|
| Status |
Public on Apr 10, 2014 |
| Title |
Aid+/+ MEF#3_p3 |
| Sample type |
SRA |
| |
|
| Source name |
Aid+/+ MEF#3_p3
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Aid+/+
cell type: MEF
modification: Nanog-GFP
strain: mix (C57BL6, DBA,129S4)
gender: male
|
| Treatment protocol |
Ｎｏ
|
| Growth protocol |
iPS cells and ES cells were cultured in DMEM supplemented with 20% FBS, 0.1 mM non-essential amino acids, 2 mM L-glutamine, 50 U/ml penicillin-streptomycin, 0.11 mM 2-mercaptoethanol, LIF on gelatin coated dishes. Two μg/mL puromycin was to the medium of iPS cells. MEFs were cultured in DMEM supplemented with 10% FBS, 50 U/ml penicillin-streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed with genome buffer (8.8 mM Tris-HCl pH8.0, 135 mM NaCl, 8.8 mM EDTA, 1% SDS, 200 μg/mL protenase K) and treated with RNase. Subsequently genomic DNA was purified with Phenol-Chloroform Isoamyl Alcohol (PCI) DNA extraction.
Genomic DNA was sonicated to 100-300 bp fragment with Covaris E210 (Covaris). Methylated DNA was enriched with EpiXplore Methylated DNA Enrichment Kit (Takara) according to manufacturer’s protocol. Multiplexed MBD-seq libraries were prepared from 10 ng of metylated DNA fragment using NEBNext ChIP-seq Library Prep Master Mix (New England BioLabs). For sequencing using GAIIx, cluster generation was performed using TruSeq SR Cluster Kit v2. Each lane of flow cells contained one sample. Sequencing was performed by a single-read run mode with total 76 cycles, including 75-bp read and one cycle for phasing.
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.1
Data were filtered using Illumina's Quality Filtering and 76th bases in reads were not used.
ChIP-seq reads were aligned to the mm9 genome assembly using BWA version 0.5.9rc1 with default parameters.
Peaks were detected using MACS version 1.4.1 with default parameter and without control samples.
Genome_build: mm9
Supplementary_files_format_and_content: Text files which contain peak information were generated using MACS version 1.4.1.
|
| |
|
| Submission date |
Nov 06, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ren Shimamoto |
| E-mail(s) |
shimamoto@cira.kyoto-u.ac.jp
|
| Organization name |
Center for iPS Cell Research and Application (CiRA)
|
| Department |
Dept. of Reprogramming Science
|
| Lab |
Shinya Yamanaka
|
| Street address |
53 Shogoin Kawahara-cho, Sakyo-ku
|
| City |
Kyoto |
| ZIP/Postal code |
606-8507 |
| Country |
Japan |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE52136 |
Effect of Aid deletion on the global DNA methylation status of iPS cells |
|
| Relations |
| BioSample |
SAMN02399491 |
| SRA |
SRX373800 |
