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Individual-specific and allele-specific chromatin signatures in diverse human populations

ABSTRACT: This dataset contains DNase-seq data and CTCF ChIP-seq data for 6 lymphoblastoid cell lines. There are 3 cell lines from a YRI trio and 3 lines from a CEU trio (HapMap GM19238, GM19239, GM 19240, GM12891, GM12892, GM12878). 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: GSE19622 | GEO | 2010/03/15

REPOSITORIES: GEO

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Individual-specific and allele-specific chromatin signatures in diverse human populations

Project description:This dataset contains DNase-seq data and CTCF ChIP-seq data for 6 lymphoblastoid cell lines. There are 3 cell lines from a YRI trio and 3 lines from a CEU trio (HapMap GM19238, GM19239, GM 19240, GM12891, GM12892, GM12878). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf DNase-seq and ChIP-seq data from each of the 6 cell lines.

2010-03-15 | E-GEOD-19622 | biostudies-arrayexpress

NFkB perturbation followed by genome-wide allelic-expression data assessment

Project description:We developed a method that perturbs transcription factor followed by monitoring genome-wide allelic expression measurements in living cells. As a model for this novel approach, we chose the factor NFÎºB. We performed TNF-Î± induction coupled to inhibition of NFÎºB in LCLs followed by Allelic Expression (AE) analysis on Illumina HumanOmni5-Quad BeadChips. Samples used included two HapMap trios: one from the CEU (GM12891, GM12892, and GM12878) and one from the YRI (GM19239, GM19238, and GM19240) population. NF-ÎºB knockdown was validated using RT-PCR of known gene targets for NFkB. Differential AE was assessed on Illumina HumanOmni5-Quad BeadChips for each experimental condition: (1) inhibition with Helenanin followed 1 hour later by activation by TNF-Î± (TN); (2) activation by TNF-Î± (tnfalpha); (3) DMSO; (4) no treatment (notmt).

2014-11-03 | E-GEOD-61254 | biostudies-arrayexpress

Germline Copy Number Variants are Associated with Methylation Variation in the Genome

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)

2020-10-05 | GSE114131 | GEO

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

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

Genotyping of human lymphoblastoid cell lines from CEU and YRI HapMap individuals

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.

2010-03-02 | E-TABM-927 | biostudies-arrayexpress

Custom array CGH validation of de novo CNVs in CEU HapMap samples

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.

2010-09-01 | GSE23575 | GEO

A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity

Project description:Large inter-individual variance has been observed in sensitivity to drugs. To comprehensively decipher the genetic contribution to these variations in drug susceptibility, we present a genome-wide model utilizing human lymphoblastoid cell lines from the International HapMap consortium, of which extensive genotypic information is available, to identify genetic variants that contribute to chemotherapeutic agent-induced cytotoxicity. Our model integrated genotype, gene expression and sensitivity of HapMap cell lines to drugs. Cell lines derived from 30 trios of European descent (CEU) and 30 trios of African descent (YRI) were utilized. Cell growth inhibition at increasing concentrations of etoposide for 72 h was determined using alamarBlue® assay. Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip® Human Exon 1.0ST Array. We evaluated associations between genotype and cytotoxicity, genotype and gene expression and correlated gene expression of the identified candidates with cytotoxicity. The analysis identified 63 genetic variants that contribute to etoposide-induced toxicity through their effect on gene expression. These include genes that may play a role in cancer (AGPAT2, IL1B and WNT5B) and genes not yet known to be associated with sensitivity to etoposide. This unbiased method can be used to elucidate genetic variants contributing to a wide range of cellular phenotypes induced by chemotherapeutic agents. Keywords: exon array

2007-05-31 | GSE7792 | GEO

Identification of Genetic Variants Contributing to Cisplatin-Induced Cytotoxicity using a Genome-wide Approach

Project description:Cisplatin, a platinating agent commonly used in treating several cancers is associated with nephrotoxicity, neurotoxicity and ototoxicity that have hindered its utility. To gain a better understanding of the genetic variants associated with cisplatin induced toxicity, we present a step-wise approach integrating genotypes, gene expression and sensitivity of HapMap cell lines to cisplatin. Cell lines derived from 30 trios of European descent (CEU) and 30 trios of African descent (YRI) were utilized to develop a preclinical model to identify genetic variants and gene expression that contribute to cisplatin induced cytotoxicity in two different populations. Cytotoxicity was determined as cell growth inhibition at increasing concentrations of cisplatin for 48 h. Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip® Human Exon 1.0 ST Array. We identified 6, 2 and 9 representative SNPs that contribute to cisplatin-induced cytotoxicity through their effects on 8, 2 and 16 gene expressions in the combined, CEPH and Yoruban populations, respectively. These genetic variants contribute to 27, 29 and 45% of the overall variation in cell sensitivity to cisplatin in the combined, CEPH and Yoruban populations, respectively. Our whole genome approach can be used to elucidate expression quantitative trait loci contributing to a wide range of cellular phenotypes. Keywords: exon array

2007-06-06 | GSE7761 | GEO

Transcription profiling of human samples show variation in african americans with genetic ancestry at most expressed genes

Project description:Variation in gene expression is a fundamental aspect of human phenotypic variation. Several studies have analyzed gene expression levels in populations of different continental ancestry, and concluded that there is variation across populations at a fraction of expressed genes. Here we analyze gene expression levels in African American cell lines, which differ from previously analyzed cell lines in that samples from this population have variable proportions of continental ancestry. We show that for most genes examined, gene expression varies with genetic ancestry. Experiment Overall Design: Lymphoblastoid cell lines (LCL) for 60 HapMap CEU, 60 HapMap YRI, and 82 AFA from the Human Variation Panel were obtained from Coriell Cell Repositories. LCLs were grown in culture, total RNA was extracted and hybridized to Affymetrix HG-FOCUS arrays.

2009-01-14 | E-GEOD-10824 | biostudies-arrayexpress

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