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| Status |
Public on Aug 01, 2021 |
| Title |
Single-cell RNA sequencing of Smek1-/- cortices and hippocampus |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
PPP4R3A, namely SMEK1 (Suppressor of Mek1 null), encodes a regulatory subunit of protein phosphatase 4 that is highly expressed in nervous system. Experimental autoimmune encephalomyelitis (EAE) is an animal disease model of multiple sclerosis (MS) that involves the immune system and central nervous system (CNS). However, it is unclear how genetic predispositions promote neuroinflammation in MS and EAE. Here, we investigated how partial loss-of-function of suppressor of SMEK1facilitates the onset of MS and EAE. Smek1 deficient mice showed more severe symptoms after EAE immunization. We performed single-cell RNA sequencing (scRNA-seq) on the cortices and hippocampus from 2-month old Smek1-/- and wild type littermates. Twelve cell types were identified in 6 tissue samples. Addtionally, we found a unique microglia subtype in Smek1-/- CNS that highly express IL-1β. Further analysis revealed enrichment of macrophage Csf1 in the novel microglia cluster. These findings confirmed that with loss of function of Smek1, a novel Csf1+ microglial cluster had a preactivated phenotype that may promote neuroinflammation.
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| Overall design |
Four samples of cortices and hippocampus from 2-month old wild type (WT) and Smek1-/- mice
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| Contributor(s) |
Duan R, Liu A, Wang A, Liu Q |
| Citation(s) |
34183017 |
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| Submission date |
Apr 13, 2021 |
| Last update date |
Aug 02, 2021 |
| Contact name |
Ruonan Duan |
| E-mail(s) |
[email protected]
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| Phone |
+8618366110727
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| Organization name |
Shandong University
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| Street address |
44# Wen Hua Xi Road
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| City |
Jinan |
| ZIP/Postal code |
250012 |
| Country |
China |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA721619 |
| SRA |
SRP314643 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE171986_RAW.tar |
35.8 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE171986_barcodes.tsv.gz |
51.4 Kb |
(ftp)(http) |
TSV |
| GSE171986_genes.tsv.gz |
423.9 Kb |
(ftp)(http) |
TSV |
| GSE171986_matrix.mtx.gz |
90.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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