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Sample GSM3594144 Query DataSets for GSM3594144
Status Public on Dec 08, 2020
Title METTL3_KO_WGBS_rep1
Sample type SRA
Source name Embryonic stem cells
Organism Mus musculus
Characteristics cell type: Embryonic stem cells
genotype: METTL3 KO
Growth protocol E14Tg2a murine embryonic stem cells (mES) were cultured in Dulbecco’ s Modified Eagle’ s Medium (DMEM) supplemented with 10% fetal bovine serum (FBSGibco #16000-044), 1% MEM non-essential amino acid (Gibco #11140), 55 mM β-Mercaptoethanol (Gibco#21985-023), 100 U/mL Penicillin/Streptomycin (Hyclone #SV30010), 1000 units/mL LIF (Millipore #ESG1107,) and MEK inhibitor PD0325901 (1μM) and GSK3β inhibitor CH99021 (3μM) at 37℃ with 5% CO2.
Extracted molecule genomic DNA
Extraction protocol The bisulphite conversion was performed using the EZ DNA Methylation Gold kit from Zymo Research (#D5005).
Post-BS library preparation was performed using Accel-NGS® Methyl-Seq DNA Library Kit from Swift Biosciences (#36024).
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model HiSeq X Ten
Data processing Raw reads were trimmed 10 bps off the 5’ end and 3’ end and then mapped to mm10 genome using bsmap (v 2.90) with the parameters “-p 10 -w 50 -v 0.1”.
Methylation ratio were calculated by with the parameters “-t 2 -m 5 -z”.
Genome_build: mm10
Supplementary_files_format_and_content: output files (.meth.txt) including methylation position and methylation ratio.
Submission date Feb 07, 2019
Last update date Dec 10, 2020
Contact name Yang Shi
Organization name Fudan university
Street address NO. 138, Yi-Xue-Yuan Road
City Shanghai
ZIP/Postal code 200032
Country China
Platform ID GPL21273
Series (2)
GSE126239 RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (WGBS)
GSE126243 RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs
BioSample SAMN10884457
SRA SRX5347776

Supplementary file Size Download File type/resource
GSM3594144_METTL3_KO_WGBS_rep1_CG.meth.txt.gz 34.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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