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Series GSE55105 Query DataSets for GSE55105
Status Public on Aug 29, 2014
Title The NF-kB genomic landscape in lymphoblastoid B-cells
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The nuclear factor kB (NF-kB) subunits RelA, RelB, c-Rel, p50 and p52 are each critical for B-cell development and function. To systematically characterize their responses to canonical and non-canonical NF-kB pathways activity, we performed ChIP-seq analysis in lymphoblastoid B-cells. We found a surprisingly complex NF-kB binding landscape, which did not readily reflect the two NF-kB pathway paradigm. Instead, ten subunit binding patterns were observed at promoters and eleven at enhancers. Surprisingly, nearly one-third of NF-kB binding sites lacked kB motifs. De novo motif finding uncovered distinct modes of NF-kB recruitment at these sites. The oncogenic forkhead box protein FOXM1 and NF-kB co-occupied many kB sites despite the absence of a FOXM1 DNA motif. FoxM1 knockdown decreased expression of key NF-kB targets and caused apoptosis. Our study highlights opportunities for selective therapeutic NF-kB blockade.
Overall design ChIP-seq was used to define the genomic landscape of NF-kB DNA binding in lymphoblastoid cells.

The raw data for GSM2628089 are not available.
Contributor(s) Zhao B, Barrera LA, Ersing I, Willox B, Schmidt S, Zhou H, Shi T, Mollo S, Greenfeld H, Takasaki K, Jiang S, Cahir-McFarland E, Kellis M, Bulyk ML, Kieff E, Gewurz B
Citation(s) 25159142, 25255445
Submission date Feb 18, 2014
Last update date May 15, 2019
Contact name Benjamin Gewurz
Organization name Brigham and Women's Hospital
Department Medicine
Street address 181 Longwood Ave
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (10)
GSM2628088 RelA ChIP-seq rep.1
GSM2628089 RelA ChIP-seq rep.2
GSM2628090 RelB ChIP-seq rep.1
BioProject PRJNA238539
SRA SRP107497

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Supplementary file Size Download File type/resource
GSE55105_RelA.TagDens.bd150.st50.wig.tdf 418.3 Mb (ftp)(http) TDF
GSE55105_RelB.TagDens.bd150.st50.wig.tdf 418.0 Mb (ftp)(http) TDF
GSE55105_cRel.TagDens.bd150.st50.wig.tdf 418.5 Mb (ftp)(http) TDF
GSE55105_p50.TagDens.bd150.st50.wig.tdf 414.0 Mb (ftp)(http) TDF
GSE55105_p52.TagDens.bd150.st50.wig.tdf 417.3 Mb (ftp)(http) TDF
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Processed data are available on Series record
Raw data are available in SRA

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