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Sample GSM5182588 Query DataSets for GSM5182588
Status Public on Feb 04, 2022
Title TMX, methylated DNA
Sample type SRA
 
Source name Skeletal muscle stem cells
Organism Mus musculus
Characteristics tissue: Hindlimb muscles
age: 9-week old
treatment: Tamoxifen
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 SAMN18352299
SRA SRX10379185

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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