Project description:A technical comparison of Agilent SureSelect Focussed Exome and TruSight One Mendeliome sequencing kits, by triplicate sequencing of the cell line DNA of NA12878, NA12891, NA12892 and NIST RM8395
Project description:Discovery of common Asian copy number variants using a novel integrated high-resolution array CGH and massively parallel DNA sequencing. We attempted to discover common Asian copy number variants (CNVs) from the DNA of 30 Asian women (10 Korean, 10 CHB (HapMap), 10 JPT (HapMap)) using a custom-designed 24M-oligonucleotide Agilent platform (1.1M X 24 slides). The reference sample for aCGH was NA10851 (HapMap CEPH). In addition to the 30 women, 3 more individuals were analyzed as controls (AK1 (Kim, J.I. et al., 2009 Nature), NA12878 and NA19240).
Project description:Illumina methylation 27 array (Illumina) analysis was performed on 24 HapMap individuals including one CEU trio (family 1463 including NA12878, NA12891, NA12892) and one YRI trio (family Y117 including NA19240, NA19238, NA19239)
Project description:Accurate functional annotation of regulatory elements is essential for understanding global gene regulation. Here, we report a genome-wide map of 827,000 transcription factor binding sites in human lymphoblastoid cell lines, which is comprised of sites correspond-ing to 239 position weight matrices of known transcription factor binding motifs, and 49 novel sequence motifs. To generate this map, we developed a probabilistic framework that integrates cell- or tissue-specific experimental data such as histone modifications and DNa-seI cleavage patterns with genomic information such as gene annotation and evolutionary conservation. Comparison to empirical ChIP-seq data suggests that our method is highly accurate yet has the advantage of targeting many factors in a single assay. We anticipate that this approach will be a valuable tool for genome-wide studies of gene regulation in a wide variety of cell-types or tissues under diverse conditions. DNaseI-Seq on two YRI Hapmap cell lines. Each individual sequenced on 8 lanes of the Illumina Genome Analyzer II
Project description:Whole human genome sequencing of an CEPH/UTAH female individual (HapMap: NA12878) using the Illumina HiSeq 2000 and paired 100 base reads
