|
| Status |
Public on Jul 13, 2022 |
| Title |
SEV3 |
| Sample type |
SRA |
| |
|
| Source name |
primary neurons
|
| Organism |
Mus musculus |
| Characteristics |
srtain: C57BL/6
tissue: cortex
passage: 0
|
| Treatment protocol |
The cells were treated with 3% sevoflurane, plus 21% O2, and 5% CO2 2 h a day for three consecutive days. Control conditions included 21% O2, and 5% CO2.
|
| Growth protocol |
Primary cortical neurons were prepared from the brains of C57 mice on embryonic day (E14.5) as described by Gerard et al 2012.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
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 |
| |
|
| Description |
Sample 6
|
| 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 |
Oct 17, 2019 |
| Last update date |
Jul 13, 2022 |
| Contact name |
yanyong cheng |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE139012 |
10x single cell sequencing for primary neurons transcriptomes after sevoflurane exposure |
|
| Relations |
| BioSample |
SAMN13048017 |
| SRA |
SRX7011552 |
