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.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

2 Datasets 20 Publications

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	Healthy volunteer collection of European Ancestry	Illumin OmniExpress v1.0 - Illumina GenomeStudio	288
EGAD00010000520	Healthy volunteer collection of European Ancestry	Illumina OmniExpress v1.0-Illumina GenomeStudio	144

Publications	Citations
Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Fairfax BP, Humburg P, Makino S, Naranbhai V, Wong D, Lau E, Jostins L, Plant K, Andrews R, McGee C, Knight JC. Science 343: 2014 1246949	638
Integration of disease association and eQTL data using a Bayesian colocalisation approach highlights six candidate causal genes in immune-mediated diseases. Guo H, Fortune MD, Burren OS, Schofield E, Todd JA, Wallace C. Hum Mol Genet 24: 2015 3305-3313	131
Genomic modulators of gene expression in human neutrophils. Naranbhai V, Fairfax BP, Makino S, Humburg P, Wong D, Ng E, Hill AV, Knight JC. Nat Commun 6: 2015 7545	118
Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression. Rakitsch B, Stegle O. Genome Biol 17: 2016 33	22
Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters. Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnström K, Downes K, Grassi L, Kostadima M, Freire-Pritchett P, Wang F, BLUEPRINT Consortium, Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M, Wallace C, Spivakov M, Fraser P. Cell 167: 2016 1369-1384.e19	855
A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the VSTM1 gene locus. Kumar D, Puan KJ, Andiappan AK, Lee B, Westerlaken GH, Haase D, Melchiotti R, Li Z, Yusof N, Lum J, Koh G, Foo S, Yeong J, Alves AC, Pekkanen J, Sun LD, Irwanto A, Fairfax BP, Naranbhai V, Common JE, Tang M, Chuang CK, Jarvelin MR, Knight JC, Zhang X, Chew FT, Prabhakar S, Jianjun L, Wang Y, Zolezzi F, Poidinger M, Lane EB, Meyaard L, Rötzschke O. Genome Med 9: 2017 18	29
Joint genetic analysis using variant sets reveals polygenic gene-context interactions. Casale FP, Horta D, Rakitsch B, Stegle O. PLoS Genet 13: 2017 e1006693	14
Sex-Interacting mRNA- and miRNA-eQTLs and Their Implications in Gene Expression Regulation and Disease. Shen JJ, Wang YF, Yang W. Front Genet 10: 2019 313	14
Tensor decomposition of stimulated monocyte and macrophage gene expression profiles identifies neurodegenerative disease-specific trans-eQTLs. Ramdhani S, Navarro E, Udine E, Efthymiou AG, Schilder BM, Parks M, Goate A, Raj T. PLoS Genet 16: 2020 e1008549	17
A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data. Lamparter D, Bhatnagar R, Hebestreit K, Belgard TG, Zhang A, Hanson-Smith V. PLoS Comput Biol 16: 2020 e1007770	2
Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants. Kolberg L, Kerimov N, Peterson H, Alasoo K. Elife 9: 2020 e58705	44
Multi-tissue transcriptome-wide association studies. Grinberg NF, Wallace C. Genet Epidemiol 45: 2021 324-337	17
EPISPOT: An epigenome-driven approach for detecting and interpreting hotspots in molecular QTL studies. Ruffieux H, Fairfax BP, Nassiri I, Vigorito E, Wallace C, Richardson S, Bottolo L. Am J Hum Genet 108: 2021 983-1000	8
A compendium of uniformly processed human gene expression and splicing quantitative trait loci. Kerimov N, Hayhurst JD, Peikova K, Manning JR, Walter P, Kolberg L, Samoviča M, Sakthivel MP, Kuzmin I, Trevanion SJ, Burdett T, Jupp S, Parkinson H, Papatheodorou I, Yates AD, Zerbino DR, Alasoo K. Nat Genet 53: 2021 1290-1299	350
Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity. Gilchrist JJ, Makino S, Naranbhai V, Sharma PK, Koturan S, Tong O, Taylor CA, Watson RA, de Los Aires AV, Cooper R, Lau E, Danielli S, Hameiri-Bowen D, Lee W, Ng E, Whalley J, Knight JC, Fairfax BP. Nat Commun 13: 2022 4073	25
A Genetic Risk Score Distinguishes Different Types of Autoantibody-Mediated Membranous Nephropathy. Gupta S, Downie ML, Cheshire C, Dufek-Kamperis S, Levine AP, Brenchley P, Hoxha E, Stahl R, Ashman N, Pepper RJ, Mason S, Norman J, Bockenhauer D, Stanescu HC, Kleta R, Gale DP. Glomerular Dis 3: 2023 116-125	2
eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs. Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ, Kanai M, Ulirsch J, Ryten M, Hardy J, Guelfi S, Trabzuni D, Kim-Hellmuth S, Rayner W, Finucane H, Peterson H, Mosaku A, Parkinson H, Alasoo K. PLoS Genet 19: 2023 e1010932	46
Scalable genetic screening for regulatory circuits using compressed Perturb-seq. Yao D, Binan L, Bezney J, Simonton B, Freedman J, Frangieh CJ, Dey K, Geiger-Schuller K, Eraslan B, Gusev A, Regev A, Cleary B. Nat Biotechnol 42: 2024 1282-1295	74
Sex bias in celiac disease: XWAS and monocyte eQTLs in women identify TMEM187 as a functional candidate gene. Hernangomez-Laderas A, Cilleros-Portet A, Martínez Velasco S, Marí S, Legarda M, González-García BP, Tutau C, García-Santisteban I, Irastorza I, Fernandez-Jimenez N, Bilbao JR. Biol Sex Differ 14: 2023 86	4
Monocyte inflammation and resilience to Alzheimer's disease: novel genetic risk genes identified by transcriptome-wide association study. Mustafa Y, Main LR, Mews M, Janve VA, Hohman TJ, Haines JL, Song YE, Griswold AJ, Pericak-Vance MA, Scott WK, Naj AC, Below JE, Dumitrescu L, Bush WS. Transl Psychiatry 15: 2025 481	0