|
Status |
Public on Aug 25, 2011 |
Title |
Methylation profiling in 3A6 MSCs |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
HPV E6/E7- and hTERT-transfected mesenchymal stem cells, HpaII/HhaI/BstuI
|
Organism |
Homo sapiens |
Characteristics |
cell line: 3A6 cell type: immortalized human mesenchymal stem cells tissue derivation: bone marrow restriction enzyme: HpaII, HhaI, BstuI transfected gene: HPV E6/E7 and hTERT
|
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- and hTERT-transfected mesenchymal stem cells, McrBC
|
Organism |
Homo sapiens |
Characteristics |
cell line: 3A6 cell type: immortalized human mesenchymal stem cells tissue derivation: bone marrow restriction enzyme: McrBC transfected gene: HPV E6/E7 and hTERT
|
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 |
3A6
|
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.
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|
|
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 |
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