Influence of feeder cells on transcriptomic analysis of pluripotent stem cells.

ABSTRACT:

Objectives

Human pluripotent stem cells (hPSCs) are of great importance in both scientific research and regenerative medicine. The most classic and widely used culture method for hPSCs is co-culture with feeder cells, usually mouse embryonic fibroblasts. However, whether these feeder cell residues can affect the transcriptomic data analysis of hPSCs, especially gene or miRNA expression quantification, is still largely unknown.

Methods and results

In this study, reanalysis of published mRNA-Seq and miRNA-Seq data sets revealed the existence of feeder cell-derived reads in the hPSC transcriptomic samples. We identified potentially influenced human genes and miRNAs due to misalignment of sequencing fragments affected by mouse feeder cells. Furthermore, we developed an optimized

SUBMITTER: Wan H 

PROVIDER: S-EPMC8828260 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature