Comment[ArrayExpressAccession]	E-GEOD-13419
Public Release Date	2009-02-02														
Investigation Title	High-throughput pyrosequencing of endogenous small RNAs from Arabidopsis thaliana wild-type and ddm1 mutant.														
Comment[Submitted Name]	High-throughput pyrosequencing of endogenous small RNAs from Arabidopsis thaliana wild-type and ddm1 mutant.
Experiment Description	DNA methylation is essential for silencing transposable elements and some genes in higher eukaryotes, implying that this modification must be tightly controlled. However, accidental changes in DNA methylation can be transmitted through mitosis, as in cancer, or meiosis, leading to epiallelic variation. Here, we demonstrate the existence of an efficient and faithful mechanism that protects against transgenerational loss of DNA methylation in the plant Arabidopsis. This process is specific to the subset of heavily methylated genomic repeats that are targeted by the RNAi machinery, and does not spread into flanking regions. Remethylation is often progressive over two to four sexual generations. This differential and incremental correction of epigenetic defects may preserve genome stability while increasing adaptive opportunities. 2 samples examined: wild type, and ddm1 mutant.														
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Term Source Name	EFO
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Term Source File	http://www.ebi.ac.uk/efo/efo.owl														
Person Last Name	Sarazin	Teixeira	Heredia	Sarazin	Roudier	Boccara	Ciaudo	Cruaud	Poulain	Berdasco	Fraga	Voinnet	Wincker	Esteller	Colot
Person First Name	Alexis	Felipe	Fabiana	Alexis	François	Martine	Constance	C	J	Maria	Mario	Olivier	P	Manel	Vincent
Person Mid Initials		K									F				
Person Email	sarazin@biologie.ens.fr														
Person Affiliation	CNRS UMR 8186 - Biologie Moléculaire des Organismes Photosynthétiques														
Person Phone	+33 1 44 32 35 24														
Person Fax	+33 1 44 32 39 35														
Person Address	Ecole Normale Supérieure, Département de Biologie, CNRS UMR 8186 - Biologie Moléculaire des Organismes Photosynthétiques, 46 rue d'Ulm, PARIS, France														
Person Roles	submitter														
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Protocol Name	P-GSE13419-2	P-GSE13419-1	P-GSE13419-4	P-GSE13419-3	P-GSE13419-5										
Protocol Description	SEQUENCE = Unique sequences identified<br>COUNT = Abundance count in Col0 ddm1 mutant	SEQUENCE = Unique sequences identified<br>COUNT = Abundance count in Col0 WT	Small RNA isolation, gel purification and cloning were performed as described in Curr Protoc Mol Biol by Pfeffer et al. in 2005.	Plants were grown under long-day conditions	Sequence reads were matched against the Arabidopsis thaliana nuclear genome (TAIR7, www.arabidopsis.org) using MUMmer v3.0, only full-length complete matches were allowed.										
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Protocol Type	bioassay_data_transformation	bioassay_data_transformation	nucleic_acid_extraction	grow	feature_extraction										
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Experimental Factor Name	STRAIN OR LINE														
Experimental Factor Type	strain or line														
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Publication Title	A role for RNAi in the selective correction of DNA methylation defects.														
Publication Author List	Teixeira FK, Heredia F, Sarazin A, Roudier F, Boccara M, Ciaudo C, Cruaud C, Poulain J, Berdasco M, Fraga MF, Voinnet O, Wincker P, Esteller M, Colot V														
PubMed ID	19179494														
Publication DOI	10.1126/science.1165313														
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Comment[SecondaryAccession]	GSE13419	SRP001257													
Comment[GEOLastUpdateDate]	2012-03-20
Comment[AEExperimentType]	RNA-seq of non coding RNA														
Comment[GEOReleaseDate]	2009-02-02
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR027950-SRR027951														
Comment[ArrayExpressSubmissionDate]	2008-10-31
SDRF File	E-GEOD-13419.sdrf.txt