Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs.

ABSTRACT: By profiling gene expression in individual cells, single-cell RNA-sequencing (scRNA-seq) can resolve cellular heterogeneity and cell-type gene expression dynamics. Its application to time-series samples can identify temporal gene programs active in different cell types, for example, immune cells' responses to viral infection. However, current scRNA-seq analysis has limitations. One is the low number of genes detected per cell. The second is insufficient replicates (often 1-2) due to high experimental cost. The third lies in the data analysis-treating individual cells as independent measurements leads to inflated statistics. To address these, we explore a new computational framework, specifically whether "metacells" constructed to maintain cellular heterogeneity within individual cell types

SUBMITTER: O'Leary K 

PROVIDER: S-EPMC10997786 | biostudies-literature | 2024 Apr

REPOSITORIES: biostudies-literature