|
| Status |
Public on Mar 28, 2011 |
| Title |
33171920fie - H3K4me3_fie_II_INPUT vs H3K4me3_fie_II_IP |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
H3K4me3_fie_II_IP
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
antibody: anti-H3K4me3
antibody catalog #: 07-473
antibody manufacturer: Upstate-Millipore
antibody lot #: 24503
genotype: fie mutant
genetic background: Col-0
tissue: seedling
|
| Treatment protocol |
no treatment
|
| Growth protocol |
seedling - 20 days on MS agar plate at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
fie_II:50ug.
|
| Label |
Cy5
|
| Label protocol |
labelling Cy3 and Cy5 indirect, amplification=yes, DNA .
|
| |
|
| Channel 2 |
| Source name |
H3K4me3_fie_II_INPUT
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
antibody: n/a
antibody catalog #: n/a
antibody manufacturer: n/a
antibody lot #: n/a
genotype: fie mutant
genetic background: Col-0
tissue: seedling
|
| Treatment protocol |
no treatment
|
| Growth protocol |
seedling - 20 days on MS agar plate at 22 degrees C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
fie_II:50ug.
|
| Label |
Cy3
|
| Label protocol |
labelling Cy3 and Cy5 indirect, amplification=yes, DNA .
|
| |
|
| |
| Hybridization protocol |
H3K4me3_fie_II_IP Cy5 / H3K4me3_fie_II_INPUT Cy3 : 80pmol.
|
| Scan protocol |
GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 700V,laser power 100%
|
| Description |
Epigenomic mapping in fie
|
| 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).
|
| |
|
| Submission date |
Sep 16, 2010 |
| Last update date |
Mar 29, 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 |
GPL10918 |
| Series (2) |
| GSE24161 |
Genome-wide analysis of H3K27me3 and H3K4me3 deposition in the fie mutant (h3k4me3_fie_col_seedlings_db) |
| GSE24163 |
Genome-wide analysis of H3K27me3 and H3K4me3 deposition in the fie mutant |
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