E-WMIT-6 - Chromatin immunoprecipitation of human cells after lipopolysaccharide stimulation, to identify binding of NF-KappaB family members

Status
Submitted on 9 May 2006, released on 9 May 2006, last updated on 2 May 2014
Organism
Homo sapiens
Samples (35)
Arrays (2)
Protocols (6)
Description
The NF-KappaB family of transcription factors plays a critical role in numerous cellular processes, particularly the immune response. Our understanding of how the different NF-kappaB subunits act coordinately to regulate gene expression is based on a limited set of genes. We used genome-scale location analysis to identify targets of all five NF-kappaB proteins before and after stimulation of monocytic cells with bacterial lipopolysaccharide (LPS). In unstimulated cells, p50 and p52 bound to a significant number of gene promoters. p50 occupied genes together with RNA polymerase II and defined a set of genes to which other NF-kappaB proteins bound after LPS induction. In stimulated cells, genes bound by multiple NF-kappaB subunits exhibited the greatest increases in RNA polymerase II occupancy and gene expression. This study identifies novel NF-kappaB target genes, reveals how the different NF-kappaB proteins coordinate their activity and maps transcriptional regulatory networks that underlie the host response to infection.
Experiment types
ChIP-chip by array, binding site identification, compound treatment
Contacts
Elizabeth Herbolsheimer, Joerg Schreiber
Citation
Coordinated Binding of NF-KappaB Family Members in the Response of Human Cells to Lipopolysaccharide. Joerg Schreiber, Richard G. Jenner, Heather L. Murray, Georg K. Gerber, David K. Gifford and Richard A. Young. Proc Natl Acad Sci U S A 103(15):5899-5904 (2006)
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-WMIT-6.idf.txt
Sample and data relationshipE-WMIT-6.sdrf.txt
Raw data (1)E-WMIT-6.raw.1.zip
Array designsA-MEXP-48.adf.txt, A-WMIT-8.adf.txt
R ExpressionSetE-WMIT-6.eSet.r
Links