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Series GSE117963 Query DataSets for GSE117963
Status Public on Sep 19, 2018
Title Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy mouse vessels
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Vascular smooth muscle cells (VSMCs) show pronounced heterogeneity across and within vascular beds, with direct implications for their function in injury response and atherosclerosis. Here we combine single-cell transcriptomics with lineage tracing to examine VSMC heterogeneity in healthy mouse vessels. The transcriptional profiles of single VSMCs consistently reflect their region-specific developmental history and show heterogeneous expression of vascular disease-associated genes involved in inflammation, adhesion and migration. We detect a rare population of VSMC-lineage cells that express the multipotent progenitor marker Sca1, progressively downregulate contractile VSMC genes and upregulate genes associated with VSMC response to inflammation and growth factors. We find that Sca1 upregulation is a hallmark of VSMCs undergoing phenotypic switching in vitro and in vivo, and reveal an equivalent population of Sca1-positive VSMC-lineage cells in atherosclerotic plaques. Together, our analyses identify disease-relevant transcriptional signatures in VSMC-lineage cells in healthy blood vessels, with implications for disease susceptibility, diagnosis and prevention.
 
Overall design This entry contains data from the following analyses: (1) Bulk RNA-seq of mouse VSMCs isolated from aortic arch (AA) and descending thoracic aorta (DT) regions in triplicates. (2) Pooled RNA-seq of mouse Sca1- VSMCs and Sca1- or Sca1+ adventitial cells in triplicates. (3) Single-cell RNA-seq of VSMCs from the AA and DT regions (143 cells). (4) VSMC lineage label positive and negative cells isolated from the medial layer of mouse aorta, which expressed or did not express the Sca1 protein (155 cells). (5) 10X single-cell RNA-seq analysis of: lineage positive plaque cells isolated from mice following 14 or 18 weeks of high fat diet feeding, cells isolated from the whole aorta and lineage positive VSMCs from the medial layer.
 
Contributor(s) Spivakov M, Jørgensen HF, Dobnikar L, Taylor AL, Chappell J, Harman JL
Citation(s) 30385745
Submission date Jul 31, 2018
Last update date Mar 21, 2019
Contact name Steven William Wingett
E-mail(s) steven.wingett@mrc-lmb.cam.ac.uk
Organization name MRC Laboratory of Molecular Biology
Department Cell Biology
Street address Francis Crick Avenue, Cambridge Biomedical Campus
City Cambridge
State/province Cambs
ZIP/Postal code CB2 0QH
Country United Kingdom
 
Platforms (3)
GPL16417 Illumina MiSeq (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (317)
GSM3315891 Bulk RNA-seq AA replicate 1
GSM3315892 Bulk RNA-seq AA replicate 2
GSM3315893 Bulk RNA-seq AA replicate 3
Relations
BioProject PRJNA483799
SRA SRP155893

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
GSE117963_10X_lineage_positive_filtered_gene_bc_matrices_h5.h5 10.8 Mb (ftp)(http) H5
GSE117963_10X_plaque_14w_filtered_gene_bc_matrices_h5.h5 11.7 Mb (ftp)(http) H5
GSE117963_10X_plaque_18w_filtered_gene_bc_matrices_h5.h5 9.7 Mb (ftp)(http) H5
GSE117963_10X_whole_aorta_filtered_gene_bc_matrices_h5.h5 12.5 Mb (ftp)(http) H5
GSE117963_normalised_aadt_counts.txt.gz 5.8 Mb (ftp)(http) TXT
GSE117963_normalised_bulk_counts.txt.gz 811.0 Kb (ftp)(http) TXT
GSE117963_normalised_counts_smartseq2_sca1.txt.gz 3.3 Mb (ftp)(http) TXT
GSE117963_normalised_pooled_counts.txt.gz 814.1 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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