|
| Status |
Public on Nov 27, 2020 |
| Title |
S3-/- 2iLIF R1 RRBS |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryo
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cell
strain: 129/Ola
genotype: Stat3 knock-out
phenotype: adherent
growth condition: 2iLIF
|
| Growth protocol |
Mouse ES cells were cultured without feeders on gelatine-coated plates (0.2% gelatine) in serum-free KSR-based medium (Life Technologies) supplemented with: 1 μM PD0325901, 3 mM CHIR99021 (2i); and 100 units/m LIF (2iLIF).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
500ng of DNA was digested at 37°C with 200U of MspI restriction endonuclease (NEB). Digested DNA was than end repaired, dA-tailed, and ligated to methylated adapters, using the Illumina TruSeq DNA Sample Prep Kit, following manufacturer’s instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing reads were mapped to mouse genome reference (mm10/GRC.m38.p6) with BSMAP (v2.89) using RRBS mode (parameters: -s 12 -D C-CGG -v 0.01 –n 1).
CpG methylation levels were extracted from aligned reads as the ratio of the number of Cs over the total number of Cs and Ts using the methratio.py script. CpG methylation ratios from both strands were combined (parameters: –g)
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited text files include single-base resolution DNA methylation measurements for each sample.
|
| |
|
| Submission date |
Aug 10, 2019 |
| Last update date |
Nov 27, 2020 |
| Contact name |
Graziano Martello |
| E-mail(s) |
graziano.martello@unipd.it
|
| Organization name |
University of Padua
|
| Department |
Department of Molecular Medicine
|
| Street address |
viale Colombo 3
|
| City |
Padua |
| ZIP/Postal code |
35121 |
| Country |
Italy |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE133926 |
RRBS profiling and Transcriptome profiling of Stat3 wild-type, Stat3 knock-out, Dnmt3a/b wild-type and Dnmt3a/b knock-out mouse embryonic stem cells (mES cells) |
|
| Relations |
| BioSample |
SAMN12549302 |
| SRA |
SRX6693283 |
