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Sample GSM1260057 Query DataSets for GSM1260057
Status Public on Mar 10, 2015
Title NSC_m6A-Seq
Sample type SRA
 
Source name Neural stem cells
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Neural stem cells (NSC)
passages: P16
enrichment antibody: m6A
enrichment antibody vendor: Synaptic Systems
enrichment antibody cat. #: 202003
enrichment antibody lot #: 22
Growth protocol Normal neural stem cells (NSCs) were isolated from E12.5 fetal brain and cultured in 1:1 mix of neurobasal medium and DMEM/F12 supplemented with 1xN2, 1xB27, 25 ug/ml BSA, 1xpenicillin/streptomycin/glutamine, 0.1 mM β-mercaptoethanol, 10 ug/ml insulin, 10 ng/ml EGF, and 10 ng/ml bFGF.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol. Highly purified and intact mRNA was enriched from total RNA and fragmented into ~100 nt fragments. For m6A-Seq, mRNA-fragments were enriched by m6A antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Data processing Base-calling were performed using RTA and CASAVA.
Sequenced reads were mapped to mouse genome (mm9) using TopHat (version 2.0.4) with a RefSeq based transcript index given to the option “--transcriptome-index”.
m6A peak-calling were done with in-house softwares by comparing the read abundance between m6A-Seq and RNA-Seq samples of the same loci.
The expression of transcripts were quantified as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and estimated by Cufflinks (version 2.0.2).
Genome_build: mm9
Supplementary_files_format_and_content: Excel file includes FPKM values and modification status of each transcript for all samples.
 
Submission date Nov 06, 2013
Last update date May 15, 2019
Contact name Tong Chen
E-mail(s) chentong_biology@163.com
Phone 86-15210822685
Organization name China Academy of Chinese Medical Sciences
Department State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica
Lab Luqi Huang's lab
Street address No 16 Nan-xiao-jie Dong-zhi-men-nei
City Beijing
ZIP/Postal code 100700
Country China
 
Platform ID GPL11002
Series (1)
GSE52125 m6A RNA Methylation Is Regulated by MicroRNAs and Promotes Reprogramming to Pluripotency
Relations
BioSample SAMN02398671
SRA SRX373635

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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