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Sample GSM589956 Query DataSets for GSM589956
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.
 
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

Data table header descriptions
ID_REF
VALUE Log10 Cy5/Cy3
Normalized_Ratio Cy5/Cy3 ratio

Data table
ID_REF VALUE Normalized_Ratio
A_17_P16499695 -0.203679223 0.625634626
A_17_P00917694 -0.176542897 0.665973737
A_17_P05822757 -0.31869195 0.48007385
A_17_P11201690 -0.239591141 0.575981931
A_17_P15518473 -0.02111683 0.952539885
A_17_P11189908 0.076950095 1.19385091
A_17_P17268257 0.052158234 1.127608223
A_17_P07299116 -0.120216123 0.758200169
A_17_P10258961 -0.122705287 0.753866966
A_17_P17240199 0.049501566 1.120731468
A_17_P08342170 0.075651606 1.190286768
A_17_P15872316 0.053328643 1.130651186
A_17_P15436892 -0.042540862 0.906690652
A_17_P05821269 0 1
A_17_P07833726 0.272630405 1.873399521
A_17_P00091682 0.245039013 1.758081538
A_17_P16463750 -0.367311297 0.429228651
A_17_P17089734 0.200787207 1.587768592
A_17_P15905399 -0.253579974 0.557724889
A_17_P16167438 -0.062606013 0.865752963

Total number of rows: 237220

Table truncated, full table size 8722 Kbytes.




Supplementary file Size Download File type/resource
GSM589956.txt.gz 68.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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