|
| Status |
Public on Jan 04, 2008 |
| Title |
DNAmeth_MethylatedDNA_532_LS replicate2 |
| Sample type |
genomic |
| |
|
| Source name |
light shoot
|
| Organism |
Oryza sativa |
| Characteristics |
Enriched for methylated DNA at all sequenced contexts
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Methylated DNA was isolated using a McrBC digestion method adapted from restriction enzyme that cleaves between two [A/G] C sites separated by 40-3000 bp, only when the C residue in [A/G] C motif is methylated.
|
| Label |
Cy3
|
| Label protocol |
About 2.0 µg recovered methylated DNA or sonicated total genomic DNA (< 500 bp) were labeled with Cy3 or Cy5 using the BioPrime Array CGH Genomic Labeling System (Invitrogen) and used for microarray hybridization.
|
| |
|
| Hybridization protocol |
Microarray slides were incubated in prehybridization buffer (5X SSC, 0.1% SDS, 1% BSA) for 30min - 1hour at 42 ºC and washed with water. Slides were then hybridized with Cy3 or Cy5- labeled DNA targets in hybridization buffer (5X SSC, 0.1% SDS, 0.5 mg/ml salmon sperm DNA, 0.5 mg/ml BSA) for 16-20 hours at 50 ºC. After hybridization, slides were washed sequentially with 2X SSC / 0.1% SDS, 0.2X SSC /0.1% SDS and 0.2X SSC for 10 min at room temperature.
|
| Scan protocol |
The dried slides were scanned with a GenePix 4200A scanner (Axon).
|
| Description |
Enriched for methylated DNA at all sequenced contexts
|
| Data processing |
Gene chip data files were processed using quantile normalization.
|
| |
|
| Submission date |
Dec 17, 2007 |
| Last update date |
Jan 03, 2008 |
| Contact name |
Hang He |
| E-mail(s) |
hehang@gmail.com
|
| Organization name |
Yale University
|
| Department |
MCDB
|
| Lab |
Deng Xing-Wang
|
| Street address |
165 Prospect St
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL6285 |
| Series (1) |
| GSE9925 |
Global mapping of epigenetic modifications of histone H3 Lysine 4 di- and trimethylation in Rice |
|
