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Series GSE248432 Query DataSets for GSE248432
Status Public on Jan 16, 2024
Title Toll-Like Receptor-Induced Nucleosome Remodeling Achieved by Broadly Acting NF-kB in Collaboration with Transcription Factors Conferring Selectivity [BMDM_ATAC_2]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
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 Bone-marrow derived macrophages (background: C57Bl/6) were stimulated with Lipid A (100 ng/mL), Pam3CSK4 (100 ng/mL) or Poly (I:C) (100 µg/ml) for 0 or 2 hours. Chromatin was collected and treated with Tn5 transposase to profile DNA accessibility.
 
Contributor(s) Feng AC, Melo FM, Smale ST
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Nov 21, 2023
Last update date Jan 17, 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 (13)
GSM7913887 PolyIC_2h_r1
GSM7913888 Pam3_2h_r1
GSM7913889 PolyIC_2h_r2
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 PRJNA1043740

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Supplementary file Size Download File type/resource
GSE248432_RAW.tar 4.5 Gb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA

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