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Sample GSM6900562 Query DataSets for GSM6900562
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

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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