|
| Status |
Public on May 17, 2011 |
| Title |
14984202Col - H3K27me3_Col_II_INPUT vs H3K27me3_Col_II_IP |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
H3K27me3_Col_II_IP
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain: col-0
age: 15 day
tissue: seedling
antibody: H3K27me3
antibody manufacturer: Upstate
antibody catalog #: 07-449
sample type: input DNA
|
| Treatment protocol |
no treatment
|
| Growth protocol |
seedling - 15 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_II:50ug. antibody: H3K27me3 (Upstate 07-449);
|
| Label |
Cy5
|
| Label protocol |
labelling Cy3 and Cy5 indirect, amplification=yes, DNA .
|
| |
|
| Channel 2 |
| Source name |
H3K27me3_Col_II_INPUT
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain: col-0
age: 15 day
tissue: seedling
|
| Treatment protocol |
no treatment
|
| Growth protocol |
seedling - 15 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_II:50ug.
|
| Label |
Cy3
|
| Label protocol |
labelling Cy3 and Cy5 indirect, amplification=yes, DNA .
|
| |
|
| |
| Hybridization protocol |
H3K27me3_Col_II_IP Cy5 / H3K27me3_Col_II_INPUT Cy3 : 80pmol.
|
| Scan protocol |
NimbleGen, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 700V,laser power 100%
|
| Description |
arabidopsis thaliana (col-0) - age: 15day 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 |
For the ChIP-chip data we performed a normalization step by an ANOVA model (Kerr et.al,2002) to remove technical biases.Let Yplfts be the log2 intensity of the probe s on the chip p and the array l, with treatment t and fluorochrome f.The considered model is: Yplfts=mu+ap+bl+abpl+cf+acpf+Eplfts, where ap+bl+abpl is the support effect (chip, array and interactions), cf is the fluorochrome effect, acpf is the chip*fluorochrome interaction and the errors Eplfts are centered Gaussian variables.We estimated the parameters of the model and we removed quantified biases from the raw data.The IP and INPUT intensities for each biological replicate were then averaged on the dye-swap to remove gene-specific dye biases.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 |
GPL10920 |
| Series (2) |
| GSE24836 |
Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions |
| GSE25052 |
h3k27me3_col(cvi)-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions |
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