|
| Status |
Public on Sep 21, 2010 |
| Title |
kyp ibm1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
H3K9me2 ChIP DNA from kyp ibm1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: kyp ibm1 mutant
sample type: ChIP fraction
antibody: CMA307, anti-H3K9me2 antibody
antibody source: Antibody used was directly provided from Dr. Hiroshi Kimura at Osaka Univ.
|
| Treatment protocol |
no treatment
|
| Growth protocol |
4 weeks on soil
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Leaves of 4-week-old plants were fixed as described previously (Saze et al, 2008). Chromatin immunoprecipitation (ChIP) was performed as described previously (Kimura et al, 2008), using antibody against H3K9me2 (CMA307, Kimura et al, 2008).
|
| Label |
Cy5
|
| Label protocol |
According to standard NimbleGen protocols (www.nimblegen.com).
|
| |
|
| Channel 2 |
| Source name |
Input DNA from kyp ibm1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: kyp ibm1 mutant
sample type: Input fraction
|
| Treatment protocol |
no treatment
|
| Growth protocol |
4 weeks on soil
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Leaves of 4-week-old plants were fixed as described previously (Saze et al, 2008). Chromatin immunoprecipitation (ChIP) was performed as described previously (Kimura et al, 2008), using antibody against H3K9me2 (CMA307, Kimura et al, 2008).
|
| Label |
Cy3
|
| Label protocol |
According to standard NimbleGen protocols (www.nimblegen.com).
|
| |
|
| |
| Hybridization protocol |
According to standard NimbleGen protocols (www.nimblegen.com)
|
| Scan protocol |
Used Agilent Microarray Scanner.
|
| Description |
ChIP-chip of H3K9me2 in kyp ibm1
|
| Data processing |
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.
Each feature on the array has a corresponding scaled log2 ratio, which is the ratio of the signals for the ChIP and input samples cohybridized to the array. The log2 ratio is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.
|
| |
|
| Submission date |
Jul 15, 2010 |
| Last update date |
Sep 21, 2010 |
| Contact name |
Soichi Inagaki |
| E-mail(s) |
soinagak@bs.naist.jp
|
| Organization name |
Nara Institute of Science and Technology
|
| Department |
Graduate School of Biological Sciences
|
| Street address |
8916-5, Takayama-cho
|
| City |
Ikoma |
| State/province |
Nara |
| ZIP/Postal code |
630-0192 |
| Country |
Japan |
| |
|
| Platform ID |
GPL10686 |
| Series (2) |
| GSE22953 |
Genome-wide analysis of H3K9me2 in ibm1, kyp, and cmt3 mutants of Arabidopsis thaliana |
| GSE23030 |
Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome |
|
