 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 19, 2019 |
| Title |
Gene expression, methylome and splicing of THP-1 monocytic cells and THP-1-derived macrophage |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
|
| Summary |
Monocytes and macrophages are essential components of the innate immune system. Herein, we report that intron retention (IR) plays an important role in the development and function of these cells. Using mRNA sequencing, bioinformatics analyses and RT-qPCR validation, we identified differential IR and altered expression of key genes involved in macrophage development and function, both in vitro and in vivo. We demonstrate that decreased IR in nuclear-detained mRNA is coupled to increased expression of genes encoding regulators of macrophage transcription, phagocytosis and inflammatory signalling, including ID2, IRF7, ENG and LAT. We further show that this dynamic IR program persists during the polarisation of resting macrophages into activated macrophages. In the presence of proinflammatory stimuli, intron-retaining CXCL2 and NFKBIZ transcripts in macrophages are rapidly spliced, leading to timely expression of these key inflammatory regulators by macrophages. Our study provides novel insights into the molecular mechanisms controlling vital regulators of the innate immune response.
|
| |
|
| Overall design |
We determined the role of intron retention in THP-1 monocytic cells and THP-1-derived macrophage cells.
NOTE: [01-24-2024] The titles of GSM3729250-GSM3729258 and GSM6573090-GSM6573092 were revised, but the associated data did not change.
|
| |
|
| Contributor(s) |
Wong J, Green I, Song R |
| Citation(s) |
32449925, 38780787 |
| |
| Submission date |
Apr 18, 2019 |
| Last update date |
Jun 05, 2024 |
| Contact name |
RENHUA SONG |
| E-mail(s) |
[email protected]
|
| Phone |
61452667663
|
| Organization name |
Centenary Institute
|
| Lab |
Epigenetics and RNA Biology Program
|
| Street address |
Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive
|
| City |
Camperdown |
| State/province |
NSW |
| ZIP/Postal code |
2050 |
| Country |
Australia |
| |
|
| Platforms (3) |
|
| Samples (23)
|
|
| Relations |
| BioProject |
PRJNA533591 |
| SRA |
SRP192966 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE130011_EXOSC10_KD_Control.txt.gz |
119.3 Kb |
(ftp)(http) |
TXT |
| GSE130011_M0_ND.tab.gz |
687.0 Kb |
(ftp)(http) |
TAB |
| GSE130011_M1_M0.tab.gz |
549.4 Kb |
(ftp)(http) |
TAB |
| GSE130011_M2_count_RNAseq.xlsx |
1.0 Mb |
(ftp)(http) |
XLSX |
| GSE130011_ND_M0_M1.rlog.txt.gz |
2.0 Mb |
(ftp)(http) |
TXT |
| GSE130011_RAW.tar |
1.1 Gb |
(http)(custom) |
TAR (of BW) |
| GSE130011_THP1_monocyte_macrophage.tsv.gz |
188.3 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...