|
| Status |
Public on Apr 19, 2011 |
| Title |
13189669 - H3K9me2_I_IP vs H3K9me2_I_INPUT |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
H3K9me2_I_INPUT
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: col-0
age: 11 day
dev.stage (boyes et al. plant cell 2001): seedling
|
| Treatment protocol |
no treatment
|
| Growth protocol |
whole plant - 11 days in liquid MS 0.5X at 22 °s C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
H3K9me2_I:15ug.
|
| Label |
Cy5
|
| Label protocol |
labelling Cy3 and Cy5 direct, amplification=yes, DNA .
|
| |
|
| Channel 2 |
| Source name |
H3K9me2_I_IP
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: col-0
age: 11 day
dev.stage (boyes et al. plant cell 2001): seedling
antibody: H3K9me2
vendor: upstate_07-441
|
| Treatment protocol |
no treatment
|
| Growth protocol |
whole plant - 11 days in liquid MS 0.5X at 22 °s C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
H3K9me2_I:15ug.
|
| Label |
Cy3
|
| Label protocol |
labelling Cy3 and Cy5 direct, amplification=yes, DNA .
|
| |
|
| |
| Hybridization protocol |
H3K9me2_I_INPUT Cy5 / H3K9me2_I_IP Cy3 : 140pmol.
|
| Scan protocol |
GenePix Pro 3.0, Cy3:pmt voltage 532nm,550V,laser power 100%, Cy5:635nm,pmt voltage 600V,laser power 100%
|
| Description |
Epigenomic mapping
|
| Data processing |
Data were normalized as ChIP-chip data in Turck e al.(2007). This method is based on the properties of dye-swaps to remove technical biases. To be specific, let Yij be the signal of the sample labeled with the dye j on the array i. Given that the second array is a technical replicate of the first one, the distribution of Y21 (respectively Y22) should be close to that of Y12 (respectively Y11). In practice, the relationship between Y21 and Y12 is linear but it is not the identity function. The parameters of the two linear models are estimated by Y21=a+bY12+N(0,sigma2) and Y22=c+dY11+N(0,sigma2),and these estimates are used to define the normalized IP and INPUT values of the second array relative to the first one: Y21=(Y21-a)/b and Y22=(Y22-c)/d.For each sample and for each tile, the values of the two arrays of the dye-swap are then averaged.To analyze data, we use ChIPmix, a method proposed by Martin-Magniette et al.(2008) that we have adapted to study several biological replicates simultaneously. The method investigates the relationship between IP and Input by a mixture model of regressions. For a probe, available observation are the two measurements IP and INPUT for the two biological replicates. These latter are assumed to be independent by definition. The (unknown) status of a probe is characterized through a label Z which is 1 if the probe is enriched and 0 if it is normal (not enriched).
|
| |
|
| Submission date |
Oct 12, 2010 |
| Last update date |
Apr 19, 2011 |
| Contact name |
François ROUDIER |
| E-mail(s) |
francois.roudier@ens-lyon.fr
|
| Organization name |
Ecole Normale Supérieure de Lyon
|
| Department |
Biologie
|
| Lab |
RDP
|
| Street address |
46 Allée d'Italie
|
| City |
Lyon |
| ZIP/Postal code |
69364 |
| Country |
France |
| |
|
| Platform ID |
GPL10772 |
| Series (2) |
| GSE24647 |
h3k9me2-Establishing a reference epigenome in arabidopsis seedlings |
| GSE24710 |
Establishing a reference epigenome in arabidopsis seedlings |
|
