|
Status |
Public on Mar 31, 2023 |
Title |
NSC, H/R_IP, rep2 |
Sample type |
SRA |
|
|
Source name |
C17.2
|
Organism |
Mus musculus |
Characteristics |
cell line: C17.2 cell type: neural stem cells genotype: WT treatment: hypoxia/reoxygenation
|
Treatment protocol |
To simulate ischemia-reperfusion in vitro, NSCs were placed in a humid anaerobic chamber perfused with 5% O2, 5% CO2, and 90% N2 at 37 °C for 12 h. NSCs were then moved to standard oxygen conditions and cultured for 48 h.
|
Growth protocol |
C17.2 NSCs were cultured in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum, 1% penicillin-streptomycin, and 1% glutamine. The culture medium was replaced every two days, and the cells were passaged every 4-5 days.
|
Extracted molecule |
total RNA |
Extraction protocol |
Immunoprecipitation of total RNA was completed using the GenSeq® m6A-IP Kit according to the manufacturer’s instructions. GenSeq® Low Input Whole RNA Library Prep Kit was used to construct RNA libraries for IP and input samples according to the manufacturer’s instructions.
|
|
|
Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
treatment(H/R)
|
Data processing |
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3) Clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4) Methylated sites on RNAs (peaks) were identified by MACS software Assembly: MM10 Supplementary files format and content: "Methylated_RNA_sites.txt" illustrated the m6A methylation sites information, including m6A peak start site, peak stop site, peak ID, m6A peak score, peak length, generated by MACS software (see column B to column F). Additional statistical enrichment information and gene annotation information was also provided Library strategy: MeRIP-seq
|
|
|
Submission date |
Dec 28, 2022 |
Last update date |
Mar 31, 2023 |
Contact name |
Bo Fang |
E-mail(s) |
bfang@cmu.edu.cn
|
Organization name |
The First Hospital of China Medical University
|
Department |
Department of Anesthesiology
|
Street address |
NO.155, North Nanjing Street
|
City |
Shenyang |
State/province |
Liaoning |
ZIP/Postal code |
110001 |
Country |
China |
|
|
Platform ID |
GPL24247 |
Series (1) |
GSE221841 |
Comprehensive analysis of the transcriptome-wide m6A methylation in mouse neural stem cells after hypoxia/reoxygenation |
|
Relations |
BioSample |
SAMN32470217 |
SRA |
SRX18863829 |