|
Status |
Public on Jun 14, 2023 |
Title |
MCAO-brain, scRNAseq |
Sample type |
SRA |
|
|
Source name |
Brain
|
Organism |
Mus musculus |
Characteristics |
tissue: Brain treatment: MCAO
|
Treatment protocol |
Mice treated middle cerebral artery occlusion (MCAO) means they were anesthetized with 3% isoflurane in 67%:30% N2O/ O2 (induction), until they were unresponsive to the tail pinch test and were then fitted with a nose cone providing 1.5% isoflurane for anesthesia maintenance. A monofilament was introduced into the common carotid artery, advanced to the origin of the middle cerebral artery, and left in position for 60 minutes until reperfusion.Sham-operated animals underwent the same anesthesia and surgical procedures except MCAO.
|
Growth protocol |
Male C57/BL6 mice were purchased from Shanghai SLAC Laboratory Animals and were housed under standard laboratory conditions (22°C and a 12‐hour light‐dark cycle with free access to food and water).
|
Extracted molecule |
total RNA |
Extraction protocol |
BD Rhapsody system was used to capture the transcriptomic information of the single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells RNA libraries were generated by BD Rhapsody singel cell RNA-seq 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 |
|
|
Description |
BD Rhapsody
|
Data processing |
Basecalls performed using CASAVA version 1.8 Umi-tools 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% < 30%; 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. Assembly: mm10 Supplementary files format and content: TXT file contain counts and barcodes for each sample
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|
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Submission date |
Aug 10, 2022 |
Last update date |
Jun 14, 2023 |
Contact name |
Yueman Zhang |
E-mail(s) |
altaszhang@gmail.com
|
Phone |
19121710063
|
Organization name |
Department of Anesthesiology, Renji Hospital, School of Medicine Shanghai Jiao Tong University, China
|
Street address |
160 Pujian Rd
|
City |
Shanghai |
ZIP/Postal code |
200127 |
Country |
China |
|
|
Platform ID |
GPL24247 |
Series (1) |
GSE210986 |
Single-Cell Analysis Uncovers Dramatic Alteration of Microglia Heterogeneity after Ischemic Stroke |
|
Relations |
BioSample |
SAMN30244891 |
SRA |
SRX17025829 |