|
| Status |
Public on Dec 30, 2009 |
| Title |
D to L_H3K27me3_rep3 |
| Sample type |
genomic |
| |
|
| Source name |
5 day-old dark grow seedlings transfered to white light for 6 hours (D to L).
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
modification and growth condition: H3K27me3 D to L
antibody: anti-H3K27me3
|
| Treatment protocol |
Chromatin immunoprecipitated with anti-H3K27me3
|
| Growth protocol |
5 day-old dark grow seedlings transfered to white light for 6 hours (D to L).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin isolation was performed with 10 g of whole seedlings tissue according to Bowler et al. (2004). The resuspended chromatin pellet was sonicated at 4°C with a Diagenode Bioruptor (Diagenode, Sparta, NJ) set at high intensity for 10 min (30 sec on, 30 sec off intervals). The DNA was sheared to approximatively 0.3-0.8 kb fragments.Three μl of the following antibodies were used for immunoprecipitation: anti-H3K9ac (Upstate 06-942), anti-H3K9me3 (Upstate 07-442), anti-H3K27ac (Upstate 07-360), anti-H3K27me3 (Upstate 07-449), and anti-H3 (Upstate 07-690).
|
| Label |
biotin
|
| Label protocol |
DNA was labeled according to Affymetrix’ Chromatin Immunoprecipitation Assay Protocol Rev.3.
|
| |
|
| Hybridization protocol |
DNA was hybridized according to Affymetrix’ Chromatin Immunoprecipitation Assay Protocol Rev.3.
|
| Scan protocol |
Whole Genome Tiling array were scanned on Affymetrix scanner G7
|
| Description |
none
|
| Data processing |
Raw microarray data were quantile normalized and modified regions were detected with TileMap using the Hidden Markov model option and the Unbalanced Mixture Subtraction (UMS) method (Ji and Wong, 2005) to provide an approximate estimate of model parameters for HMM (false discovery rate).
|
| |
|
| Submission date |
Apr 07, 2009 |
| Last update date |
Aug 28, 2009 |
| 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 |
GPL8416 |
| Series (1) |
| GSE15597 |
Epigenetic Control of Light-Regulated Gene Expression in Arabidopsis |
|
