wiki:DataSets
Last modified 20 months ago

Example data sets

Below a list of publicly available datasets in XGAP format.
Please email m.a.swertz@… to publish your data to this list.

Table of Contents

    1. Unpublished epigenetic data example
    2. Unpublished alternative splicing data example
    3. Baile et al.
    4. Beamer et al.
    5. Lyons et al.
    6. Fu et al.
    7. Myers et al.
    8. Stranger/Human?
    9. Keurentjes/Arabidopsis?
    10. Bystrykh/Mouse?
    11. Heap/Human?
    12. Myers/Human?
    13. Li/C.elegans

Unpublished epigenetic data example

Example of an epigenetic experiment using ChIP-on-chip for methylation detection.

Unpublished alternative splicing data example

Example of isoform data that uses tiling arrays for detection of alternative splicing

Baile et al.

Identification of QTL for locomotor activation and anxiety using related inbred strains B6 and C58/J

Beamer et al.

Bone mineral density in F2 progeny from a C57BL/6J x CAST/EiJ intercross

Lyons et al.

QTL analysis: Plasma lipids and susceptibility to gallstones in F2 progeny of DBA/2J x CAST/EiJ on a high-fat diet'

Fu et al.

MetaNetwork example dataset

Myers et al.

This set includes Genotypes, SNP locations, and Expression data.

Stranger/Human?

Whole-genome gene expression variation in 210 unrelated HapMap individuals. This set includes genotype and expression data and panel, gene and clone annotations.

Keurentjes/Arabidopsis?

Genetic analysis of natural variation in the metabolite composition in Arabidopsis thaliana using empirical untargeted metabolomics using liquid chromatography-time of flight mass spectrometry (LC-QTOF MS). This set includes gene expression, genotype, and lcms data sets and qtls and gene, invidiual, marker, masspeak, and sample annotations.

Bystrykh/Mouse?

mRNA gene expression in hematopoietic stem cells from adult female BXD mice using Affymetrix U74Av2 chips. This set includes genotype, probe level gene expression and probset level gene expression data and individual, marker, probe, probeset and strain annotations.

  •  Download data in xgap format (zip)
  •  View data on xgap server
  •  View pubmed:15711547 - Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'. Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, Wiltshire T, Su AI, Vellenga E, Wang J, Manly KF, Lu L, Chesler EJ, Alberts R, Jansen RC, Williams RW, Cooke MP, de Haan G. Nat Genet. 2005 Mar;37(3):225-32. Epub 2005 Feb 13.

Heap/Human?

Primary human leucocyte RNA expression of unrelated celiac disease cases and unrelated healthy controls. This set includes genotype and gene expression data sets and probe, marker, and sample annotations.

Myers/Human?

This set includes Genotypes, SNP locations, and Expression data. Also available from http://labs.med.miami.edu/myers/LFuN/data.html.

  •  Download data in xgap format (zip)
  •  View data on xgap server
  •  View pubmed:17982457 - A survey of genetic human cortical gene expression. Myers AJ, Gibbs JR, Webster JA, Rohrer K, Zhao A, Marlowe L, Kaleem M, Leung D, Bryden L, Nath P, Zismann VL, Joshipura K, Huentelman MJ, Hu-Lince D, Coon KD, Craig DW, Pearson JV, Holmans P, Heward CB, Reiman EM, Stephan D, Hardy J. Nat Genet. 2007 Dec;39(12):1494-9. Epub 2007 Nov 4.

Li/C.elegans

Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. This set includes Probe, Gene, Marker, Paired sample and Strain annotations and Genotype and Expression datasets.