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Sample GSM6443691 Query DataSets for GSM6443691
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
 
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
 
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

Supplementary file Size Download File type/resource
GSM6443691_MCAO.cellname.txt.gz 40.7 Kb (ftp)(http) TXT
GSM6443691_MCAO.counts.tsv.gz 14.2 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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