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Lung mRNA expression from Affymetrix M430 2.0 microarrays in a recombinant inbred intercross between C57BL/6J and DBA/2J was analyzed across 51 strains (HZI BXD Lung M430v2 (Apr08) RMA). Four NCoR1 probe sets from this microarray were selected: 1423200_at (3�� UTR), 1435914_at (3�� UTR), 1423202_a_at (exonic and 3��UTR), and 1423201_at (exonic). For all four probe sets, the top 2000 Pearson's trait correlations within the same microarray were calculated ( Table S4. List of Genes whose Expression Covaries with NCoR1 in Muscle, Related to Figure?4?and?Table S5. List of Genes whose Expression Covaries with NCoR1 in Lung, Related to Figure?4). Strong correlates were selected for validation by qRT-PCR (e.g., Mck; r?= �C0.63 and Mef2d; r?= �C0.73, both p?[http://en.wikipedia.org/wiki/Ribonucleotide_reductase Ribonucleotide reductase] metabolic roles, and genes with significant correlations were selected for qRT-PCR as well (e.g., Cs; r?= �C0.35, p?= 0.01). Mouse embryonic fibroblasts (MEFs) from NCoR1L2/L2 floxed mice were prepared and immortalized. Then, GFP- or Cre recombinase-expressing adenovirus (Ad-GFP or -Cre) were infected at a MOI?= 20 to generate NCoR1+/+ or ?/? MEFs, respectively. C2C12 skeletal muscle cells were grown and differentiated as described previously ( Lagouge et?al., 2006). In order to knockdown NCoR1 expression, two different [http://www.selleckchem.com/products/VX-770.html Selleck VX770] shRNA containing adenoviruses [http://www.selleckchem.com/products/ch5424802.html CH5424802 mouse] were made by BLOCK-iT Adenoviral RNAi Expression System (Invitrogen) and each set of oligonucleotides was used following the manufacturer's instructions: Set 1: FWD, 5��-CACCGCGTCAGCTTTCTGTGATTCCCCAAGGAATCACAGAAAGCTGACGC-3��; REV, 5��-AAAAGCGTCAGCTTTCTGTGATTCCTTCGGGAATCACAGAAAGCTGACGC-3��. Set 2: FWD, 5��-CACCGGGTCTATCTCTCTGGGATTGCGAACAATCCCAGAGAGATAGACCC-3��; REV, 5��-AAAAGGGTCTATCTCTCTGGGATTGTTCGCAATCCCAGAGAGATAGACCC-3. C2C12 cells were infected with either these two different shRNA-containing adenoviruses or shRNA for LacZ (control) at a MOI?= 20. In one set of ChIP experiments to evaluate the recruitment of NCoR1 to the promoters of the mouse Pdk4 and Ucp3 genes, we used NIH 3T3 cells (10x106 cells) transfected with pCMX-NCoR1-FLAG, pcDNA3-VTS-mPPAR�� (V5-tagged PPAR��/�� expression vector), and pcDNA-HA-ERR�� with lipofectamine 2000 according to the manufacturers protocol. We also used pCMX-NCoR1-FLAG- and pcDNA-HA-ERR��-transfected HEK293 cells for the analysis of human Pdk4 promoter. We adapted the ChIP protocol described previously ( M��tivier et?al., 2008). In another set of experiments, we used non-transfected C2C12 myotubes and a homemade NCoR1 polyclonal antibody to detect the recruitment of endogenous NCoR1 to known PPAR��/�� and ERR�� binding sites of Ucp3, and Pdk4.