|
| Status |
Public on Nov 04, 2013 |
| Title |
H9 Embryonic stem (ES) cells 2 |
| Sample type |
genomic |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Embryonic stem (ES) cells H9
passages: 35-38
quantification: MethylFlash methylated DNA quantification kit (Epigentek, Catalog No. P-1035)
cell line: H9
|
| Growth protocol |
Differentiation of the hES cell line H9 (WiCell, Madison, WI, USA; passages 35-38) into NP cells and terminally into DA neurons was performed as described (Ko et al., 2007).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (1 µg) from each sample was bisulfite converted using the EZ DNA methylation kit (Zymo Research), and 200 ng of the converted DNA was used for amplification.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
standard Illumina protocol
|
| |
|
| Hybridization protocol |
Amplified DNA was hybridized on the Infinium HumanMethylation 450 BeadChip (Illumina), following the Illumina Infinium HD Methylation protocol.
|
| Scan protocol |
The arrays were imaged using the Illumina HiScan SQ scanner, and image processing and extraction of intensity data were performed according to Illumina’s instructions.
|
| Description |
Embryonic stem(ES) cells H9
|
| Data processing |
Each methylation signal was used to compute the β value, which is a quantitative measure of DNA methylation ranging from 0 (for completely unmethylated cytosines) to 1 (for completely methylated cytosines) (Bibikova et al., 2006).
|
| |
|
| Submission date |
May 24, 2012 |
| Last update date |
Nov 04, 2013 |
| Contact name |
Mirang Kim |
| E-mail(s) |
mirnag@kribb.re.kr
|
| Organization name |
KRIBB(Korea Research Institute of Bioscience and Biotechnology
|
| Department |
Personalized Genomic Medicine Research Center
|
| Street address |
125 Gwahak-ro, Yuseong-gu
|
| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE38214 |
Dynamic changes of DNA methylome and hydroxymethylome during neural differentiation of hES cell (hMeDIP-Seq and MBD-Seq) |
| GSE38216 |
Dynamic changes of DNA methylome and hydroxymethylome during neural differentiation of hES cells (Methylation BeadChip) |
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