|
| Status |
Public on Jan 04, 2020 |
| Title |
Accessible chromatin profiles of IL-4 stimulated mouse peritoneal macrophages derived from different cellular lineages |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Interleukin-4 (IL-4) activates macrophages to adopt a distinct phenotype important for tissue repair and helminth infection, but the molecular basis of chromatin remodeling in response to IL-4 stimulation is not understood. We find that IL-4 activation of terminally differentiated macrophages in mice is accompanied by cell-type-specific chromatin remodeling in regions enriched with binding motifs of the pioneer transcription factor PU.1. Mutation studies based on natural genetic variation between C57BL/6 and BALB/c mouse strains demonstrate that accessibility of these IL-4 induced regions can be regulated through differences in DNA shape, without disruption of pioneer factor motifs. We propose a model whereby DNA shape features of stimulation-dependent genomic elements contribute to differences in the accessible chromatin landscape of alternatively activated macrophages on different genetic backgrounds.
|
| |
|
| Overall design |
We FACS-sorted resting and IL-4 stimulated mouse peritoneal macrophages of F4/80hi CD206- (tissue resident) and F4/80int CD206+ (monocyte-derived) phenotypes for accessible chromatin profiling by ATAC-Seq.
|
| |
|
| Contributor(s) |
Tang M, Loke P |
| Citation(s) |
32661179 |
| |
| Submission date |
Jun 21, 2018 |
| Last update date |
Aug 24, 2020 |
| Contact name |
Mei San Tang |
| Organization name |
Washington University in St Louis
|
| Department |
Pathology & Immunology
|
| Street address |
660 S Euclid, Campus Box 8118
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63108 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (35)
|
|
| This SubSeries is part of SuperSeries: |
| GSE116108 |
Profiles of IL-4 stimulated mouse peritoneal macrophages |
|
| Relations |
| BioProject |
PRJNA477289 |
| SRA |
SRP151025 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE116107_ATACSeqB6BalbcIL4c_union_peaks_max100.txt.gz |
923.7 Kb |
(ftp)(http) |
TXT |
| GSE116107_ATACSeqIL4cMacs_union_peaks_max100.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE116107_B6_IL4c_dedup_nochrMY_posSorted_merged.tdf.gz |
222.6 Mb |
(ftp)(http) |
TDF |
| GSE116107_B6_ThioIL4c_dedup_nochrMY_posSorted_merged.tdf.gz |
225.5 Mb |
(ftp)(http) |
TDF |
| GSE116107_Balbc_IL4c_dedup_nochrMY_posSorted_merged.tdf.gz |
161.5 Mb |
(ftp)(http) |
TDF |
| GSE116107_Balbc_ThioIL4c_dedup_nochrMY_posSorted_merged.tdf.gz |
203.4 Mb |
(ftp)(http) |
TDF |
| GSE116107_M0_merged_runs_nochrMY_dedup.tdf.gz |
132.9 Mb |
(ftp)(http) |
TDF |
| GSE116107_M1_merged_runs_nochrMY_dedup.tdf.gz |
136.2 Mb |
(ftp)(http) |
TDF |
| GSE116107_M2_merged_runs_nochrMY_dedup.tdf.gz |
184.8 Mb |
(ftp)(http) |
TDF |
| GSE116107_M3_merged_runs_nochrMY_dedup.tdf.gz |
136.0 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
Less...
More...