Data Set Group2: GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11)

Data Set: GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA GN Accession: GN373 GEO Series: GSE16780 Title: Hybrid Mouse diversity Panel Liver Expression Profile Organism: Mouse (Mus musculus, mm10) Group: BXD Tissue: Liver mRNA Dataset Status: Public Platforms: Affy Mouse Genome 430A, 430B, 430A 2.0 (GPL339,GPL340) Normalization: RMA

Contact Information Aldons Lusis University of California, Los Angeles UCLA Med-Cardio/Microbio BOX 951679 Los Angeles, CA 90095 USA Tel. 310 825-1359 jlusis@mednet.ucla.edu Website Download datasets and supplementary data files

Specifics of this Data Set:

None

Summary:

Novel, systems-based approach to mouse genetics.

About the cases used to generate this set of data:

For complete information please refer to Bennett BJ, Farber CR, Orozco L, Kang HM, Ghazalpour A, Siemers N, Neubauer M, Neuhaus I, Yordanova R, Guan B, Truong A, Yang WP, He A, Kayne P, Gargalovic P, Kirchgessner T, Pan C, Castellani LW, Kostem E, Furlotte N, Drake TA, Eskin E, Lusis AJ (2010) A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Research 20:281-90 PMID: 20054062

About the tissue used to generate this set of data:

Hybrid Mouse diversity Panel Liver Expression Profile

About the array platform:

Platform GPL8759 [HT_MG-430A] Affymetrix HT Mouse Genome 430A Array The probe sets were selected from sequences derived from GenBank®, dbEST and RefSeq. The sequence clusters were created from the UniGene database (Build 107, June 2002) and then refined by analysis and comparison with the publicly available draft assembly of the mouse genome from the Whitehead Institute Center for Genome Research (MSCG, April 2002). Oligonucleotide probes complementary to each corresponding sequence are synthesized in situ on the array. Eleven pairs of oligonucleotide probes, including a perfect match and mismatch probe, are used to measure the level of transcription of each sequence represented on the GeneChip® HT Mouse Genome 430 Array Plate Set.

About data values and data processing:

For complete information please refer to A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Res 2010 Feb;20(2):281-90. PMID: 20054062

Notes:

Raw data provided as supplementary file at GEO Series GSE16780

Experiment Type:

Expression profiling by array. Expression Profiles from 99 strains of inbred and recombinant inbred mice. Most assayed in triplicate. Two of 288 chips were excluded from the final analysis due to low QC scores.

Contributor:

Bennett BJ, Ghazalpour A

Citation:

Bennett BJ, Farber CR, Orozco L, Kang HM et al. A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Res 2010 Feb;20(2):281-90. PMID: 20054062

Data source acknowledgment:

Bennett BJ, Ghazalpour A

Study Id:

136

• 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)