MPD - Available gene expression strain survey data sets

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Available gene expression strain survey data sets

When using MPD's gene expression functionality you'll have the opportunity to select specific data sets.
Each data set has an MPD project identifier as well as a short tag that conveys info about the basics of the study.

[Show strains]

Data set (short tag)	Number of probesets and platform	Number of strains, sexes and ages	Number of replicates per strain/ sex	Description	Investigators, papers, GEO
GX-Gatti1 (liver_Gatti1)	N = 20,291 Agilent G4121A	36 inbred strains; males age 7-9wks	2 (most)	liver RNA	Gatti DM, Harrill A, Threadgill DW, Rusyn I (2009) PMID:19609828 GSE14563
GX-Lusis1 (liver_HMDP_Lusis1)	N = 22,164 Affy M430	99 HMDP strains; males age 16wks	3	whole liver RNA	Bennett BJ, Farber CR, Kang HM, Orozco L, Eskin E, Lusis AJ (2010) PMID:20054062 GSE16780
GX-Orozco1 (macrophage_HMDP_Oro1_ctrl)	N = 21,885 Affy M430	85 HMDP strains; males age 16wks	1-2	macrophage RNA, control group	Orozco L, Bennett BJ, Lusis AJ (2012) PMID:23101632 GSE38705
GX-Orozco2 (macrophage_HMDP_Oro2_LPS)	N = 21,885 Affy M430	88 HMDP strains; males age 16wks	1-2	macrophage RNA, treated with lipopolysaccharide (LPS)	Orozco L, Bennett BJ, Lusis AJ (2012) PMID:23101632 GSE38705
GX-Orozco3 (macrophage_HMDP_Oro3_OxPAPC)	N = 21,885 Affy M430	79 HMDP strains; males age 16wks	1-2	macrophage RNA, treated with OxPAPC	Orozco L, Bennett BJ, Lusis AJ (2012) PMID:23101632 GSE38705
GX-Rusyn3 (liver_Rusyn3_ctrl)	N = 25,229 Agilent G4122F	16 inbred strains; males age 6-8wks	2-3	whole liver RNA, vehicle controls	Rusyn I, Threadgill DW (2010) PMID:21135412 GSE24278
GX-Rusyn4 (liver_Rusyn4_TCE)	N = 25,229 Agilent G4122F	16 inbred strains; males age 6-8wks	2-3	whole liver RNA, treated with trichloroethylene (TCE)	Rusyn I, Threadgill DW (2010) PMID:21135412 GSE24278
GX-Shockley1 (liver_Sho1_baseline)	N = 43,110 Affy M430	10 inbred strains; females, males age 10-13wks	3	whole liver RNA, control cohort for high-fat diet study	Shockley K, Churchill GA (2008) PMID:19671657 GSE10493
GX-Shockley2 (liver_Sho2_highfat)	N = 43,110 Affy M430	10 inbred strains; females, males age 10-13wks	3	whole liver RNA, high-fat cohort (4wks on high-fat diet)	Shockley K, Churchill GA (2008) PMID:19671657 GSE10493
GX-Su1 (liver_Su1)	N = 21,184 Merck Rosetta	22 inbred strains; females, males age 20wks	7-11	whole liver RNA	Schadt EE, Su WL (2010) PMID:20135320 GSE13870
GX-Tabakoff1 (brain_Tabakoff1)	N = 39,985 Affy M430	20 inbred strains; males age 10-12wks	4-6	whole brain mRNA	Tabakoff B, Bhave S, Saba L (2007) PMID:17760997 PMID:21054686
GX-Tabakoff2 (brain_LXS_Tabakoff2)	N = 16,334 Affy na31	61 ILSXISS strains; males age 10-13wks	3-6	whole brain RNA	Tabakoff B, Saba L (2011)

Build and annotation notes

All chromosome locations were converted to GRCm38 on Dec 20 '12. The platform vendor's probeset mm9 location annotation was converted to GRCm38 using UCSC liftOver utility, then gene symbols were reassigned based on these GRCm38 locations and the current MGI gene info.

Affymetrix Mouse430_2_Annotations (version 30) were downloaded from Affymetrix web site in Nov 2009.

Merck Rosetta annotations were downloaded from GEO's GPL3677 page in Sept 2010, and gene symbols found by running Entrez gene ids through MGI batch query system. Rosetta annotations do not include basepair locations; for Rosetta these were added by MPD using the midpoint coordinate of the annotated gene.

Agilent annotations for G4122F were downloaded from GEO's GPL7202 page in March 2011. Additional annotations for G4121A downloaded from GEO's GPL6466 page in March 2012.

Affymetrix Mouse Gene ST 1.0 transcript cluster annotations (version 32) downloaded from Affymetrix web site Feb 2012.

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