HCA Data Explorer

Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs

Access Granted
Updated June 19, 2024

Genome-wide association studies have identified thousands of genetic variants that are associated with disease1. Most of these variants have small effect sizes, but their downstream expression effects, so-called expression quantitative trait loci (eQTLs), are often large and celltype-specific. To identify these celltype-specific eQTLs using an unbiased approach, we used single-cell RNA sequencing to generate expression profiles of ~25,000 peripheral blood mononuclear cells from 45 donors. We identified previously reported cis-eQTLs, but also identified new celltype-specific cis-eQTLs. Finally, we generated personalized co-expression networks and identified genetic variants that significantly alter co-expression relationships (which we termed ‘co-expression QTLs’). Single-cell eQTL analysis thus allows for the identification of genetic variants that impact regulatory networks.

Lude FrankeUniversity of Groningen, University Medical Center Groningenlude@ludesign.nl
Monique GP van der Wijst1
Harm Brugge1
Dylan H de Vries1
Patrick Deelen1
Morris A Swertz1
Lude Franke1
1University of Groningen, University Medical Center Groningen
Ami Day

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/40272c3b-4697-4bd4-ba3f-82fa96b9bf71

Supplementary links are provided by contributors and represent items such as additional data which can’t be hosted here; code that was used to analyze this data; or tools and visualizations associated with this specific dataset.

1.https://molgenis26.gcc.rug.nl/downloads/scrna-seq/
EGA Accessions:

Analysis Portals

None

Project Label

SingleCelleQTLCoexpressionAnalysis

Species

Homo sapiens

Sample Type

specimens

Anatomical Entity

blood

Organ Part

Unspecified

Selected Cell Types

peripheral blood mononuclear cell

Disease Status (Specimen)

normal

Disease Status (Donor)

normal

Development Stage

human adult stage

Library Construction Method

10x 3' v2

Nucleic Acid Source

single cell

Paired End

false

Analysis Protocol

analysis_protocol_cell_types, analysis_protocol_eQTL, analysis_protocol_eQTL_coexpression, analysis_protocol_gene_expression

File Format

3 file formats

Cell Count Estimate

25.0k

Donor Count

45
md51 file(s)xlsx1 file(s)zip5 file(s)