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Series GSE19481 Query DataSets for GSE19481
Status Public on Mar 22, 2010
Title Human variation in PolII and NF-KappaB binding (RNA-seq study with TNF-alpha induced)
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary 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.
 
Overall design Genome-wide comparison of Pol II and NF-KappaB binding in ten individuals. RNA-seq study with TNF-alpha treatment.
 
Contributor(s) Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong M, Weissman SM, Gerstein MB, Korbel JO, Snyder M
Citation(s) 20299548
Submission date Dec 15, 2009
Last update date May 15, 2019
Contact name Flora Vaccarino
Organization name Yale University
Department Child Study Center
Lab Vaccarino
Street address 230 South Frontage Road
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (10)
GSM485682 GM10847_RNA-SEQ_induced_Rep1
GSM485683 GM12878_RNA-SEQ_induced_Rep1
GSM485684 GM12891_RNA-SEQ_induced_Rep1
This SubSeries is part of SuperSeries:
GSE19486 Human variation in PolII and NF-KappaB binding
Relations
SRA SRP002128
BioProject PRJNA123947

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE19481_RAW.tar 5.5 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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