Genome-wide baseline microRNA expression quantification in HapMap phase I CEU and YRI samples
ABSTRACT: Baseline microRNA (miRNA) expression was evaluated in 107 HapMap lymphoblastoid cell lines (LCLs; 53 CEU and 54 YRI) using Exiqon miRCURY LNA arrays v10.0 (Exiqon array). Total RNA from each of the 107 HapMap sample was labeled and hybridized onto an Exiqon array
Project description:Paired genomic DNA and cDNA samples obtained from lymphoblastoid cell lines from CEU and YRI HapMap individuals were hybridized to custom Illumina SNP arrays to study allele-specific expression in this tissue.
Project description:This SuperSeries is composed of the following subset Series: GSE23572: Custom array CGH validation of de novo CNVs in asthma samples GSE23575: Custom array CGH validation of de novo CNVs in CEU HapMap samples Refer to individual Series
Project description:This is the validation data for candidate de novo CNV calls made in the CEU Hapmap by Itsara et al., Genome Research 2010. In this study, de novo CNV calls were initially made with Illumina 1M SNP arrays. Validation of CNV calls was performed with Nimblegen custom array CGH using the extended CEPH pedigrees. A truly de novo CNV would be unobserved in the first generation (CEU trio parents), validated in the second generation (CEU trio children), and assuming no selective effects, transmitted to approximately half of the individuals in the third generation. We attempted validation of 4 de novo CNVs in 3 extended CEPH pedigrees: 1358, 1408, and 1459. 12 samples were hybridized in each of the three pedigrees (36 samples total) against a previously well-characterized reference (GM15510; see Tuzun et al., Nat Genet 2005).