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Series GSE89970 Query DataSets for GSE89970
Status Public on Jun 06, 2017
Title Genome-wide map of HAEC chromatin landscape under resting and TNFa, IL1b, and OxPAPC stimulation, with corresponding transcription factor binding and RNA expression
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary We report the dynamic enhancer landscape of HAEC at baseline and under inflammatory stimulation, and also show the cistromes of ETS, AP-1 as well as key signal dependent transcription factors, with corresponding gene expression. We also describe the inflammatory transcriptional profile caused by inhibition of the ETS factor ERG with siRNA.
Overall design We use ChIP-seq for two histone modifications and ATAC-seq datasets to describe EC enhancers, poly-A selected RNA sequencing to show gene expression, and ChIP-seq to characterize the binding profile of EC transcription factors in relation to enhancers. ERG siRNA knockdown followed by RNA-seq was used to characterize the ERG knockdown phenotype.
Contributor(s) Romanoski CE, Hogan NT
Citation(s) 28585919
NIH grant(s)
Grant ID Grant title Affiliation Name
R00 HL123485 Systems Genetic Analysis of Atherogenic Transcriptional Regulation in Human Cells ABOR, UNIVERSITY OF ARIZONA CASEY E ROMANOSKI
Submission date Nov 17, 2016
Last update date May 15, 2019
Contact name Casey E Romanoski
Organization name University of Arizona
Department Cellular & Molecular Medicine
Street address 1657 E. Helen St.
City Tucson
State/province AZ
ZIP/Postal code 85721
Country USA
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (75)
GSM2394391 HAEC.atac.control.4h.rep1
GSM2394392 HAEC.atac.control.4h.rep2
GSM2394393 HAEC.atac.il1b.4h.rep1
BioProject PRJNA354352
SRA SRP093727

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
GSE89970_HAEC.rna.rpkm.txt.gz 4.6 Mb (ftp)(http) TXT
GSE89970_RAW.tar 45.3 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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