Transcriptomics

Dataset Information

298

Human variation in PolII and NF-KappaB binding (RNA-seq study with TNF-alpha induced)


ABSTRACT: We examined genome-wide variation in transcription factor binding in different individuals and a chimpanzee using chromatin immunoprecipitation followed by massively-parallel sequencing (ChIP-Seq). The binding sites of RNA Polymerase II (Pol II) as well as a key regulator of immune responses, NFkB, were mapped in ten HapMap lymphoblastoid cell lines derived from individuals of African, European, and Asian ancestry, including a parent-offspring trio. We also mapped gene expression in all ten human cell lines for two treatment conditions: a) no treatment and b) following induction by TNF-alpha. Genome-wide comparison of Pol II and NF-KappaB binding in ten individuals. RNA-seq study with TNF-alpha treatment.

ORGANISM(S): Homo sapiens  

SUBMITTER: Fabian Grubert   Minyi Shi  Michael P Wilson  Maya Kasowski  Lukas Habegger  Manoj Hariharan  Joel Rozowsky  Akwasi Asabere  Mi-Young Hong  Christopher Heffelfinger  Mark B Gerstein  Alexander E Urban  Jan O Korbel  Sebastian M Waszak  Sherman M Weissman  Michael Snyder 

PROVIDER: E-GEOD-19481 | ArrayExpress | 2010-03-22

SECONDARY ACCESSION(S): SRP002128GSE19481PRJNA123947

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications


Differences in gene expression may play a major role in speciation and phenotypic diversity. We examined genome-wide differences in transcription factor (TF) binding in several humans and a single chimpanzee by using chromatin immunoprecipitation followed by sequencing. The binding sites of RNA polymerase II (PolII) and a key regulator of immune responses, nuclear factor kappaB (p65), were mapped in 10 lymphoblastoid cell lines, and 25 and 7.5% of the respective binding regions were found to dif  ...[more]

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