|
| Status |
Public on Aug 25, 2011 |
| Title |
Methylation profiling in KP MSCs |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
HPV E6/E7-transfected mesenchymal stem cells, HpaII/HhaI/BstuI
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KP
cell type: immortalized human mesenchymal stem cells
tissue derivation: bone marrow
restriction enzyme: HpaII, HhaI, BstuI
transfected gene: HPV E6/E7
|
| Growth protocol |
KP and 3A6 MSCs were kept in DMEM-LG medium with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from samples using the Qiagen QIAamp DNA mini kit.
|
| Label |
Cy5
|
| Label protocol |
The HpaII/HhaI/BstuI-digested samples and the McrBC-digested samples were differentially labeled with Cy5- or Cy3-conjugated dUTP using the Agilent Genomic DNA Labeling Kit PLUS.
|
| |
|
| Channel 2 |
| Source name |
HPV E6/E7-transfected mesenchymal stem cells, McrBC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KP
cell type: immortalized human mesenchymal stem cells
tissue derivation: bone marrow
restriction enzyme: McrBC
transfected gene: HPV E6/E7
|
| Growth protocol |
KP and 3A6 MSCs were kept in DMEM-LG medium with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from samples using the Qiagen QIAamp DNA mini kit.
|
| Label |
Cy3
|
| Label protocol |
The HpaII/HhaI/BstuI-digested samples and the McrBC-digested samples were differentially labeled with Cy5- or Cy3-conjugated dUTP using the Agilent Genomic DNA Labeling Kit PLUS.
|
| |
|
| |
| Hybridization protocol |
Labeled DNA was hybridized to a human CpG island microarray at 65°C for 40 h.
|
| Scan protocol |
Arrays were scanned on the Agilent microarray scanner G2505B (Agilent Technologies, USA).
Images were quantified using Feature Extraction 9.1 software (Agilent Technologies, USA).
|
| Description |
KP
|
| Data processing |
Microarray data were firstly normalized with print-tip loess, followed by background-correction, normalization and analysis by the limma package within the R environment. The methylation level was determined as the ratio of Cy5/Cy3 in each spot.
|
| |
|
| Submission date |
Sep 01, 2010 |
| Last update date |
Aug 25, 2011 |
| Contact name |
Chih Chien Tsai |
| E-mail(s) |
n_asnas@yahoo.com.tw
|
| Organization name |
Taipei Vaterans General Hospital
|
| Street address |
No. 201, Sec. 2, Shih-Pai Road, Taipei 112, Taiwan
|
| City |
Taipei |
| ZIP/Postal code |
112 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL9767 |
| Series (1) |
| GSE23936 |
Homo sapiens immortalized MSCs: KP vs. 3A6 |
|
