Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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MSNP data for normal blood, normal bone marrow, CD34+ cells and placenta samples

ABSTRACT: A novel method for detecting genome-wide ASM (allele-specific methylation) was developed by modification of the Affymetrix 250K StyI SNP arrays. Using this method, and the above mentioned samples, we consistently detected ASM in non-imprinted regions of the genome. Interestingly, ASM appears to be strongly correlated with the SNP sequences in cis. DNA from various sources (6 normal blood, 2 normal bone marrow, 2 CD34+ bone marrow, and 3 placenta samples) was genotyped and ASM was scored as an allele call conversion from 'AB' (heterozygous) to 'AA' or 'BB' (homozygous) in the StyI+HpaII genomic representation, compared to the StyI-only representation. Each sample was subjected to 5 runs of genotyping on the 250K StyI array, including 2 StyI alone, 2 StyI+HpaII and 1 StyI+MspI.

ORGANISM(S): Homo sapiens

SUBMITTER: Le Jiang 

PROVIDER: E-GEOD-11409 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation.

Kerkel Kristi K   Spadola Alexandra A   Yuan Eric E   Kosek Jolanta J   Jiang Le L   Hod Eldad E   Li Kerry K   Murty Vundavalli V VV   Schupf Nicole N   Vilain Eric E   Morris Mitzi M   Haghighi Fatemeh F   Tycko Benjamin B  

Nature genetics 20080622 7

Allele-specific DNA methylation (ASM) is a hallmark of imprinted genes, but ASM in the larger nonimprinted fraction of the genome is less well characterized. Using methylation-sensitive SNP analysis (MSNP), we surveyed the human genome at 50K and 250K resolution, identifying ASM as recurrent genotype call conversions from heterozygosity to homozygosity when genomic DNAs were predigested with the methylation-sensitive restriction enzyme HpaII. Using independent assays, we confirmed ASM at 16 SNP-  ...[more]

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