CPEB1 and CPEB4-associated mRNAs in mice striatum

To identify CPEB1 and CPEB4 regulated RNA we performed CPEB1 and CPEB4 RNA immunoprecipitation (RIP) followed by microarray hybridization analysis with striatal (St) RNA from wild-type (WT) and R6/1 mice (HD mice). Four male WT and HD mice were sacrified at the age of 7-8 months. Striatum tissue was pooled by genotype. mRNA-protein complexes were crosslinked with formaldehyde in PBS and samples were homogenized in lysis buffer. Lysates were precleared with unconjugated dynabeads and aliquot was stored (INPUT). The rest of the extract was immunoprecipitated with the antibody-conjugated dynabeads (anti-CPEB1, anti-CPEB4 and rabbit igG). Input and immunoprecipitated RNAs were extracted, purified and amplified. cDNA was hybridized in GeneChip mouse arrays and CEL files were generated from DAT files using Affymetrix Command Console software.