NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE107776 Query DataSets for GSE107776
Status Public on Aug 21, 2019
Title Damage-associated molecular patterns induce macrophage polarization toward an M1 pro-inflammatory phenotype
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Dying cells release Damage-Associated Molecular Patterns (DAMPs) that can initiate and perpetuate sterile inflammatory responses. However, the effect of DAMPs on macrophages biology remains unclear. We therefore studied the effect of DAMPs on primary peritoneal macrophages (PPM) in vitro. We first performed unbiased transcriptomic profiling with RNA-seq of PPMs cultured for up to 72 hours in the presence and absence of: 1) liposaccharide (LPS), which is known to provoke an “M1” phenotype, 2) IL-4, which is known to provoke an “M2” phenotype, or 3) cytosolic extracts (CEs) from necrotic H9C2 cells to mimic the release of cardiomyocyte DAMPs. We found that the transcriptional profile of PPMs stimulated with CEs resembled the transcriptional profile of PPMs stimulated with LPS.
 
Overall design All primary peritoneal macrophages were derived from the same initial isolate (pooled from multiple mice). Three to four replicates of each timepoint and condition were used for RNA extraction, RNAseq library preparation with Diagenode CATS procedures, and single-end 50 bp Illumina sequencing.
 
Contributor(s) Matkovich SJ, Jiang W, Mann DL
Citation(s) 31162139
Submission date Dec 06, 2017
Last update date Aug 21, 2019
Contact name Scot J Matkovich
E-mail(s) smatkovich@gmail.com
Organization name Washington University School of Medicine
Department Center for Cardiovascular Research
Street address 660 S Euclid Ave, box 8086
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
 
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (44)
GSM2878986 24 h treatment with 10 ug/mL H9c2 cell extract, repl 2
GSM2878987 24 h treatment with 10 ug/mL H9c2 cell extract, repl 3
GSM2878988 24 h treatment with 10 ug/mL H9c2 cell extract, repl 4
Relations
BioProject PRJNA421349
SRA SRP126282

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
GSE107776_peritoneal_macrophage_stimulation_HTSeq.txt.gz 1.5 Mb (ftp)(http) TXT
GSE107776_remove_CATSadapters_cutadapt.sh.txt.gz 530 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap