2021
DOI: 10.1186/s12864-020-07334-y
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scReQTL: an approach to correlate SNVs to gene expression from individual scRNA-seq datasets

Abstract: Background Recently, pioneering expression quantitative trait loci (eQTL) studies on single cell RNA sequencing (scRNA-seq) data have revealed new and cell-specific regulatory single nucleotide variants (SNVs). Here, we present an alternative QTL-related approach applicable to transcribed SNV loci from scRNA-seq data: scReQTL. ScReQTL uses Variant Allele Fraction (VAFRNA) at expressed biallelic loci, and corelates it to gene expression from the corresponding cell. … Show more

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Cited by 14 publications
(29 citation statements)
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“…In this study we find 20 significant cis-scReQTLs. This number is expected given the input size (up to 70 SNVs and up to 3000 cells per dataset), and, based on our previous studies is likely to be significantly higher in larger datasets [11,18].…”
Section: Discussionmentioning
confidence: 67%
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“…In this study we find 20 significant cis-scReQTLs. This number is expected given the input size (up to 70 SNVs and up to 3000 cells per dataset), and, based on our previous studies is likely to be significantly higher in larger datasets [11,18].…”
Section: Discussionmentioning
confidence: 67%
“…To explore if cells bearing certain scSNVs have related gene expression features, we assessed the scSNV expression in the individual cells after graph-based cell-clustering. For this analysis we processed the scRNA-seq datasets as we have previously described [11,18]. Briefly, after alignment with STARsolo [12] and quality filtering, the gene-expression matrices were processed using Seurat [24] to normalize gene expression and correct for batch-and cell-cycle effects; the normalized gene expression values were then used to assign likely cell types using SingleR [25] (Methods).…”
Section: Scsnvs Expressionmentioning
confidence: 99%
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