Dataset Information

Genotype (CNV and SNP) by Illumina 1MDuo and CBS from ENCODE/HudsonAlpha

ABSTRACT: This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Florencia Pauli mailto:fpauli@hudsonalpha.org). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). This track is produced as part of the ENCODE project. The track displays copy number variation (CNV) as determined by the Illumina Human 1M-Duo Infinium HD BeadChip assay and circular binary segmentation (CBS). The Human 1M-Duo contains more than 1,100,000 tagSNP markers and a set of ~60,000 additional CNV-targeted markers. The median spacing between markers is 1.5 kb and the mean spacing is 2.4 kb. The B-allele frequency and genotyping single nucleotide polymorphism (SNP) data generated by the experiment are not displayed, but are available for download from the Downloads page. Where applicable, biological replicates of each cell line are reported separately. Possible uses of the data include correction of copy number in peak-calling for ChIP-seq, transcriptome, DNase hypersensitivity, and methylation determinations. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

ORGANISM(S): Homo sapiens

PROVIDER: GSE40698 | GEO | 2012/09/07

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Florencia Pauli mailto:fpauli@hudsonalpha.org). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). This track is produced as part of the ENCODE project. The track displays copy number variation (CNV) as determined by the Illumina Human 1M-Duo Infinium HD BeadChip assay and circular binary segmentation (CBS). The Human 1M-Duo contains more than 1,100,000 tagSNP markers and a set of ~60,000 additional CNV-targeted markers. The median spacing between markers is 1.5 kb and the mean spacing is 2.4 kb. The B-allele frequency and genotyping single nucleotide polymorphism (SNP) data generated by the experiment are not displayed, but are available for download from the Downloads page. Where applicable, biological replicates of each cell line are reported separately. Possible uses of the data include correction of copy number in peak-calling for ChIP-seq, transcriptome, DNase hypersensitivity, and methylation determinations. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Isolation of genomic DNA and hybridization: Cells were grown according to the approved ENCODE cell culture protocols by the Myers lab and by other ENCODE production groups. The production group is reported in the metadata. Genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen). DNA concentration and quality were determined by fluorescence (Invitrogen Quant-iT dsDNA High Sensitivity Kit and Qubit Fluorometer), and 400 nanograms of each sample were hybridized to Illumina 1M-Duo DNA Analysis BeadChips. Processing and Analysis: The genotypes from the 1M-Duo Arrays were ascertained with BeadStudio by using default settings and formatting with the A/B genotype designation for each SNP. Primary QC for each sample was a cut-off at a call rate of 0.95. Copy Number Variation (CNV) analysis was performed with circular binary segmentation (DNAcopy) of the log R ratio values at each probe (Olshen et al., 2004). The parameters used were alpha=0.001, nperm=5000, sd.undo=1. The copy number segments are reported with the mean log R ratio for each chromosomal segment called by CBS. Log ratios of ~-0.2 to -1.5 can be considered heterozygous deletions, < -1.5 homozygous deletions, and > 0.2 amplifications. Primary QC for each sample was SD of < 0.6.

Dataset Information

Genotype (CNV and SNP) by Illumina 1MDuo and CBS from ENCODE/HudsonAlpha

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets