Question: Should I deplete red blood cells from my sample before loading?
Answer: Different sample types have different ranges of Red Blood Cell (RBC) content, as seen in the image below:
Depending on how your sample was isolated and the expected red blood cell (RBCs) content, removing RBCs may not be necessary before loading your sample. However, if they are not removed, they will contribute to the total number of loaded cells and increase the amount of sequencing you will need to perform to detect the other cell populations of interest. A list of suggested usage scenarios is listed below.
If choosing to skip RBC lysis, it is possible to “ignore” the RBCs by counting cells with fluorescent DNA markers (AO/PI), load normally for the PBMC count, and increase the sequencing to account for RBCs loading.
Note: RBC-specific transcripts may appear in the cDNA QC trace as a sharp peak at ~700 bp. This is normal and does not affect downstream library quality. More RBC data should be expected from samples such as these.
Instructions for removing RBCs during sample prep and analysis can be found here: How can I remove red blood cells from my sample?
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