Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control.

ABSTRACT:

Motivation

Quality control (QC) is a critical step in single-cell RNA-seq (scRNA-seq) data analysis. Low-quality cells are removed from the analysis during the QC process to avoid misinterpretation of the data. An important QC metric is the mitochondrial proportion (mtDNA%), which is used as a threshold to filter out low-quality cells. Early publications in the field established a threshold of 5% and since then, it has been used as a default in several software packages for scRNA-seq data analysis, and adopted as a standard in many scRNA-seq studies. However, the validity of using a uniform threshold across different species, single-cell technologies, tissues and cell types has not been adequately assessed.

Results

We systematically analyzed 5 530 106 cells reported in 1349

SUBMITTER: Osorio D 

PROVIDER: S-EPMC8599307 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature