{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["François ROUDIER"],"organism":["Arabidopsis thaliana"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-25050"],"description":["a2e_heterosis - h3k27me3_colxcvi - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K27me3 profiling in ColxCvi hybrids 4 dye-swap - chip-chip"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Processing - no treatment","Hybridization - H3K27me3_ColxCvi_II_IP Cy5 / H3K27me3_ColxCvi_II_INPUT Cy3 : 80pmol.","Nucleic Acid Extraction - ColxCvi_I:20ug.","Nucleic Acid Extraction - ColxCvi_II:20ug.","Hybridization - H3K27me3_ColxCvi_I_INPUT Cy5 / H3K27me3_ColxCvi_I_IP Cy3 : 80pmol.","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.","Nucleic Acid Extraction - ColxCvi_I:20ug. antibody: H3K27me3 (Upstate 07-449);","Labeling - labelling Cy3 and Cy5 indirect, amplification=yes, DNA .","Hybridization - H3K27me3_ColxCvi_I_IP Cy5 / H3K27me3_ColxCvi_I_INPUT Cy3 : 80pmol.","Hybridization - H3K27me3_ColxCvi_II_INPUT Cy5 / H3K27me3_ColxCvi_II_IP Cy3 : 80pmol.","Nucleic Acid Extraction - ColxCvi_II:20ug. antibody: H3K27me3 (Upstate 07-449);"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Feature Extraction - 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).","Assay Data Transformation - 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","Assay Data Transformation - 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","Image Adquisition - NimbleGen, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 700V,laser power 100%"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["Plant genomes are earmarked with defined patterns of chromatin marks. Little is known about the stability of these epigenomes when related, but distinct genomes are brought together by intra-species hybridization. Arabidopsis thaliana accessions and their reciprocal hybrids were used as a model system to investigate the dynamics of histone modification patterns. The genome-wide distribution of histone modifications H3K4me2 and H3K27me3 in the inbred parental accessions Col-0, C24 and Cvi and their hybrid offspring was compared by chromatin immunoprecipitation in combination with genome tiling array hybridization. The analysis revealed that, in addition to DNA sequence polymorphisms, chromatin modification variations exist among accessions of A. thaliana. The range of these variations was higher for H3K27me3 (typically a repressive mark) than for H3K4me2 (typically an active mark). H3K4me2 and H3K27me3 were rather stable in response to intra-species hybridization, with mainly additive inheritance in hybrid offspring. In conclusion, intra-species hybridization does not result in gross changes to chromatin modifications."],"study_type":["ChIP-chip by tiling array"],"species":["Arabidopsis thaliana"],"pubmed_title":["Additive inheritance of histone modifications in Arabidopsis thaliana intra-specific hybrids."],"pubmed_authors":["François ROUDIER","Vincent Colot","Moghaddam AM, Roudier F, Seifert M, B�rard C, Magniette ML, Ashtiyani RK, Houben A, Colot V, Mette MF","Marie-Laure Martin-Magniette","Francois Roudier"],"additional_accession":[]},"is_claimable":false,"name":"h3k27me3_colxcvi-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions","description":"a2e_heterosis - h3k27me3_colxcvi - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K27me3 profiling in ColxCvi hybrids 4 dye-swap - chip-chip","dates":{"release":"2011-05-17T00:00:00Z","modification":"2023-08-15T02:29:48.837Z","creation":"2022-03-10T03:13:56.273Z"},"accession":"E-GEOD-25050","cross_references":{"GEO":["GSE25050"],"pubmed":["21554454"],"EFO":["EFO_0002762"],"doi":["10.1111/j.1365-313X.2011.04628.x"]}}