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| Status |
Public on Nov 18, 2022 |
| Title |
20-month brain |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 20-month
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| Extracted molecule |
total RNA |
| Extraction protocol |
Brain tissues were surgically removed and minced into small pieces (approximately 1mm3) on ice and digested by 200 U/mL Papine (Diamond) and Cysteine-HCL (Sigma). Then samples were sieved through 70 µm cell strainers, centrifuged at 300 g for 10 min, and further cleaned for red blood cells using red blood cell lysis buffer (Miltenyi Biotec).
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols
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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 |
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria: MT% < 40%; Cell Gene Number < Median Gene Number * 2; Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples. Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes
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| Submission date |
Mar 25, 2021 |
| Last update date |
Nov 18, 2022 |
| Contact name |
Junjie Gao |
| E-mail(s) |
Junjie.gao@shsmu.edu.cn
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| Phone |
+8615067175608
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| Organization name |
Shanghai Jiao Tong University Affiliated Shanghai Sixth People’s Hospital
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| Street address |
600 Yishan Road
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| City |
Shanghai |
| ZIP/Postal code |
200233 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE169606 |
Single-cell transcriptome analysis of aging brain |
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| Relations |
| BioSample |
SAMN18489560 |
| SRA |
SRX10442191 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5210612_WT20m.barcodes.tsv.gz |
39.8 Kb |
(ftp)(http) |
TSV |
| GSM5210612_WT20m.genes.tsv.gz |
243.5 Kb |
(ftp)(http) |
TSV |
| GSM5210612_WT20m.matrix.mtx.gz |
64.5 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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