GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE136662 Query DataSets for GSE136662
Status Public on Jun 29, 2020
Title NCX1 represents an ionic Na+ sensing mechanism in macrophages
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Inflammation and infection can trigger local tissue Na+-accumulation. This Na+-rich environment boosts pro-inflammatory activation of monocyte/macrophage-like cells (MΦ) and their antimicrobial activity. Enhanced Na+-driven MΦ-function requires the osmoprotective transcription factor nuclear factor of activated T cells 5 (NFAT5), which augments NO production and contributes to increased autophagy. However, the mechanism of Na+-sensing in MΦ remained unclear. High extracellular Na+ levels (HS) trigger a substantial Na+-influx and Ca2+ loss. Here, we show that the Na+/ Ca2+-exchanger 1 (NCX1/ solute carrier family 8 member A1 (SLC8A1)) plays a critical role in HS-triggered Na+-influx, concomitant Ca2+ efflux and subsequent NFAT5 accumulation. Moreover, interfering with NCX1-activity impairs HS-boosted inflammatory signaling, infection-triggered autolysosome formation and subsequent antibacterial activity. Taken together, this demonstrates that NCX1 is able to sense Na+ and is required for amplifying inflammatory and antimicrobial MΦ responses upon HS exposure. Manipulating NCX1 offers a new strategy to regulate MΦ function.
Overall design Examination of Slc8a1 (NCX1) isoform expression in RNA-seq data of 3 unstimulated murine BMDM samples.

We analyzed the isoform expression of Slc8a1 (NCX1) in RNA-seq data of murine bone-marrow derived macrophages (BMDM). RNA of 3 samples differentiated in vitro for 8 days using M-CSF was isolated with trizol and miRNeasy micro kit (Qiagen) according to the manufacturer’s protocol and 100 ng of RNA was converted into cDNA libraries using the TruSeq RNA library preparation kit v2 for 75 bp single read sequencing performed on a HiSeq1500. We aligned the reads using Hisat2 and and performed genome-guided transcriptome assembly using Stringtie followed by transcript abundance estimation using Ballgown as delineated in the "new tuxedo" protocol (Pertea et al., 2016: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown). The transcriptome assembly identified two additional multi-exon transcripts variants for Slc8a1 and transcript abundance estimation determined one of the novel variants to be dominantly expressed.
Contributor(s) Schulte-Schrepping J, Neubert P, Schultze JL, Jantsch J, Kolanus W
Citation(s) 32569301
Submission date Aug 30, 2019
Last update date Jun 29, 2020
Contact name Joachim Schultze
Organization name LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)
Department Genomics and Immunoregulation
Street address Carl-Troll-Strasse 31
City Bonn
State/province NRW
ZIP/Postal code 53115
Country Germany
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (3)
GSM4054738 BMDM_1
GSM4054739 BMDM_2
GSM4054740 BMDM_3
BioProject PRJNA563000
SRA SRP219733

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
GSE136662_Stringtie_mergedTranscripts.gtf.gz 10.1 Mb (ftp)(http) GTF
GSE136662_transcriptExpression.csv.gz 4.6 Mb (ftp)(http) CSV
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