Genetics_of_gene_expression_in_human_macrophage_response_to_Salmonella

This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

Type: Transcriptome Analysis
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 4 Publications

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Dataset ID	Description	Technology	Samples
EGAD00001003204	Understanding how cells sense and respond to their environment, and how these responses are modulated by genetic variation, are fundamental biological problems, particularly for understanding how pathogenic organisms invade and manipulate the cells of the human immune system. Macrophages recognize and respond to many important human pathogens including HIV-1, Mycobacteria tuberculosis and Salmonella. This study will focus on the cellular response of human macrophages to Salmonella infection and how this response is modulated by the genetic bacground of the individual as well as additional pro-inflammatory stimulus (interferon-gamma priming). We will acquire 100 human induced pluripotent stem cell lines from the HipSci project, differentiate the cells in vitro into macrophages and expose them to four environmental conditions: (i) no stimulation, (ii) interferon-gamma (18h), (iii) Salmonella typhimurium SL1344 (5h), (iv) interferon-gamma (18h) + Salmonella (5h).Subsequently, we will isolate RNA from the samples for sequencing.	Illumina HiSeq 2500	236

Publications	Citations
Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response. Alasoo K, Rodrigues J, Mukhopadhyay S, Knights AJ, Mann AL, Kundu K, HIPSCI Consortium, Hale C, Dougan G, Gaffney DJ. Nat Genet 50: 2018 424-431	161
Genetic effects on promoter usage are highly context-specific and contribute to complex traits. Alasoo K, Rodrigues J, Danesh J, Freitag DF, Paul DS, Gaffney DJ. Elife 8: 2019 e41673	38
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	180
Genetics of the human microglia regulome refines Alzheimer's disease risk loci. Kosoy R, Fullard JF, Zeng B, Bendl J, Dong P, Rahman S, Kleopoulos SP, Shao Z, Girdhar K, Humphrey J, de Paiva Lopes K, Charney AW, Kopell BH, Raj T, Bennett D, Kellner CP, Haroutunian V, Hoffman GE, Roussos P. Nat Genet 54: 2022 1145-1154	53