Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments.

ABSTRACT: A mechanistic understanding of the biological and technical factors that impact transcript measurements is essential to designing and analyzing single-cell and single-nucleus RNA sequencing experiments. Nuclei contain the same pre-mRNA population as cells, but they contain a small subset of the mRNAs. Nonetheless, early studies argued that single-nucleus analysis yielded results comparable to cellular samples if pre-mRNA measurements were included. However, typical workflows do not distinguish between pre-mRNA and mRNA when estimating gene expression, and variation in their relative abundances across cell types has received limited attention. These gaps are especially important given that incorporating pre-mRNA has become commonplace for both assays, despite known gene length bias in pre-m

SUBMITTER: Chamberlin JT 

PROVIDER: S-EPMC10984380 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature