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DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

ABSTRACT: We measured the methylation status at 27,578 CpG sites using the Human Methylation27 DNA array in 77 HapMap Yoruba lymphoblastoid cell lines.

ORGANISM(S): Homo sapiens

PROVIDER: GSE26133 | GEO | 2011/01/05

SECONDARY ACCESSION(S): PRJNA135379

REPOSITORIES: GEO

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DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

Project description:We measured the methylation status at 27,578 CpG sites using the Human Methylation27 DNA array in 77 HapMap Yoruba lymphoblastoid cell lines. Bisulphite converted DNA from 77 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip

2011-01-05 | E-GEOD-26133 | biostudies-arrayexpress

CTCF HAPMAP VARIATION

Project description:This study will look at variation in CTCF binding in humans as assayed by ChIP-seq on 60 HapMap lymphoblastoid cell lines.

2013-09-04 | E-ERAD-141 | biostudies-arrayexpress

BLUEPRINT methylome of the HapMap cell line GM18507 (Coriell cell line NA18507)

Project description:Whole genome bisulfite sequencing (WGBS) of the NA18507 (Yoruba) lymphoblastoid cell line

2016-02-25 | GSE66285 | GEO

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines.

Project description: Not available

| S-EPMC3091299 | biostudies-literature

BLUEPRINT methylome of the HapMap cell line GM18507 (Coriell cell line NA18507)

Project description:Whole genome bisulfite sequencing (WGBS) of the NA18507 (Yoruba) lymphoblastoid cell line high resolution methylome of one cell type

2016-02-25 | E-GEOD-66285 | biostudies-arrayexpress

Homo sapiens strain:(YRI) Yoruba HapMap population

Project description:CompleteGenomics sequencing of (YRI) Yoruba HapMap population

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Genome-wide baseline microRNA expression quantification in HapMap phase I CEU and YRI samples

Project description: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).

2012-07-29 | GSE34406 | GEO

Homo sapiens strain:(YRI) Yoruba HapMap population

Project description:Whole genome sequencing of (YRI) Yoruba HapMap population

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Identification of genetic variants that affect histone modifications in human cells

Project description:Histone modifications are important markers of function and chromatin state, yet the DNA elements that direct them to specific locations in the genome are poorly understood. Here we use the genetic variation in Yoruba lymphoblastoid cell lines as a natural experiment to identify genetic differences that affect histone marks and to better understand their relationship with transcriptional regulation. Across the genome, we identified hundreds of quantitative trait loci that impact histone modification or RNA polymerase (PolII) occupancy. In many cases the same variant is associated with quantitative changes in multiple histone marks and PolII, as well as in DNaseI sensitivity and nucleosome positioning, indicating that these molecular phenotypes often share a single underlying genetic cause. Variants that impact chromatin at distal regulatory sites frequently also direct changes in chromatin and gene expression at associated promoters; while most of these distal regulators enhance promoter activity, some act as distal chromatin silencers. Finally, we find that polymorphisms in transcription factor binding sites are often causally responsible for variation in local histone modification. In summary, the class of variants identified here generate coordinated changes in chromatin both locally and sometimes at distant locations, frequently drive changes in gene expression, and likely play an important role in the genetics of complex traits. ChIP-seq of RNA Polymerase II and 4 histone modifications (H3K4me1, H3K4me3, H3K27ac, H3K27me3) in 10 unrelated Yoruba HapMap lymphoblastoid cell lines

2013-10-01 | E-GEOD-47991 | biostudies-arrayexpress

Genome-wide baseline microRNA expression quantification in HapMap phase I CEU and YRI samples

Project description: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

2012-07-28 | E-GEOD-34406 | biostudies-arrayexpress

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