|
| Status |
Public on Jan 04, 2008 |
| Title |
H3K4Me2_MethylatedDNA_532_LS replicate1 |
| Sample type |
genomic |
| |
|
| Source name |
light shoot
|
| Organism |
Oryza sativa |
| Characteristics |
Enriched for ChIP at all sequenced contexts
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin from light-grown shoots and cultured cells was immunoprecipitated with antibodies against H3K4Me2 (Upstate), H3K4Me3 (Abcam) (Nagaki et al., 2004) as described in Gendrel et al, 2005. ChIP (enriched) and iInput (whole cell extract) DNA samples were amplified using a random amplification procedure as described (Lippman et al., 2005).
|
| Label |
Cy3
|
| Label protocol |
2.0 µg amplified ChIP or Input DNA was 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 ChIP 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 |
GPL6286 |
| Series (1) |
| GSE9925 |
Global mapping of epigenetic modifications of histone H3 Lysine 4 di- and trimethylation in Rice |
|
