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Series GSE130710 Query DataSets for GSE130710
Status Public on May 04, 2019
Title Quantitative proteomic and single-nucleus transcriptomics map of the sinus node elucidates the foundation of cardiac pacemaking
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The sinus node is a collection of highly specialised cells constituting the heart’s pacemaker. It is keenly debated whether the so-called membrane or alternatively Ca2+ clocks provide the molecular substrate of pacemaking. By high-resolution mass spectrometry, we quantified >7,000 proteins from sinus node and neighbouring atrial muscle. The abundances of 575 proteins differed between the two tissues, including particular differences in metabolic profiles and extracellular matrix composition. Most notably, the data reveal significant differences between the tissues in the ion channels responsible for the membrane clock, but not in Ca2+ clock proteins, suggesting that the membrane clock underpins pacemaking. By performing single-nucleus RNA sequencing of sinus node biopsies, we attributed protein abundances to specific cell types. Consistent with these results, incorporation of the ion channel expression differences into a biophysically-detailed atrial action potential model resulted in pacemaking and a sinus node-like action potential. Combining our quantitative proteomics data with computational modeling, we estimate ion channel copy numbers for sinus node myocytes. Our findings provide detailed insights into the unique molecular make-up of the pacemaker of the heart.
Overall design Single-nucleus transcriptomics using the 10X Genomics Chromium system.
Contributor(s) Schrölkamp M, Egerod KL, Thompson JJ, Pers TH, Lundby A
Citation(s) 31253831
Submission date May 03, 2019
Last update date Jul 09, 2019
Contact name Tune Hannes Pers
Organization name University of Copenhagen
Department Novo Nordisk Foundation Center for Basic Metabolic Research
Lab Tune Pers
Street address Blegdamsvej 3B
City Copenhagen
ZIP/Postal code 2200
Country Denmark
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (2)
GSM3748100 Single-nucleus from the sinus nodes of 8 mice (pooled) [H4_S1]
GSM3748101 Single-nucleus from the sinus nodes of 8 mice (pooled) [H5_S2]
BioProject PRJNA541019
SRA SRP194998

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

Supplementary file Size Download File type/resource
GSE130710_metadata.csv.gz 189.2 Kb (ftp)(http) CSV
GSE130710_normdata.csv.gz 130.4 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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