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Status |
Public on Dec 08, 2020 |
Title |
rescue_WT_WGBS_rep1 |
Sample type |
SRA |
|
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Source name |
Embryonic stem cells
|
Organism |
Mus musculus |
Characteristics |
cell type: Embryonic stem cells genotype: METTL3 KO+WT METTL3
|
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).
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|
|
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 methratio.py with the parameters “-t 2 -m 5 -z”. Genome_build: mm10 Supplementary_files_format_and_content: methratio.py output files (.meth.txt) including methylation position and methylation ratio.
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|
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Submission date |
Feb 07, 2019 |
Last update date |
Dec 10, 2020 |
Contact name |
Yang Shi |
E-mail(s) |
yshi@hms.harvard.edu
|
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 |
|
Relations |
BioSample |
SAMN10884455 |
SRA |
SRX5347778 |