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Sample GSM227267 Query DataSets for GSM227267
Status Public on Jan 28, 2008
Title Promoter CpG Methylation in Mouse ES Cells (2/2) replicate 1
Sample type genomic
 
Channel 1
Source name Wildtype Mouse ES Cell DNA
Organism Mus musculus
Characteristics Wildtype DNA from J1 Mouse ES Cells
Extracted molecule genomic DNA
Extraction protocol Phenol:Chloroform Extracted DNA
Label Cy3
Label protocol Cy3 Labelled with Agilent CGH protocol
 
Channel 2
Source name TKO Mouse ES Cells
Organism Mus musculus
Characteristics Dnmt3a/3b -/-; Dnmt1 KD Mouse ES Cells (Meissner et al., 2005. Nucleic Acid Research. 33:5868-77).
Extracted molecule genomic DNA
Extraction protocol Phenol:Chloroform Extracted DNA
Label Cy5
Label protocol Cy5 Labelled with Agilent CGH protocol
 
 
Hybridization protocol 250ng of DNA for each channel was labelled using Agilent CGH labelling protocol. Labelled DNA mixed with mouse Cot-1 DNA, yeast tRNA and Agilent 10x Control targets. This mix was hybridized to arrays for 40 hours at 65C. Arrays were washed as per Agilent protocol and scanned immediately
Scan protocol The arrays were scanned with Agilent DNA microarray scanner (G2565BA), and probe features were extracted using Feature Extraction Software (version 8.5)
Description All cell cultures were maintained at 37 °C with 5% CO2. The culture of mouse ESCs were maintained in DMEM supplemented with 15% heat-inactivated FBS , LIF and penicillin/streptomycin. mESCs were grown in feeder-free for 2 passages before harvesting of DNA. After genomic DNA isolation, the DNA was RNase treated and 2ug was used for methylated DNA immunoprecipitation (Weber et al., 2005. Nat Genetics. 37, 853-62. Zhang et al., 2006. Cell. 126:1189-1201.) Immunoprecipitated DNA was checked with Q-PCR to ensure that it was enriched for methylated DNA. This DNA was then used for labelling.
Data processing Arrays were processed using Agilent Feature Extraction (Version 8.5). Log 10 ratio were calculated from processed Cy5/ processed Cy3 signals
 
Submission date Sep 05, 2007
Last update date Aug 14, 2011
Contact name Yin Shen
E-mail(s) yshen@mednet.ucla.edu
Organization name UCLA
Street address 695 Charles E. Young Dr.
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL5805
Series (1)
GSE9172 Mapping Promoter CpG Methylation in mESCs

Data table header descriptions
ID_REF
VALUE Log10 Ratio (Cy5/Cy3)
gProcessedSignal Processed Cy3 signal
rProcessedSignal Processed Cy5 Signal

Data table
ID_REF VALUE gProcessedSignal rProcessedSignal
1 -9.40E-01 2.14E+03 2.45E+02
2 0.00E+00 8.30E+00 1.89E+01
3 -1.42E-01 2.26E+02 1.63E+02
4 -2.27E-01 1.32E+03 7.79E+02
5 -2.68E-02 1.69E+03 1.59E+03
6 -7.93E-03 8.04E+03 7.90E+03
7 -7.16E-01 2.72E+03 5.23E+02
8 -1.55E-02 4.35E+01 4.19E+01
9 -4.68E-02 5.79E+02 5.20E+02
10 -1.85E-01 3.41E+02 2.23E+02
11 -4.70E-02 1.90E+03 1.71E+03
12 1.02E-01 6.15E+01 7.78E+01
13 -6.69E-02 5.68E+01 4.87E+01
14 -7.31E-01 2.67E+03 4.96E+02
15 -5.84E-02 6.41E+02 5.61E+02
16 9.13E-02 1.56E+02 1.93E+02
17 -3.18E-02 7.00E+02 6.51E+02
18 -1.11E-01 4.07E+02 3.15E+02
19 -5.17E-03 9.60E+02 9.49E+02
20 -1.29E-01 3.29E+01 2.45E+01

Total number of rows: 43804

Table truncated, full table size 1423 Kbytes.




Supplementary file Size Download File type/resource
GSM227267.txt.gz 10.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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