|
| Status |
Public on May 30, 2024 |
| Title |
mouse-acc |
| Sample type |
SRA |
| |
|
| Source name |
nucleus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain
brain region: Anterior cingulate cortex (ACC)
passage: 0
|
| Treatment protocol |
without treatment
|
| Growth protocol |
The tissues samples of ACC and RSC were surgically removed and the frozen tissue was used to intact nucleus isolation. The nucleus was isolated and purified as previously described with some modifications
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sample washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
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% < 20%; 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. Graphcluster and K-mean 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&Mmul_10
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes
|
| |
|
| Submission date |
Aug 30, 2021 |
| Last update date |
May 30, 2024 |
| Contact name |
yanyong cheng |
| E-mail(s) |
cheng_yanyong@163.com
|
| Organization name |
Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine
|
| Department |
Department of Anesthesiology
|
| Street address |
639 Zhizaoju Road
|
| City |
shanghai |
| ZIP/Postal code |
200011 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE183052 |
Single-cell RNA-sequencing analysis for the molecular taxonomy of primate Anterior cingulate cortex (ACC) and Retro splenial cortex (RSC), as well as rodents |
|
| Relations |
| BioSample |
SAMN21040365 |
| SRA |
SRX11966609 |
