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| Status |
Public on Jan 30, 2024 |
| Title |
APOE-/- sham mice + PBS |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
cell type: CD45intCD11b+ cells
genotype: APOE konckout
treatment: Sham induction + PBS
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell suspensions were prepared from pooled mouse brain tissues at day 4 after sham or NMOSD induction. CD45intCD11b+ cells were isolated at 4°C using flow-cytometry.
Library was performed according to the manufacter’s instructions (single-cell 3' v.2 kit, 10× Genomics).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw files (FASTQ format) were processed with Cell Ranger software (v5.0.1), which performed mapping to the mm10 transcriptome, filtering, barcode counting, and UMI counting and finally generated feature-by-barcode UMI matrix. Seurat (v4.3.0) was used for downstream analysis. Low-quality cells, with < 1000 genes expressed or < 1000 UMIs, were excluded at the initial quality-control step. Cells > 10% mitochondrial UMIs were removed. Doublets were identified by the R package DoubletFinder with default settings. We first used the “SCTransform” function to perform the workflow of data normalization, identification of highly variable genes (HVGs), and data scaling, and then used the “RunPCA” function to perform PCA dimensionality reduction. Selected top PCs were retained using the elbow method for computing the UMAP dimensional reduction. Cells were clustered with Seurat’s “FindClusters” function.
Assembly: mm10
Supplementary files format and content: tsv and mtx file
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| Submission date |
Dec 21, 2023 |
| Last update date |
Jan 30, 2024 |
| Contact name |
Wei-Na Jin |
| Organization name |
Beijing Tiantan Hospital, Capital Medical University
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| Department |
China National Clinical Research Center for Neurological Diseases
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| Street address |
NO.119, Southwest of the Fourth Ring Road, Fengtai District
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100070 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE251774 |
Molecular characteristics of microglia in APOE-/-mice treated with APOE130-149 or control peptides after NMOSD induction |
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| Relations |
| BioSample |
SAMN39049360 |
| SRA |
SRX22993319 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7987610_Sham_induction_+_PBS_filtered_feature_bc_matrix_barcodes.tsv.gz |
24.3 Kb |
(ftp)(http) |
TSV |
| GSM7987610_Sham_induction_+_PBS_filtered_feature_bc_matrix_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM7987610_Sham_induction_+_PBS_filtered_feature_bc_matrix_matrix.mtx.gz |
37.8 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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