|
| Status |
Public on Feb 04, 2022 |
| Title |
OIL, methylated DNA |
| Sample type |
SRA |
| |
|
| Source name |
Skeletal muscle stem cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Hindlimb muscles
age: 9-week old
treatment: Oil
|
| Treatment protocol |
Tamoxifen (150 µl of 20 mg/ml) (Sigma, Cat# T5648) dissolved in corn oil (Sigma, Cat# C8267) were injected intraperitoneally for a total of 5 consecutive days to induce Cre-mediated recombination.
|
| Growth protocol |
Isolated satellite cells were resuspended in the DMEM/F12 (gibco, Cat# 10565-018) containing 20% FBS, 2% Ultroser G (Pall, Cat# 15950-017), and Antibiotic-Antimycotic. Cells were cultured for 3 days in 8-well chamber slide (Thermo Scientific, Cat# 177445) with 1 mg/ml of Matrigel (Corning, Cat# 354230) at 5000 cells/cm2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated and purified with NucleoSpin Tissure Kit (MACHEREY-NAGEL, Cat# 740952).
Purified DNA was sheared with Covaris S220 with microTUBE AFA (Covaris, Cat# 520045). Methylated and non-methylated DNA fragments were separated using EpiXplore Methylated DNA Enrichment Kit (Clontech, Cat# PT5034-2). Libraries were generated with DNA SMART ChIP-Seq Kit (Takara, Cat# 634865). The libraries were selected into 250-350-bp fragments by E-Gel 2% SizeSelect electrophoresis (Invitrogen, Cat# G661012).
MBD2-Seq
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were down-sampled to 50 million reads for each condition to avoid biases due to different sequencing depths.
The reads were trimmed using TrimGalore and were mapped using HISAT2 (Kim et al., 2015).
Peaks were obtained using MACS2 (version 2.2.6) (Zhang et al., 2008) using TMX treated mice-derived cells as ‘control’ with following options (--slocal 0 --llocal 0 -q 0.0001).
ChIPpeakAnno (Zhu et al., 2010) was used to annotate and visualize the peaks.
Genome_build: mm10
Supplementary_files_format_and_content: peaks file
|
| |
|
| Submission date |
Mar 18, 2021 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Hiroshi Sakai |
| E-mail(s) |
sakai.hiroshi.wh@ehime-u.ac.jp
|
| Phone |
+81-89-960-5925
|
| Organization name |
Ehime University
|
| Department |
Proteo-Science Center
|
| Lab |
Division of Integrative Pathophysiology
|
| Street address |
Shitsukawa
|
| City |
Toon |
| State/province |
Ehime |
| ZIP/Postal code |
791-0295 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE169184 |
Uhrf1 control the proliferation and the differentiation of satellite cells [MBD-seq] |
| GSE169193 |
Uhrf1 control the proliferation and the differentiation of satellite cells |
|
| Relations |
| BioSample |
SAMN18352289 |
| SRA |
SRX10379184 |
