A targeted sequencing extension for transcript genotyping in single-cell transcriptomics.

ABSTRACT: As no existing methods within the single-cell RNA sequencing repertoire combine genotyping of specific genomic loci with high throughput, we evaluated a straightforward, targeted sequencing approach as an extension to high-throughput droplet-based single-cell RNA sequencing. Overlaying standard gene expression data with transcript level genotype information provides a strategy to study the impact of genetic variants. Here, we describe this targeted sequencing extension, explain how to process the data and evaluate how technical parameters such as amount of input cDNA, number of amplification rounds, and sequencing depth influence the number of transcripts detected. Finally, we demonstrate how targeted sequencing can be used in two contexts: (1) simultaneous investigation of the presence of

SUBMITTER: Van Horebeek L 

PROVIDER: S-EPMC10494938 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature