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Status |
Public on Aug 23, 2011 |
Title |
13460812 - hen1.6_2_H3K4me2 vs Col_2_H3K4me2 |
Sample type |
genomic |
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Channel 1 |
Source name |
Col_2_H3K4me2
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Organism |
Arabidopsis thaliana |
Characteristics |
ecotype: columbia genotype/variation: control harvest date: 22-09-06 antibody: H3K4me2 antibody vendor: upstate antibody catalog #: 07-030
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Treatment protocol |
no treatment
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Growth protocol |
aerial - Media : soil hygrometry : 50-60% temperature : day : 21.5°C, night : 17°C light : 16h day/8h night
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Extracted molecule |
genomic DNA |
Extraction protocol |
Col_1:20ug. antibody: H3K4me2 (upstate_07-030); (Plant_ChIP_protocol_06.doc)
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Label |
Cy5
|
Label protocol |
labelling Cy3 and Cy5 direct, amplification=yes, DNA . (ChIP_amplification_roundA+B.doc)
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Channel 2 |
Source name |
hen1.6_2_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_2:10ug. 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)
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|
|
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Hybridization protocol |
Col_2_H3K4me2 Cy5 / hen1.6_2_H3K4me2 Cy3 : 65pmol. (4_chip_hybridisation.doc)
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Scan protocol |
GenePix Pro 3.0, Cy3:pmt voltage 532nm,550V,laser power 100%, Cy5:635nm,pmt voltage 600V,laser power 100%
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Description |
What are the genes that are differentially regulated in various tissues derived from silencing suppressor plants or miRNA mutants?
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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.
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Submission date |
Oct 14, 2010 |
Last update date |
Aug 23, 2011 |
Contact name |
Véronique BRUNAUD |
E-mail(s) |
veronique.brunaud@inrae.fr
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Organization name |
INRA - CNRS - UPSUD
|
Lab |
IPS2
|
Street address |
rue Noetzlin
|
City |
Gif-sur-Yvette |
ZIP/Postal code |
91190 |
Country |
France |
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|
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 |
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