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Title: NFkB perturbation followed by genome-wide allelic-expression data assessment      
dateReleased:
11-03-2014
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 NFκB. We performed TNF-α induction coupled to inhibition of NFκB 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-κB 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-α (TN); (2) activation by TNF-α (tnfalpha); (3) DMSO; (4) no treatment (notmt).
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-61254
refinement:
raw
alternateIdentifiers:
61254
keywords:
functional genomics
dateModified:
11-08-2014
availability:
available
types:
gene expression
name:
Homo sapiens
ID:
A-GEOD-14157
name:
Illumina HumanOmni5-Quad BeadChip (HumanOmni5-4v1_B)
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-61254/E-GEOD-61254.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-61254/E-GEOD-61254.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61254
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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