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| 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 [ATAC_MQ] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| 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.
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| Overall design |
J2 virus immortalized Bone-marrow derived macrophages stimulated with lipid-A for 0, 30, 60 or 120 minutes. Chromatin was collected and treated with Tn5 transposase to profile DNA accessibility.
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| 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 14, 2023 |
| Last update date |
Jan 17, 2024 |
| Contact name |
Stephen Smale |
| E-mail(s) |
smale.geo.uploads@gmail.com
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| Organization name |
University of California Los Angeles
|
| Department |
MIMG
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| Lab |
Smale Lab
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| Street address |
6-730 MRL 675 Charles E. Young Drive South
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| City |
Los Angeles |
| State/province |
Ca |
| ZIP/Postal code |
90024 |
| Country |
USA |
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| Platforms (2) |
| GPL21493 |
Illumina HiSeq 3000 (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (35)
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| 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 |
PRJNA983736 |
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