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Series GSE130011 Query DataSets for GSE130011
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
Submission date Apr 18, 2019
Last update date Jan 24, 2024
Contact name RENHUA SONG
E-mail(s) Renhua.song1989@gmail.com
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)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL24106 MinION (Homo sapiens)
Samples (23)
GSM3729250 Mo THP-1_RNA-seq [Mo_1]
GSM3729251 Mo THP-1_RNA-seq [Mo_2]
GSM3729252 Mo THP-1_RNA-seq [Mo_3]
Relations
BioProject PRJNA533591
SRA SRP192966

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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 SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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