|
| Status |
Public on Dec 08, 2020 |
| Title |
rescue_WT_WGBS_rep1 |
| Sample type |
SRA |
| |
|
| 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).
|
| |
|
| 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.
|
| |
|
| 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 |
