Estimating the Allele-Specific Expression of SNVs From 10× Genomics Single-Cell RNA-Sequencing Data.
RNA-seq
SNV
VAFRNA
genetic variation
monoallelic expression
sc-RNA-seq
sc-VAFRNA
single cell
single-cell RNA-sequencing
Journal
Genes
ISSN: 2073-4425
Titre abrégé: Genes (Basel)
Pays: Switzerland
ID NLM: 101551097
Informations de publication
Date de publication:
25 02 2020
25 02 2020
Historique:
received:
22
12
2019
revised:
10
02
2020
accepted:
19
02
2020
entrez:
29
2
2020
pubmed:
29
2
2020
medline:
3
2
2021
Statut:
epublish
Résumé
With the recent advances in single-cell RNA-sequencing (scRNA-seq) technologies, the estimation of allele expression from single cells is becoming increasingly reliable. Allele expression is both quantitative and dynamic and is an essential component of the genomic interactome. Here, we systematically estimate the allele expression from heterozygous single nucleotide variant (SNV) loci using scRNA-seq data generated on the 10×Genomics Chromium platform. We analyzed 26,640 human adipose-derived mesenchymal stem cells (from three healthy donors), sequenced to an average of 150K sequencing reads per cell (more than 4 billion scRNA-seq reads in total). High-quality SNV calls assessed in our study contained approximately 15% exonic and >50% intronic loci. To analyze the allele expression, we estimated the expressed variant allele fraction (VAF
Identifiants
pubmed: 32106453
pii: genes11030240
doi: 10.3390/genes11030240
pmc: PMC7140866
pii:
doi:
Substances chimiques
RNA
63231-63-0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
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