Genetic Determinants of Transcriptional Variation in Primary Human Monocytes Across Multiple Contexts

Monocytes undergo global gene expression changes upon stimulation, thus a significant proportion of eQTL are specific to activation state. Here we systematically explore determinants of gene and transcript expression in monocytes from 185 individuals in the untreated state and post-exposure to IFNγ or lipopolysaccharide (LPS).

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

1 Dataset 2 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
EGAD00001010176	These data correspond to samples used in the following papers: 1. GWAS and meta-analysis identifies 49 genetic variants underlying critical Covid-19 2. Genetic determinants of monocyte splicing are enriched for disease susceptibility loci including for COVID-19. 3. Identification of Genetic Determinants of Transcriptional Response to Metformin in Primary Human Monocytes. They are the raw RNA sequencing files as used in all downstream analysis.	Illumina HiSeq 4000	611

Publications	Citations
GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19. Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, GenOMICC Investigators, SCOURGE Consortium, ISARICC Investigators, 23andMe COVID-19 Team, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK. Nature 617: 2023 764-768	56
Characterization of the genetic determinants of context-specific DNA methylation in primary monocytes. Gilchrist JJ, Fang H, Danielli S, Tomkova M, Nassiri I, Ng E, Tong O, Taylor C, Muldoon D, Cohen LRZ, Al-Mossawi H, Lau E, Neville M, Schuster-Boeckler B, Knight JC, Fairfax BP. Cell Genom 4: 2024 100541	0

Publications

Citations

GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.
Pairo-Castineira E, Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, Oosthuyzen W, Kousathanas A, Richmond A, Millar J, Russell CD, Malinauskas T, Thwaites R, Morrice K, Keating S, Maslove D, Nichol A, Semple MG, Knight J, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Begg C, Walsh T, Tenesa A, Flores C, Riancho JA, Rojas-Martinez A, Lapunzina P, GenOMICC Investigators, SCOURGE Consortium, ISARICC Investigators, 23andMe COVID-19 Team, Yang J, Ponting CP, Wilson JF, Vitart V, Abedalthagafi M, Luchessi AD, Parra EJ, Cruz R, Carracedo A, Fawkes A, Murphy L, Rowan K, Pereira AC, Law A, Fairfax B, Hendry SC, Baillie JK. Nature 617: 2023 764-768

Characterization of the genetic determinants of context-specific DNA methylation in primary monocytes.
Gilchrist JJ, Fang H, Danielli S, Tomkova M, Nassiri I, Ng E, Tong O, Taylor C, Muldoon D, Cohen LRZ, Al-Mossawi H, Lau E, Neville M, Schuster-Boeckler B, Knight JC, Fairfax BP. Cell Genom 4: 2024 100541