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Data Set Group: OX UK HS ILM6v1.1 Lung (May 2010) modify this page

Data Set: OX UK HS ILM6v1.1 Lung (May 2010) RankInv modify this page
GN Accession: GN270
GEO Series: No Geo series yet
Organism: Mouse (mm10)
Group: HS
Tissue: Lung mRNA
Dataset Status: Public
Platforms: Illumina Mouse WG-6 v1, v1.1 (GPL6105)
Normalization: RankInv
Contact Information
Richard Mott
The Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford, OX 7BN UK
Tel. unknown
Download datasets and supplementary data files

Specifics of this Data Set:


A proportion of the genetic variants underlying complex phenotypes do so through their effects on gene expression, so an important challenge in complex trait analysis is to discover the genetic basis for the variation in transcript abundance. So far, the potential of mapping both quantitative trait loci (QTLs) and expression quantitative trait loci (eQTLs) in rodents has been limited by the low mapping resolution inherent in crosses between inbred strains. We provide a megabase resolution map of thousands of eQTLs in hippocampus, lung, and liver samples from heterogeneous stock (HS) mice in which 843 QTLs have also been mapped at megabase resolution. We exploit dense mouse SNP data to show that artifacts due to allele-specific hybridization occur in _30% of the cis-acting eQTLs and, by comparison with exon expression data, we show that alternative splicing of the 3_ end of the genes accounts for <1% of cis-acting eQTLs. Approximately one third of cis-acting eQTLs and one half of trans-acting eQTLs are tissue specific. We have created an important systems biology resource for the genetic analysis of complex traits in a key model organism.

About the cases used to generate this set of data:

HS Northport stock (see https://www.nature.com/articles/ng1840) descended from eight inbred progenitor strains (A/J, AKR/J, BALBc/J, CBA/J, C3H/HeJ, C57BL/6J, DBA/2J and LP/J). For details, please see Demarest, K., Koyner, J., McCaughran, J. Jr., Cipp, L. & Hitzemann, R. Further characterization and high-resolution mapping of quantitative trait loci for ethanol-induced locomotor activityBehav. Genet.31, 79–91 (2001).

About the tissue used to generate this set of data:

About the array platform:

Organism: Mus musculus. Tissue: Lung. Array design: A-MEXP-533 - Illumina Mouse-6 v1 Expression BeadChip

About data values and data processing:


Experiment Type:



Citations: High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues. Huang GJ, Shifman S, Valdar W, Johannesson M, Yalcin B, Taylor MS, Taylor JM, Mott R, Flint J. Genome Res 19(6):1133-40 (Genome Res), PubMed 19376938

Contact: Richard Mott. Email: Richard.Mott at well.ox.ac.uk University of Oxford

Data entered by A. Centeno on May 20, 2010

Data source acknowledgment:

Study Id:

CITG Web services initiated January, 1994 as Portable Dictionary of the Mouse Genome; June 15, 2001 as WebQTL; and Jan 5, 2005 as GeneNetwork. This site is currently operated by Rob Williams, Pjotr Prins, Zachary Sloan, Arthur Centeno. Design and code by Pjotr Prins, Zach Sloan, Arthur Centeno, Danny Arends, Christian Fischer, Sam Ockman, Lei Yan, Xiaodong Zhou, Christian Fernandez, Ning Liu, Rudi Alberts, Elissa Chesler, Sujoy Roy, Evan G. Williams, Alexander G. Williams, Kenneth Manly, Jintao Wang, and Robert W. Williams, colleagues. Python Powered Registered with Nif
GeneNetwork support from:
  • The UT Center for Integrative and Translational Genomics
  • 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)
  • NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
  • NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
  • NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)
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