Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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

ABSTRACT: 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).

ORGANISM(S): Homo sapiens

SUBMITTER: Tomi Pastinen

PROVIDER: E-GEOD-61254 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs.

Adoue Veronique V Schiavi Alicia A Light Nicholas N Almlöf Jonas Carlsson JC Lundmark Per P Ge Bing B Kwan Tony T Caron Maxime M Rönnblom Lars L Wang Chuan C Chen Shu-Huang SH Goodall Alison H AH Cambien Francois F Deloukas Panos P Ouwehand Willem H WH Syvänen Ann-Christine AC Pastinen Tomi T

Molecular systems biology 20141016

Most complex disease-associated genetic variants are located in non-coding regions and are therefore thought to be regulatory in nature. Association mapping of differential allelic expression (AE) is a powerful method to identify SNPs with direct cis-regulatory impact (cis-rSNPs). We used AE mapping to identify cis-rSNPs regulating gene expression in 55 and 63 HapMap lymphoblastoid cell lines from a Caucasian and an African population, respectively, 70 fibroblast cell lines, and 188 purified mon ...[more]

PMID: 25326100

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Dataset Information

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

Publications

Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs.

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