Question: Should I deplete red blood cells from my sample before loading?
Answer: Removing red blood cells (RBCs) may not be necessary before loading your sample. However, if they are not removed, they will contribute to the total number of cells that are loaded and will increase the amount of sequencing you will need to perform to detect the other cell populations of interest. It is possible to remove the RBC population bioinformatically during Loupe Cell Browser analysis if you do not, or cannot, remove them during sample prep.
If you are interested in removing RBCs before loading your sample, our Demonstrated Protocol for tumor dissociation includes a RBC lysis step: https://support.10xgenomics.com/single-cell-gene-expression/index/doc/demonstrated-protocol-tumor-dissociation-for-single-cell-rna-sequencing
We also have customers successfully use Ficoll purification to remove RBCs from PBMC samples prior to loading the cells.
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.
Products: Single Cell 3', VDJ