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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 21, 2019 |
| Title |
Single cell RNA sequencing of aortic CX3CR1-derived monocyte/macrophage from atherosclerotic aorta during progression and regression |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In atherosclerosis progression and regression, monocytes or monocyte-derived macrophages are the major immune cells in the plaque. It is important to understand the fate and characteristics of monocyte/macrophage during the plaque progression and regression. To characterize the fate of monocytes/macrophages, we performed single cell RNA sequencing of fate-mapped aortic CX3CR1-derived monocytes/macrophages from Cx3cr1CreERT2-IRES-YFP/+Rosa26floxed-tdTomato/+ mice with AAV-PCSK9 injection and fed a Western Diet. The single cell RNA-seq analyses revealed the heterogeneity of aortic macrophages and identified a stem-like cell cluster in atherosclerotic aorta.
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| Overall design |
Single cell RNA sequencing of aortic sorted TdTomato+CD11b+Dump- cells (Dump- are excluding CD3+, CD19+, CD49b+, Siglec-F+, Ly6G+ cells) from atherosclerotic Cx3cr1CreERT2-IRES-YFP/+Rosa26floxed-tdTomato/+ mice (n=8, 1012 AAV-PCSK9 at 8wk old mice, then WD for 18 wks). Then 4 mice continue on WD for further 2wks as progression group, 3157 cells identified, Using Illumina HiSeq4000. The other 4 mice were switched into chow diet for further 2wks and also i.p. treated with ApoB-ASO (50 mg/kg, 2 doses/wk, 2wks) as regression group, 2198 cells identified, Using Illumina HiSeq4000.
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| Contributor(s) |
Lin J, Nishi H, Poles J, Niu X, Brown EJ, Ramsey SA, Fisher EA, Loke P |
| Citation(s) |
30830865 |
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| Submission date |
Dec 10, 2018 |
| Last update date |
Mar 26, 2019 |
| Contact name |
Emily Brown |
| E-mail(s) |
emily.brown2@nyulangone.org
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| Organization name |
NYU Langone
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| Department |
Medicine
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| Street address |
435 E 30th St
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (2) |
| GSM3507490 |
Total TdTomato+CD11b+Dump- cells from progression group |
| GSM3507491 |
Total TdTomato+CD11b+Dump- cells from regression group |
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| Relations |
| BioProject |
PRJNA509262 |
| SRA |
SRP173255 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE123587_RAW.tar |
19.9 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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