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Data Set Group2: HMS Spleen CD4+ T cells MDP Affy Mouse Gene 1.0 ST (Jul16) modify this page

Data Set: HMS Spleen CD4+ T cells MDP Affy Mouse Gene 1.0 ST (Jul16) Gene Level modify this page
GN Accession: GN801
GEO Series: GSE60337
Title: Variation and genetic control of gene expression in primary immunocytes across inbred mouse strains.
Organism: Mouse (Mus musculus, mm10)
Group: MDP
Tissue: Spleen mRNA
Dataset Status: Public
Platforms: Affy Mouse Gene 1.0 ST (GPL6246)
Normalization: RMA
Contact Information
Sara Mostafavi
The University of British Columbia
Earth Sciences Building, 3178-2207 Main Mall
Vancouver, British Columbia V6T 1Z4 Canada
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Specifics of this Data Set:
Gene Level


To determine the breadth and underpinning of changes in immunocyte gene expression due to genetic variation in mice, we performed, as part of the Immunological Genome Project, gene expression profiling for CD4(+) T cells and neutrophils purified from 39 inbred strains of the Mouse Phenome Database. Considering both cell types, a large number of transcripts showed significant variation across the inbred strains, with 22% of the transcriptome varying by 2-fold or more. These included 119 loci with apparent complete loss of function, where the corresponding transcript was not expressed in some of the strains, representing a useful resource of "natural knockouts." We identified 1222 cis-expression quantitative trait loci (cis-eQTL) that control some of this variation. Most (60%) cis-eQTLs were shared between T cells and neutrophils, but a significant portion uniquely impacted one of the cell types, suggesting cell type-specific regulatory mechanisms. Using a conditional regression algorithm, we predicted regulatory interactions between transcription factors and potential targets, and we demonstrated that these predictions overlap with regulatory interactions inferred from transcriptional changes during immunocyte differentiation. Finally, comparison of these and parallel data from CD4(+) T cells of healthy humans demonstrated intriguing similarities in variability of a gene's expression: the most variable genes tended to be the same in both species, and there was an overlap in genes subject to strong cis-acting genetic variants. We speculate that this "conservation of variation" reflects a differential constraint on intraspecies variation in expression levels of different genes, either through lower pressure for some genes, or by favoring variability for others.

About the cases used to generate this set of data:

About the tissue used to generate this set of data:

About the array platform:

About data values and data processing:


Experiment Type:



Blair DADustin MLShinton SAHardy RRShay TRegev ACohen NBrennan PBrenner MKim FRao TNWagers AHeng TEricson JRothamel KOrtiz-Lopez AMathis DBenoist CKreslavsky TFletcher AElpek KBellemare-Pelletier AMalhotra DTurley SMiller JBrown BMerad MGautier ELJakubzick CRandolph GJMonach PBest AJKnell JGoldrath AJojic VKoller DLaidlaw DCollins JGazit RRossi DJMalhotra NSylvia KKang JBezman NASun JCMin-Oo GKim CCLanier LL.

  • 1 Department of Computer Science, Stanford University, Stanford, CA 94305;
  • 2 Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; and.
  • 3 The Jackson Laboratory, Bar Harbor, ME 04609.
  • 4 Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115; and cbdm@hms.harvard.edu.


Data source acknowledgment:

Study Id:

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  • NIGMS Systems Genetics and Precision Medicine project (R01 GM123489, 2017-2021)
  • NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
  • NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
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