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| Status |
Public on Aug 17, 2022 |
| Title |
A_control |
| Sample type |
SRA |
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| Source name |
hippocampus
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| Organism |
Mus musculus |
| Characteristics |
age: PND10
strain: C57/BL6
agent: Control
tissue: brain
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| Treatment protocol |
PND7 mice were injected with low-dose Propofol and sacrificed at PND10
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mice hippocampus were isolated rapidly with cuting into pieces <0.5cm and were homogenized using a glass dounce tissue grinder (Sigma, #D8938). First, nuclei were isolated with EZ PREP buffer(Sigma, #NUC-101). The number of isolated nuclei was adjusted to 300000 nuclei/ml with suspension buffer and Ficoll PM-400 was added to the nuclei suspension buffer. Second, nuclei were loaded at a concentration of 200 nuclei per microliter. Third, the emulsion was kept on ice for 30 minutes to allow release of nuclear RNA.
Single-cell suspensions were loaded to 10x Chromium to capture single nuclei according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) .The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by LC-Bio Technology co.ltd., (HangZhou,China) at a minimum depth of 20,000 reads per cell.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
One sample from hippocampus of C57/BL6 in Control group
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| Data processing |
Cellranger standard processing
**Cell filter** Seurat allows to easily explore QC metrics and filter cells, we can visualize gene and molecule counts, plot their relationship, and exclude cells with a clear outlier number of genes detected as potential multiplets. Followed criteria were used to filter cells: 1.gene counts 500-Inf per cell. 2.UMI counts 3. the percentage of mitochondrial genes < 25% %(customized). 4.DoubletFinder for detecting doublets.
**Cell clustering** Cell clustering contains the following steps: 1)Normalizing the data After removing unwanted cells from the dataset, the next step is to normalize the data. By default, we employ a global-scaling normalization method “LogNormalize” that normalizes the gene expression measurements for each cell by the total expression.
2)PCA(Principal component analysis) To overcome the extensive technical noise in any single gene for snRNA-seq data, Seurat clusters cells based on their PCA scores, with each PC essentially representing a ‘metagene’ that combines information across a correlated gene set.
4)UMAP (Uniform Manifold Approximation and Projection) visualization Seurat continues to use UMAP as a powerful tool to visualize and explore these datasets. The UMAP aims to place cells with similar local neighborhoods in high-dimensional space together in low-dimensional space.
Genome_build: Mus_musculus.GRCm38.96
Supplementary_files_format_and_content: gene-barcode counts
Supplementary_files_format_and_content: gene files
Supplementary_files_format_and_content: cell barcode files
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| Submission date |
Oct 20, 2021 |
| Last update date |
Aug 17, 2022 |
| Contact name |
Dihan Lu |
| E-mail(s) |
ludihan@sina.com
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| Organization name |
First Affiliated Hospital, Sun Yat-sen University
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| Department |
Department of Anesthesiology
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| Street address |
No.58, Zhong Shan Er Lu, Guangzhou, P. R. China.
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510080 |
| Country |
China |
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| Platform ID |
GPL9185 |
| Series (1) |
| GSE186216 |
Enhanced hippocampal neurogenesis mediated by PGC-1α-activated OXPHOS after neonatal subclinical dose of Propofol exposure revealed by single-nuclei transcriptomic profiling |
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| Relations |
| BioSample |
SAMN22425956 |
| SRA |
SRX12700616 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5640790_A_barcodes.tsv.gz |
46.5 Kb |
(ftp)(http) |
TSV |
| GSM5640790_A_genes.tsv.gz |
423.9 Kb |
(ftp)(http) |
TSV |
| GSM5640790_A_matrix.mtx.gz |
113.1 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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