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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 29, 2019 |
| Title |
Single cell analysis of smooth muscle cell phenotypic modulation in vivo during disease in mice and humans [mouse CITE-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In response to various stimuli, vascular smooth muscle cells (SMCs) can de-differentiate, proliferate and migrate in a process known as phenotypic modulation. However, the phenotype of modulated SMCs in vivo during atherosclerosis and the influence of this process on coronary artery disease (CAD) risk have not been clearly established. Using single cell RNA sequencing, we comprehensively characterized the transcriptomic phenotype of modulated SMCs in vivo in atherosclerotic lesions of both mouse and human. We performed CITE-seq in mouse atherosclerotic lesions using antibodies directed against several macrophage surface markers. In the mice, we also performed SMC-specific knockout of TCF21, a causal CAD gene, to determine the effect of this gene on SMC phenotypic modulation. Finally, we performed ChIP-seq for the transcription factor TCF21 in a pooled DNA sample comprised of 52 different human coronary artery smooth muscle cell (HCASMC) lines to determine TCF21 target genes.
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| Overall design |
We performed single-cell RNAseq (scRNAseq) of cells from the aortic root and ascending aorta (up to the level of the brachiocephalic artery) in ApoE-/- mice. All mice contained the Myh11-Cre and ROSA tdTomato (tdT) alleles for smooth muscle cell (SMC) lineage tracing. Some mice also contained a floxed Tcf21 allele and are termed ‘KO’. Mice with the wild-type Tcf21 allele are termed ‘WT’. All mice underwent gavage with tamoxifen at 7 weeks of age, prior to the onset of high-fat diet feeding. Mice were then sacrificed at baseline (approximately 72 hours post gavage), after 8 weeks of high-fat diet (HFD) feeding or after 16 weeks of HFD feeding. Single-cell suspensions from these mice were separated by FACS into tdT-positive (‘SMC’) and tdT-negative (‘nonSMC’) populations and processed by a 10X Chromium instrument using 3’ reagents (version 2 chemistry).
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| Contributor(s) |
Wirka RC, Wagh D, Paik DT, Pjanic M, Nguyen T, Miller CL, Kundu R, Nagao M, Coller J, Koyano T, Fong R, Woo YJ, Liu B, Montgomery SB, Wu JC, Zhu K, Chang R, Alamprese M, Tallquist MD, Kim JB, Quertermous T |
| Citation(s) |
31359001 |
| Submission date |
May 25, 2019 |
| Last update date |
Oct 13, 2019 |
| Contact name |
Thomas Quertermous |
| E-mail(s) |
tomq1@stanford.edu
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| Phone |
650-723-5012
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| Organization name |
Stanford University
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| Department |
Medicine Cardiology
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| Lab |
Quertermous
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| Street address |
300 Pasteur Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE131780 |
Single cell analysis of smooth muscle cell phenotypic modulation in vivo during disease in mice and humans |
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| Relations |
| BioProject |
PRJNA544956 |
| SRA |
SRP199579 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE131777_mouse_16wk_citeseq_ADT_wirka_et_al_GEO.txt.gz |
58.8 Kb |
(ftp)(http) |
TXT |
| GSE131777_mouse_16wk_citeseq_RNA_wirka_et_al_GEO.txt.gz |
13.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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