|
| Status |
Public on Jun 23, 2017 |
| Title |
Type I IFNs and TNF Cooperatively Reprogram Epigenomic Landscape of Human Macrophages to Promote Inflammatory Activation [ChIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Crossregulation of TLR responses by cytokines is essential for effective host defense, avoidance of toxicity, and homeostasis, but underlying mechanisms are not well understood. A comprehensive approach integrating RNA-seq, ChIP-seq and ATAC-seq digital footprinting showed that TNF and type I IFNs extensively remodel chromatin states in human macrophages to differentially regulate transcriptional induction of NF-κB, STAT, antiviral, and metabolic genes by LPS. IFN-α potentiated TNF inflammatory function by abrogating feedback silencing of inflammatory genes via priming of chromatin to enable robust transcriptional responses to weak upstream signals. Similar chromatin regulation occurred in human diseases. Our findings provide insights into epigenomic mechanisms by which cytokines reprogram inflammatory responses, and identify new functions and mechanisms of action of TNF and IFNs.
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| |
|
| Overall design |
Analysis of transcriptional changes in human macrophages stimulated with or without TNF and LPS
|
| |
|
| Contributor(s) |
Park S |
| Citation(s) |
28825701 |
| |
| Submission date |
Jun 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Lionel Ivashkiv |
| Organization name |
Hospital For Special Surgery
|
| Street address |
535 E 70th St
|
| City |
New York |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (36)
|
|
| This SubSeries is part of SuperSeries: |
| GSE100383 |
Type I IFNs and TNF Cooperatively Reprogram Epigenomic Landscape of Human Macrophages to Promote Inflammatory Activation |
|
| Relations |
| BioProject |
PRJNA391491 |
| SRA |
SRP110186 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE100381_H2BUb_IFN_L_Peaks.bed.gz |
957.2 Kb |
(ftp)(http) |
BED |
| GSE100381_H2BUb_IFN_N_Peaks.bed.gz |
1.2 Mb |
(ftp)(http) |
BED |
| GSE100381_H2BUb_IFN_TL_Peaks.bed.gz |
945.7 Kb |
(ftp)(http) |
BED |
| GSE100381_H2BUb_IFN_T_Peaks.bed.gz |
1.0 Mb |
(ftp)(http) |
BED |
| GSE100381_H2BUb_L_Peaks.bed.gz |
953.6 Kb |
(ftp)(http) |
BED |
| GSE100381_H2BUb_N_Peaks.bed.gz |
1.2 Mb |
(ftp)(http) |
BED |
| GSE100381_H2BUb_TL_Peaks.bed.gz |
1.0 Mb |
(ftp)(http) |
BED |
| GSE100381_H2BUb_T_Peaks.bed.gz |
1.1 Mb |
(ftp)(http) |
BED |
| GSE100381_H3K27ac_L_Peaks.bed.gz |
957.2 Kb |
(ftp)(http) |
BED |
| GSE100381_H3K27ac_N_Peaks.bed.gz |
1001.6 Kb |
(ftp)(http) |
BED |
| GSE100381_H3K27ac_TL_Peaks.bed.gz |
923.9 Kb |
(ftp)(http) |
BED |
| GSE100381_H3K27ac_T_Peaks.bed.gz |
793.2 Kb |
(ftp)(http) |
BED |
| GSE100381_H3K4me3_IFN_L_Peaks.bed.gz |
288.1 Kb |
(ftp)(http) |
BED |
| GSE100381_H3K4me3_IFN_N_Peaks.bed.gz |
307.6 Kb |
(ftp)(http) |
BED |
| GSE100381_H3K4me3_IFN_TL_Peaks.bed.gz |
319.0 Kb |
(ftp)(http) |
BED |
| GSE100381_H3K4me3_IFN_T_Peaks.bed.gz |
323.4 Kb |
(ftp)(http) |
BED |
| GSE100381_H3K4me3_L_Peaks.bed.gz |
345.1 Kb |
(ftp)(http) |
BED |
| GSE100381_H3K4me3_N_Peaks.bed.gz |
313.4 Kb |
(ftp)(http) |
BED |
| GSE100381_H3K4me3_TL_Peaks.bed.gz |
323.8 Kb |
(ftp)(http) |
BED |
| GSE100381_H3K4me3_T_Peaks.bed.gz |
283.1 Kb |
(ftp)(http) |
BED |
| GSE100381_H4ac_L_peaks.bed.gz |
173.7 Kb |
(ftp)(http) |
BED |
| GSE100381_H4ac_N_peaks.bed.gz |
263.7 Kb |
(ftp)(http) |
BED |
| GSE100381_H4ac_TL_peaks.bed.gz |
161.0 Kb |
(ftp)(http) |
BED |
| GSE100381_H4ac_T_peaks.bed.gz |
238.9 Kb |
(ftp)(http) |
BED |
| GSE100381_IRF1_IFN_T_peaks.bed.gz |
158.7 Kb |
(ftp)(http) |
BED |
| GSE100381_IRF1_N_peaks.bed.gz |
65.5 Kb |
(ftp)(http) |
BED |
| GSE100381_p65_N_peaks.bed.gz |
317.6 Kb |
(ftp)(http) |
BED |
| GSE100381_p65_T_peaks.bed.gz |
525.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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