Add mitochondrial, ribosomal, and hemoglobin percentages to a Seurat object.

Detected by gene symbol prefix, case-insensitively so the same patterns match both human (MT-, RPS/RPL, HBA/HBB) and mouse (mt-, Rps/Rpl, Hba-a1/Hbb-bs) naming. RPS6K* (ribosomal protein S6 kinase) is excluded from pct_ribo - it matches the RPS prefix but is a signaling kinase, not a ribosomal protein.

Usage

add_gene_class_percent(x)

Arguments

x

A Seurat object.

Value

Seurat object with pct_mito, pct_ribo, and pct_hb metadata columns added.

Details

High expression levels of mitochondrial genes could be an indicator of poor sample quality, leading to a high fraction of apoptotic or lysing cells (see reference below).

pct_ribo is normally 15-45%; the exact fraction varies by cell type and overall cell health. "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." (see reference below)

High pct_hb is a contamination signal in PBMC and most solid tissue: per-sample pct_hb flags incomplete red blood cell lysis in PBMC preps, or inadequate perfusion in solid tissue.

References

pct_mito: https://kb.10xgenomics.com/s/article/360001086611-Why-do-I-see-a-high-level-of-mitochondrial-gene-expression

pct_ribo: https://kb.10xgenomics.com/s/article/218169723-What-fraction-of-reads-map-to-ribosomal-proteins