|
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 |