|
| Status |
Public on Mar 08, 2013 |
| Title |
Tet2CD_hMeDIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblasts (MEFs)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: OG2 transgenic mouse embryonic fibroblasts (MEFs)
passage: P2
strain: 1/2 129SVJ+3/8 C57B6+1/8 CBA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted by Wizard@ Genomic DNA Purification Kit (Promega, A1125). Genome DNA was sonicated to 100-500 base pairs (bp) for library construction.
Illumina adaptors were ligated before hmeDIP following NEBNext® DNA Library Prep Reagent Set for Illumina® instruction manual, and then the adaptor-ligated DNA was denatured and DIP using hmC-antibody. After hmeDIP, DNA was purified and amplified.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
extracting genomic DNA at D1 after infection
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
hMeDIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 2.1.0 with the parameters（ --end-to-end --sensitive)
peaks were called using MACS (1.4.2) with the following parameters ( --nomodel -p 1e-5 )
genome build: mm9
files format: bed files were generated using MACS, showing the results of peaks calling.
|
| |
|
| Submission date |
Mar 06, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Lihui Lin |
| E-mail(s) |
lin_lihui@gibh.ac.cn
|
| Phone |
020-32015291
|
| Organization name |
Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science
|
| Department |
Stem cell
|
| Lab |
Pei Duanqing
|
| Street address |
No.190, Kaiyuan Street
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
GD20 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE44935 |
The Role of Tet1 During Somatic Cell Reprogramming |
|
| Relations |
| SRA |
SRX247079 |
| BioSample |
SAMN01940690 |
