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Sample GSM4604866 Query DataSets for GSM4604866
Status Public on Jun 09, 2023
Title sev1-1
Sample type SRA
 
Source name prefrontal cortex
Organism Mus musculus
Characteristics tissue: prefrontal cortex
age: post natal day 6
Treatment protocol Mus musculus of both sexes were exposed to about 3% sevoflurane inhalation anesthesia on post-natal day 6 and then sacrificed after exposure at post-natal day 6
Growth protocol The animal studies were performed according to the guidelines and regulations of the Institute of Laboratory Animal Science, Peking Union Medical College and Chinese Academy of Medical Science (Peking, China).
Extracted molecule total RNA
Extraction protocol prefrontal cortex were harvested , flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Single Cell RNA sequencing library were generated using the 10x Genomics Chromium Platform and sequenced on the Illumina NovaSeq 6000.
 
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
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% < 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
Supplementary_files_format_and_content: TXT file contain counts for each sample
 
Submission date Jun 09, 2020
Last update date Jun 09, 2023
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)
GSE152149 RNA sequencing of mouse after single sevoflurane exposure
Relations
BioSample SAMN15192308
SRA SRX8512688

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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