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Sample GSM2471051 Query DataSets for GSM2471051
Status Public on Mar 14, 2018
Title Sample_scr_m6A_Input_rep1
Sample type SRA
 
Source name murine embryonic stem cell
Organism Mus musculus
Characteristics developmental stage: E14
genotype/variation: scr
Treatment protocol RNA was fragmented and subject to immunoprecipitation with a m6A specific antibody. 
Growth protocol E14 murine embryonic stem cell was cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum, 1% none essential amino acid, 0.1% beta-mercaptoethanol, 100u/ml penicillin/ Streptomycin and 1000u LIF.
Extracted molecule total RNA
Extraction protocol Total RNAs from mESCs were isolated using Trizol reagent according to the manufacturer’s instruction (Life technology, 15596018). Polyadenylated RNAs were extracted by oligodT beads (NEB, S1419S), followed by removal of contaminated rRNA with RiboMinus transcriptome isolation kit (Life technologies, A15026).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Data processing Library strategy: m6A-seq
Basecalls performed using CASAVA version 1.4
m6A-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf --max-multihits 1 --prefilter-multihits -o m6A_thout mm9_assemblies m6A.fq
RNA-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf -o RNA-seq_thout mm9_assemblies RNA-seq.fq
m6A peaks were called by exomePeak 2.13 package of of Bioconductor under default parameters.
Transcriptome is assemblied using cufflinks;differential expressed genes were identified by cuffdiff.
Mapped m6A reads were transfer to bedgraph files for visualization using bedtools.
FPKM value of Ensembl genes were calculated by cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content:
bed files include m6A peak lists identified by exomePeaks;and bg files include the averaged m6A enriched density.
tab-delimited text file include the FPKM values of Ensembl genes in Mus musculus genome;
 
Submission date Jan 27, 2017
Last update date Mar 14, 2018
Contact name Ruitu Lyu
E-mail(s) lvruitu@gmail.com
Organization name Institutes of Biomedical Sciences Fudan University
Lab Epigenetics lab
Street address 138 Yixueyuan Road Xuhui District
City Shanghai
ZIP/Postal code 200030
Country China
 
Platform ID GPL17021
Series (1)
GSE94148 A novel RNA m6A modulator Zc3h13 plays an anchor role in facilitating nuclear RNA methylation and mouse embryonic stem cell self-renewal
Relations
BioSample SAMN06308556
SRA SRX2541295

Supplementary file Size Download File type/resource
GSM2471051_Sample_WT_m6A_Input_rep1.bedGraph.gz 49.0 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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