|
| Status |
Public on May 17, 2011 |
| Title |
13455534 - C24_I vs Col_I |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Col_I
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: col-0
age: 15day
developmental stage: seedling (Boyes et al. Plant Cell 2001)
|
| 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_I:10ug. (DNeasy_Plant_Qiagen.pdf)
|
| Label |
Cy5
|
| Label protocol |
labelling Cy3 and Cy5 direct, amplification=no, DNA .
|
| |
|
| Channel 2 |
| Source name |
C24_I
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: c24
age: 15day
developmental stage: seedling (Boyes et al. Plant Cell 2001)
|
| 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 |
C24_I:10ug. (DNeasy_Plant_Qiagen.pdf)
|
| Label |
Cy3
|
| Label protocol |
labelling Cy3 and Cy5 direct, amplification=no, DNA .
|
| |
|
| |
| Hybridization protocol |
Col_I Cy5 / C24_I Cy3 : 120pmol. (CGH_hybridization_protocol.doc)
|
| 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 accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between
|
| Data processing |
The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.
|
| |
|
| Submission date |
Oct 04, 2010 |
| Last update date |
May 17, 2011 |
| Contact name |
Véronique BRUNAUD |
| E-mail(s) |
veronique.brunaud@inrae.fr
|
| Organization name |
INRA - CNRS - UPSUD
|
| Lab |
IPS2
|
| Street address |
rue Noetzlin
|
| City |
Gif-sur-Yvette |
| ZIP/Postal code |
91190 |
| Country |
France |
| |
|
| Platform ID |
GPL10772 |
| Series (2) |
| GSE24494 |
cgh_colvsc24_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions |
| GSE24836 |
Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions |
|
