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Series GSE67343 Query DataSets for GSE67343
Status Public on Jan 18, 2016
Title A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Much has been learned about transcriptional cascades and networks from large-scale systems analyses of high-throughput data sets. However, analysis methods that optimize statistical power through simultaneous evaluation of thousands of ChIP-seq peaks or differentially expressed genes possess substantial limitations in their ability to uncover mechanistic principles of transcriptional control. By examining nascent transcript RNA-seq, ChIP-seq, and binding motif data sets from lipid A-stimulated macrophages with increased attention to the quantitative distribution of signals, we identified unexpected relationships between the in vivo binding properties of inducible transcription factors, motif strength, and transcription. Furthermore, rather than emphasizing common features of large clusters of co-regulated genes, our results highlight the extent to which unique mechanisms regulate individual genes with key biological functions. Our findings demonstrate the mechanistic value of stringent interrogation of well- defined sets of genes as a complement to broader systems analyses of transcriptional cascades and networks.
 
Overall design Bone marrow-derived macrophages were stimulated with lipid A for 0, 15, 30, 60, and 120 minutes. Chromatin was immunoprecipitated with antibodies against RelA, SRF, or IRF3.
 
Contributor(s) Tong A
Citation(s) 26924576
Submission date Mar 27, 2015
Last update date Jan 25, 2024
Contact name Stephen Smale
E-mail(s) smale.geo.uploads@gmail.com
Organization name University of California Los Angeles
Department MIMG
Lab Smale Lab
Street address 6-730 MRL 675 Charles E. Young Drive South
City Los Angeles
State/province Ca
ZIP/Postal code 90024
Country USA
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (30)
GSM1645112 RELA-0
GSM1645113 RELA-0-Rep2
GSM1645114 RELA-15
This SubSeries is part of SuperSeries:
GSE67357 A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation
Relations
BioProject PRJNA279552
SRA SRP056618

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
GSE67343_RAW.tar 4.4 Gb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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