Comment[ArrayExpressAccession] E-GEOD-24652
Public Release Date 2011-04-19
Investigation Title h3k27me2-Establishing a reference epigenome in arabidopsis seedlings
Comment[Submitted Name] h3k27me2-Establishing a reference epigenome in arabidopsis seedlings
Experiment Description gfe_epigenome - h3k27me2 - Epigenomic mapping - H3K27me2 ChIP-chip 2 dye-swap - chip-chip
Date of Experiment
Term Source Name EFO
Term Source Version
Term Source File http://bar.ebi.ac.uk:8080/trac/browser/branches/curator/ExperimentalFactorOntology/ExFactorInOWL/currentrelease/eforelease/efo.owl
Person Last Name ROUDIER Colot Roudier Martin-Magniette
Person First Name François Vincent Francois Marie-Laure
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Person Email roudier@biologie.ens.fr
Person Affiliation Institut de Biologie de l'Ecole Normale Supérieure
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Person Address Institut de Biologie de l'Ecole Normale Supérieure, 46 rue d'Ulm, Paris, France
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Protocol Name P-GSE24652-2 P-GSE24652-1 P-GSE24652-15 P-GSE24652-14 P-GSE24652-11 P-GSE24652-8 P-GSE24652-4 P-GSE24652-10 P-GSE24652-9 P-GSE24652-3 P-GSE24652-13 P-GSE24652-12 P-GSE24652-5 P-GSE24652-7 P-GSE24652-6
Protocol Description ID_REF = ID
VALUE = Normalized log ratio base 2 IP/INPUT (INPUT=reference)
Intensity_cy5 = Normalized intensity of Ch1(Cy5) = INPUT
Intensity_cy3 = Normalized intensity of Ch2(Cy3) = IP
STATUS = (0/1) 1 if the FDR.BH < 0.01 and 0 otherwise
FDR.BH = The false discovery rate (FDR) were controlled at the 1% level using a Benjamini and Hochberg correction probability ID_REF = ID
VALUE = Normalized log ratio base 2 IP/INPUT (INPUT=reference)
Intensity_cy5 = Normalized intensity of Ch1(Cy5) = IP
Intensity_cy3 = Normalized intensity of Ch2(Cy3) = INPUT
STATUS = (0/1) 1 if the FDR.BH < 0.01 and 0 otherwise
FDR.BH = The false discovery rate (FDR) were controlled at the 1% level using a Benjamini and Hochberg correction probability H3K27me2_I_INPUT Cy5 / H3K27me2_I_IP Cy3 : 120pmol. H3K27me2_I_IP Cy5 / H3K27me2_I_INPUT Cy3 : 120pmol. H3K27me2_II_INPUT Cy5 / H3K27me2_II_IP Cy3 : 120pmol. H3K27me2_II_IP Cy5 / H3K27me2_II_INPUT Cy3 : 120pmol. seedling - 10-11 days in liquid MS 0.5X at 22 °s C. Cool white light at 100 uEm-2s-1, 16 hour photoperiod. Data were normalized as ChIP-chip data in Turck e al.(2007). This method is based on the properties of dye-swaps to remove technical biases. To be specific, let Yij be the signal of the sample labeled with the dye j on the array i. Given that the second array is a technical replicate of the first one, the distribution of Y21 (respectively Y22) should be close to that of Y12 (respectively Y11). In practice, the relationship between Y21 and Y12 is linear but it is not the identity function. The parameters of the two linear models are estimated by Y21=a+bY12+N(0,sigma2) and Y22=c+dY11+N(0,sigma2),and these estimates are used to define the normalized IP and INPUT values of the second array relative to the first one: Y21=(Y21-a)/b and Y22=(Y22-c)/d.For each sample and for each tile, the values of the two arrays of the dye-swap are then averaged.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). GenePix Pro 3.0, Cy3:pmt voltage 532nm,550V,laser power 100%, Cy5:635nm,pmt voltage 600V,laser power 100% no treatment H3K27me2_I_INPUT:15ug. H3K27me2_I_IP:15ug. H3K27me2_II_IP:15ug. H3K27me2_II_INPUT:15ug. labelling Cy3 and Cy5 direct, amplification=yes, DNA .
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Protocol Type bioassay_data_transformation bioassay_data_transformation hybridization hybridization hybridization hybridization grow feature_extraction image_aquisition specified_biomaterial_action nucleic_acid_extraction nucleic_acid_extraction nucleic_acid_extraction nucleic_acid_extraction labeling
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Publication Title Integrative epigenomic mapping defines four main chromatin states in Arabidopsis.
Publication Author List Roudier F, Ahmed I, Bérard C, Sarazin A, Mary-Huard T, Cortijo S, Bouyer D, Caillieux E, Duvernois-Berthet E, Al-Shikhley L, Giraut L, Després B, Drevensek S, Barneche F, Dèrozier S, Brunaud V, Aubourg S, Schnittger A, Bowler C, Martin-Magniette ML, Robin S, Caboche M, Colot V
PubMed ID 21487388
Publication DOI 10.1038/emboj.2011.103
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Comment[SecondaryAccession] GSE24652
Comment[GEOLastUpdateDate] 2011-04-18
Comment[AEExperimentType] ChIP-chip by tiling array
Comment[GEOReleaseDate] 2011-04-18
Comment[ArrayExpressSubmissionDate] 2010-10-11
SDRF File E-GEOD-24652.sdrf.txt