|
| Status |
Public on Aug 16, 2022 |
| Title |
mESC_RRBS+UMI |
| Sample type |
SRA |
| |
|
| Source name |
E14
|
| Organism |
Mus musculus |
| Characteristics |
cell_type: mESC
genotype: WT
|
| Growth protocol |
mESCs were cultured under standard feeder-free conditions on gelatinized tissue culture dishes and maintained in DMEM (Gibco, Thermo Fisher Scientific) supplemented with 100 uM 2-mercaptoethanol (Sigma), 1 mM sodium pyruvate, 2 mM L-glutamine, 1x penicillin–streptomycin, 15% fetal calf serum (HyClone) and 103 U/ml leukemia inhibitory factor (LIF, Millipore).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
we used 100–200 ng of genomic DNA according to Illumina's instructions. Libraries were generated and sequenced at IGA Technology Services (Italy), by using the NuGEN Ovation RRBS Methyl-Seq Library System and sequenced on paired-end 150 bp mode on NovaSeq6000 (Illumina, San Diego, CA)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
We performed the trimming and quality step using TrimGalore v. 0.6.6 using the RRBS mode (--rrbs). We aligned the reads against the Mus musculs genome (mm10) using Bismark v.0.23.0 with default parameters.We removed the duplicate reads using UMI-tools v.1.1.1 with default parameters and then we use Bismark methylation extractor to obtain the methylation level of the CpGs covered.
Assembly: mm10
Supplementary files format and content: bedGraph containing the methylation profile of the CpGs
|
| |
|
| Submission date |
May 28, 2022 |
| Last update date |
Aug 16, 2022 |
| Contact name |
Francesco Cecere |
| E-mail(s) |
francesco.cecerengs@gmail.com
|
| Phone |
3888903265
|
| Organization name |
University of Campania "Luigi Vanvitelli"
|
| Department |
DiStABiF
|
| Lab |
Riccio
|
| Street address |
Via A. Vivaldi, n. 43
|
| City |
Caserta |
| State/province |
Caserta |
| ZIP/Postal code |
81100 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE205042 |
The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex (RRBS) |
| GSE205043 |
The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex |
|
| Relations |
| BioSample |
SAMN28728451 |
| SRA |
SRX15492533 |
