Question: What fraction of reads map to ribosomal proteins?
Answer: Single Cell 3’ v2 libraries do contain reads mapping to ribosomal protein transcripts (Rps, Rpl). The fraction of reads varies based on cell type and overall cell health. Below is the fraction of reads we observe for the following cell types:
|Cell type||Fraction of reads mapping to ribosomal proteins|
|Barnyard Cells (1:1 HEK293T:3T3)||25-35%|
|Isolated Pan T Cells||40-45%|
In order to address ribosomal gene expression during data analysis, one could do any of the following:
- Exclude PCs (Principal Components) that correlate with ribosomal protein genes. This amounts to subtracting effects that are presumably technical.
- Only include in the PC analysis genes that are "highly variable". We do this by selecting the genes with the highest dispersion across the dataset and performing PCA on those genes only. The Seurat package uses a similar approach.
We encourage users to carefully analyze their data with Cell Ranger and Loupe Cell Browser to determine the prevalence of ribosomal protein gene expression in their data and analyze its effect on their analysis.
Although both ribosomal proteins and ribosomal RNA (rRNA) make up the ribosome complex, ribosomal protein transcripts are not equivalent to ribosomal RNA (rRNA). Ribosomal protein transcript detection will not necessarily correlate with either rRNA or mitochondrial transcripts.
- The 10x 2020-A references do not annotate the rRNA transcripts, and therefore rRNA transcripts will not show up as counts.
- High mitochondrial transcripts are an indicator of poor cell health. See https://kb.10xgenomics.com/hc/en-us/articles/360001086611 for details.
Products: Single Cell 3'