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Genetics of gene expression in primary human immune cells

The purpose of this study was to identify cell specific expression quantitative trait loci in freshly isolated highly purified primary B-cells and monocytes from healthy subjects of European ancestry. Cells were purified from Ficoll gradient prepared peripheral blood mononuclear cell fractions using positive selection via magnetic bead labelling of the B-cell marker CD19 and monocyte marker CD14. RNA was extracted from 287 B-cell samples and 288 monocyte samples. RNA was then hybridised to HumanHT-12 v4 BeadChips whole genome expression arrays (Illumina). Individuals were genotyped on HumanOmniExpress-12v1.0 BeadChips (Illumina) at 733202 genetic markers. Data presented include the raw expression values and Robust Spline Normalised values (RSN) for expression for each cell type per individual. Additional genotype data per individual is available on request.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00010000144 Illumin OmniExpress v1.0 - Illumina GenomeStudio 288
EGAD00010000520 Illumina OmniExpress v1.0-Illumina GenomeStudio 144
Publications Citations
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Integration of disease association and eQTL data using a Bayesian colocalisation approach highlights six candidate causal genes in immune-mediated diseases.
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Genomic modulators of gene expression in human neutrophils.
Nat Commun 6: 2015 7545
Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression.
Genome Biol 17: 2016 33
Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.
Cell 167: 2016 1369-1384.e19
A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the VSTM1 gene locus.
Genome Med 9: 2017 18
Joint genetic analysis using variant sets reveals polygenic gene-context interactions.
PLoS Genet 13: 2017 e1006693
Sex-Interacting mRNA- and miRNA-eQTLs and Their Implications in Gene Expression Regulation and Disease.
Front Genet 10: 2019 313
Tensor decomposition of stimulated monocyte and macrophage gene expression profiles identifies neurodegenerative disease-specific trans-eQTLs.
PLoS Genet 16: 2020 e1008549
A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data.
PLoS Comput Biol 16: 2020 e1007770
Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants.
Elife 9: 2020 e58705
Multi-tissue transcriptome-wide association studies.
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EPISPOT: An epigenome-driven approach for detecting and interpreting hotspots in molecular QTL studies.
Am J Hum Genet 108: 2021 983-1000
A compendium of uniformly processed human gene expression and splicing quantitative trait loci.
Nat Genet 53: 2021 1290-1299
Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity.
Nat Commun 13: 2022 4073
A Genetic Risk Score Distinguishes Different Types of Autoantibody-Mediated Membranous Nephropathy.
Glomerular Dis 3: 2023 116-125