Single cell analysis - My short summaries collection

1. In single-cell RNA sequencing, mitochondrial (mt), ribosomal (ribo), and hemoglobin (Hb) gene expression levels serve as quality indicators:

• mt Genes: High levels indicate cell stress or damage. (Should be less 5-10%)
• ribo Genes: Elevated levels suggest RNA isolation or library preparation issues. (no standard cutoff)  
  
  
• Hb Genes: High expression in non-blood cells flags potential red blood cell contamination. (maybe 50% in RBC but no standard cutoff)

2. The choice between RNA velocity and pseudotime them depends on the specific research context and data quality, with RNA velocity requiring data on both spliced and unspliced transcripts, while pseudotime focuses on overall gene expression changes.