FOR USE WITH

• Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, 16 rxns PN-120237
• Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, 4 rxns PN-120267
• Chromium™ Single Cell 5’ Library & Gel Bead Kit, 16 rxns PN-1000006
• Chromium™ Single Cell 5’ Library & Gel Bead Kit, 4 rxns PN-1000014
• Chromium™ Single Cell V(D)J Enrichment Kit, Human T Cell, 96 rxns PN-1000005
• Chromium™ Single Cell A Chip Kit, 48 rxns PN-120236
• Chromium™ Single Cell A Chip Kit, 16 rxns PN-1000009
• Chromium™ i7 Multiplex Kit, 96 rxns PN-120262