SCIFER: approach for analysis of LINE-1 mRNA expression in single cells at a single locus resolution.

ABSTRACT:

Background

Endogenous expression of L1 mRNA is the first step in an L1-initiated mutagenesis event. However, the contribution of individual cell types to patterns of organ-specific L1 mRNA expression remains poorly understood, especially at single-locus resolution. We introduce a method to quantify expression of mobile elements at the single-locus resolution in scRNA-Seq datasets called Single Cell Implementation to Find Expressed Retrotransposons (SCIFER). SCIFER aligns scRNA-Seq reads uniquely to the genome and extracts alignments from single cells by cell-specific barcodes. In contrast to the alignment performed using default parameters, this alignment strategy increases accuracy of L1 locus identification by retaining only reads that are uniquely mapped to individual L1 loci. L

SUBMITTER: Stow EC 

PROVIDER: S-EPMC9413895 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature