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Datasets.md

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List of datasets included in the eQTL Catalogue

RNA-seq datasets

Dataset Cell types or tissues Conditions Donors Samples Expression Atlas Raw expression data Raw genotype data
Alasoo_2018 macrophages IFNg, Salmonella, IFNg + Salmonella 336 84 EGAD00001003204; PRJEB18997 EGAD00010001147; PRJEB11752
BLUEPRINT monocytes, neutrophils, T-cells 554 197 EGAD00001002671; EGAD00001002674; EGAD00001002675 EGAD00001002663
GENCORD LCLs1, fibroblasts, T-cells 560 195 EGAD00001000425 EGAD00001000428
GEUVADIS LCLs1 445 445 E-GEUV-1 1000 Genomes
HipSci iPSCs2 322 322 E-MTAB-4748 EGAD00001003529; PRJEB7388 EGAD00010001147; PRJEB11752
Nedelec_2016 macrophages Listeria, Salmonella 493 168 GSE81046 Not deposited
Quach_2016 monocytes LPS, Pam3CSK4, R848, IAV 969 200 EGAD00001002714 EGAD00010001131
Schwartzentruber_2018 sensory neurons 98 98 EGAD00001003145; PRJEB18630 EGAD00010001147; PRJEB11752
TwinsUK fat, LCLs1, skin, blood 1364 433 EGAD00001001086; EGAD00001001087; EGAD00001001088; EGAD00001001089 Not deposited
van_de_Bunt_2015 pancreatic islets 117 117 EGAD00001001601 EGAD00001001601

Microarray datasets

Dataset Cell types or tissues Conditions Samples Donors Expression Atlas Raw expression data Raw genotype data
CEDAR CD4 and CD8 T-cells, monocytes, neutrophils, platelet, B-cells, ileum, rectum, transverse colon 2388 322 E-MTAB-6667 E-MTAB-6666
Fairfax_2012 B-cells 282 282 E-MTAB-945 EGAD00010000144; EGAD00010000520
Fairfax_2014 monocytes IFN24, LPS2, LPS24 1372 424 E-MTAB-2232 EGAD00010000144; EGAD00010000520
Kasela_2017 CD4 and CD8 T-cells 553 297 GSE78840 Not deposited
Naranbhai_2015 neutrophils 93 93 E-MTAB-3536 EGAD00010000144; EGAD00010000520

Citation

In addition to citing the eQTL Catalogue resource, please also cite the orginal publications producing the raw data and aknowledge the funding that they received.

BLUEPRINT

Publication: Chen, Lu, et al. "Genetic drivers of epigenetic and transcriptional variation in human immune cells." Cell 167.5 (2016): 1398-1414.

Funding statement: "This study makes use of data generated by the Blueprint Consortium. A full list of the investigators who contributed to the generation of the data is available from www.blueprint-epigenome.eu. Funding for the project was provided by the European Union's Seventh Framework Programme (FP7/2007- 2013) under grant agreement no 282510 - BLUEPRINT."

Fairax_2012, Fairfax_2014, Naranbhai_2015

Publications:

  • Fairfax, Benjamin P., et al. "Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression." Science 343.6175 (2014): 1246949.
  • Fairfax, Benjamin P., et al. "Genetics of gene expression in primary immune cells identifies cell type–specific master regulators and roles of HLA alleles." Nature genetics 44.5 (2012): 502.
  • Naranbhai, Vivek, et al. "Genomic modulators of gene expression in human neutrophils." Nature communications 6 (2015): 7545.

Funding statement: "Funding for the project was provided by the Wellcome Trust under awards Grants 088891 [B.P.F.], 074318 [J.C.K.] and 075491/Z/04 to the core facilities at the Wellcome Trust Centre for Human Genetics), the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) (281824 to J.C.K.), the Medical Research Council (98082, J.C.K.) and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre"

TwinsUK

Publication: "Buil, Alfonso, et al. "Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins." Nature genetics 47.1 (2015): 88."

Funding statement: "TwinsUK is funded by the Wellcome Trust, Medical Research Council, European Union, the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust in partnership with King’s College London."

Footnotes

  1. lymphoblastoid cell lines ↩ ↩2 ↩3

  2. induced pluripotent stem cells ↩