NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE270366 Query DataSets for GSE270366
Status Public on Jun 21, 2024
Title The transcription factor NF-κB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling [CHiC]
Organism Mus musculus
Experiment type Other
Summary Macrophages play a critical role in bridging the innate and adaptive immune systems, which requires timely and precise transcription control when responding to danger signals. Gene expression networks in macrophages have been profiled extensively in recent decades with the advancement of high-throughput sequencing technologies. However, unveiling critical mechanistic insights into control of diverse transcriptional networks has proven to be challenging. Recent evidence has suggested that the accessibility of chromatin structure can provide an integral means of transcription regulation. We have used the relatively recent Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq) method to assess chromatin accessibility with optimal resolution in mouse bone marrow derived macrophages during the course of lipid- A stimulation. This advanced method enabled us to characterize the chromatin state of genome-wide regulatory regions. By applying a quantitative systematic approach, we obtained mechanistic insights into the highly selective role of the major transcription factors, NF-κB and IRF3, in nucleosome remodeling and transcription regulation.
 
Overall design Long distant interactions to promoters were captured for DNA sequencing in WT clone. Data generated from bone marrow-derived macrophages stimulated with lipid-A for 0 and 120 minutes.
 
Contributor(s) Feng A, Thomas BJ, Smale ST
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jun 20, 2024
Last update date Jun 21, 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)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (4)
GSM8340298 WT_clone_0h_r1, CHiC
GSM8340299 WT_clone_2h_r1, CHiC
GSM8340300 WT_clone_0h_r2, CHiC
This SubSeries is part of SuperSeries:
GSE234914 Toll-Like Receptor-Induced Nucleosome Remodeling Achieved by Broadly Acting NF-kB in Collaboration with Transcription Factors Conferring Selectivity
Relations
BioProject PRJNA1126259

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
GSE270366_RAW.tar 1.1 Gb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap