|
| Status |
Public on Aug 23, 2011 |
| Title |
13455895 - hen1.6_1_H3K4me2 vs Col_1_H3K4me2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Col_1_H3K4me2
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: columbia
genotype/variation: control
harvest date: 22-09-06
antibody: H3K4me2
antibody vendor: upstate
antibody catalog #: 07-030
|
| Treatment protocol |
no treatment
|
| Growth protocol |
aerial - Media : soil hygrometry : 50-60% temperature : day : 21.5°C, night : 17°C light : 16h day/8h night
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Col_1:20ug. antibody: H3K4me2 (upstate_07-030); (Plant_ChIP_protocol_06.doc)
|
| Label |
Cy5
|
| Label protocol |
labelling Cy3 and Cy5 direct, amplification=yes, DNA . (ChIP_amplification_roundA+B.doc)
|
| |
|
| Channel 2 |
| Source name |
hen1.6_1_H3K4me2
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: columbia
genotype/variation: mutant (hen1.6)
harvest date: 24-10-06
antibody: H3K4me2
antibody vendor: upstate
antibody catalog #: 07-030
|
| Treatment protocol |
no treatment
|
| Growth protocol |
aerial - Media : soil hygrometry : 50-60% temperature : day : 21.5°C, night : 17°C light : 16h day/8h night
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
hen1.6_1:20ug. antibody: H3K4me2 (upstate_07-030); (Plant_ChIP_protocol_06.doc)
|
| Label |
Cy3
|
| Label protocol |
labelling Cy3 and Cy5 direct, amplification=yes, DNA . (ChIP_amplification_roundA+B.doc)
|
| |
|
| |
| Hybridization protocol |
Col_1_H3K4me2 Cy5 / hen1.6_1_H3K4me2 Cy3 : 30pmol. (4_chip_hybridisation.doc)
|
| Scan protocol |
GenePix Pro 3.0, Cy3:pmt voltage 532nm,550V,laser power 100%, Cy5:635nm,pmt voltage 600V,laser power 100%
|
| Description |
What are the genes that are differentially regulated in various tissues derived from silencing suppressor plants or miRNA mutants?
|
| 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 14, 2010 |
| Last update date |
Aug 23, 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) |
| GSE24692 |
chip in silencing suppressor plants or in mirna plants-Transcriptional and post-transcriptional changes in Arabidopsis plants that constitutively express suppressors of RNA silencing |
| GSE24837 |
Transcriptional and post-transcriptional changes in Arabidopsis plants that constitutively express suppressors of RNA silencing |
|
