|
| Status |
Public on Dec 31, 2010 |
| Title |
WL_control_rep2 |
| Sample type |
genomic |
| |
|
| Source name |
4-day-old whole seedlings grown under WL, input
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia (Col-0)
genotype: wild type
age: 4 days
tissue: whole seedling
growth condition: wild type light (WL)
|
| Growth protocol |
4-day-old whole seedlings were grown under WL.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin isolation was performed with 4-day-old whole seedlings grown under WL or 8hr darkness treatment according to Bowler et al. (2004). The resuspended chromatin pellet was sonicated at 4°C with a Diagenode Bioruptor set at high intensity for 10 min (30 s on, 30 s off intervals). An aliquot of untreated sonicated chromatin was reverse cross-linked and used as a total input DNA control for ChIP-PCR experiments.
|
| Label |
biotin
|
| Label protocol |
DNA was labeled according to the Affymetrix Chromatin Immunoprecipitation Assay Protocol Rev.3.
|
| |
|
| Hybridization protocol |
DNA was hybridized according to the Affymetrix Chromatin Immunoprecipitation Assay Protocol Rev.3.
|
| Scan protocol |
Whole Genome Tiling arrays were scanned on an Affymetrix scanner G7.
|
| Description |
ChIP-chip
|
| Data processing |
Raw microarray data were log2 transformed and quantile normalized using Cisgenome (http://www.biostat.jhsph.edu/~hji/cisgenome). A two sample comparison test was performed on the processed data using TileMap Version2 with the HMM method to detect the peaks in the light and dark.
The GSE24973 supplementary file 'GSE24973_processed_data.txt' contains the log2 normalized intensities of the probes.
|
| |
|
| Submission date |
Oct 27, 2010 |
| Last update date |
Dec 31, 2010 |
| 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 (2) |
| GSE24973 |
Genome-wide mapping of the HY5-mediated gene networks in Arabidopsis that involve both transcriptional and post-transcriptional regulations: ChIP-Chip |
| GSE24974 |
Genome-wide mapping of the HY5-mediated gene networks in Arabidopsis that involve both transcriptional and post-transcriptional regulations |
|
