|
| Status |
Public on Apr 21, 2011 |
| Title |
TET1_CpG_Methylation_bisulfite_sequencing |
| Sample type |
SRA |
| |
|
| Source name |
J1 ES cells, Tet1 siRNA
|
| Organism |
Mus musculus |
| Characteristics |
cell line: J1
cell type: mouse embryonic stem (MES) cells
sirna treatment: Tet1 siRNA
|
| Treatment protocol |
J1 ES cells were transfected with control siRNA or Tet1 siRNA and harvested four days after transfection. The genomic DNA was purified, and bisulfite conversion was performed with the EZ-Methylation Gold kit (Zymo Research).
|
| Growth protocol |
J1 ES cells were co-cultured with MEF feeder cells in standard ES cell medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
A library of 55,000 long oligonucleotides was designed to capture the transcription start sites of 908 genes on mouse chromosomes X and Y, 114 imprinted genes, 493 miRNA genes and 88 additional targets. The oligonucleotide library was PCR-amplified and converted into functional padlock probes through a series of enzymatic reactions as described previously (Zhang et al., 2009). The genomic DNA was purified using the DNeasy kit (Qiagen), and bisulfite conversion was performed with the EZ-Methylation Gold kit (Zymo Research). Target capture was performed on 200ng of bisulfite-converted DNA with 100x excess of padlock probes. The detailed protocol is described in the reference: Deng, J. et al. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotech, 2009, 27, 353-360 (PMID 19330000).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
CpG DNA methylation.
library strategy: USER-S1-Ligation
library selection: padlock capture
|
| Data processing |
Reads were aligned to captured target sequences. CpG methylation levels were extracted from mapped reads. The resulting values are real numbers ranging from 0 to 1, which correspond to completely unmethylated and completely methylated, respectively.
|
| |
|
| Submission date |
Apr 11, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Feizhen Wu |
| E-mail(s) |
wufz@fudan.edu.cn
|
| Phone |
86-21-54237821
|
| Organization name |
Fudan Univ, Shanghai, China
|
| Department |
Institutes of Biomedical Sciences
|
| Lab |
Epigenetics lab
|
| Street address |
Dongan Road 131, Rm 511 Mingdao Building
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE28500 |
Genome-wide Regulation of 5hmC, 5mC and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells |
| GSE28533 |
Genome-wide Regulation of 5hmC, 5mC and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells (bisulfite sequencing data) |
|
| Relations |
| SRA |
SRX057754 |
| BioSample |
SAMN02198512 |
| Named Annotation |
GSM706686_TET1_CpG_Methylation_bisulfite_sequencing.BED.gz |
