|
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
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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 |
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