|
| Status |
Public on May 17, 2011 |
| Title |
13460815-13455531 - H3K4me2_Col_III_IP vs H3K4me2_Col_III_INPUT |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
H3K4me2_Col_III_INPUT
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain: col-0
age: 10 day
tissue: seedling
sample type: input DNA
|
| Treatment protocol |
no treatment
|
| Growth protocol |
seedling - 10 days in liquid MS 0.5X at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Col_seedlings_III:50ug.
|
| Label |
Cy5
|
| Label protocol |
labelling Cy3 and Cy5 direct, amplification=yes, DNA .
|
| |
|
| Channel 2 |
| Source name |
H3K4me2_Col_III_IP
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain: col-0
age: 10 day
tissue: seedling
antibody: H3K4me2
antibody manufacturer: upstate
antibody catalog #: 07-030
|
| Treatment protocol |
no treatment
|
| Growth protocol |
seedling - 10 days in liquid MS 0.5X at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Col_seedlings_II:50ug. antibody: H3K4me2 (upstate_07-030);
|
| Label |
Cy3
|
| Label protocol |
labelling Cy3 and Cy5 direct, amplification=yes, DNA .
|
| |
|
| |
| Hybridization protocol |
H3K4me2_Col_III_INPUT Cy5 / H3K4me2_Col_III_IP Cy3 : 80pmol.
|
| Scan protocol |
GenePix Pro 3.0, Cy3:pmt voltage 532nm,550V,laser power 100%, Cy5:635nm,pmt voltage 600V,laser power 100%
|
| Description |
arabidopsis thaliana (col-0) - age: 10day dev.stage (Boyes et al. Plant Cell 2001):seedling
Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between
|
| 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).
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| |
|
| Submission date |
Nov 01, 2010 |
| Last update date |
May 17, 2011 |
| Contact name |
François ROUDIER |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE24836 |
Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions |
| GSE25061 |
h3k4me2_col_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions |
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