Cell type-specific weighting-factors to solve solid organs-specific limitations of single cell RNA-sequencing.

ABSTRACT: While single-cell RNA-sequencing (scRNA-seq) is a popular method to analyze gene expression and cellular composition at single-cell resolution, it harbors shortcomings: The failure to account for cell-to-cell variations of transcriptome-size (i.e., the total number of transcripts per cell) and also cell dissociation/processing-induced cryptic gene expression. This is particularly a problem when analyzing highly heterogeneous solid tissues/organs, which requires cell dissociation for the analysis. As a result, there exists a discrepancy between bulk RNA-seq result and virtually reconstituted bulk RNA-seq result using its composite scRNA-seq data. To fix this problem, we propose a computationally calculated coefficient, "cell type-specific weighting-factor (cWF)". Here, we introduce a concep

SUBMITTER: Tejima K 

PROVIDER: S-EPMC11573148 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature