Comment[ArrayExpressAccession]	E-GEOD-58789
MAGE-TAB Version	1.1						
Public Release Date	2015-01-29
Investigation Title	ChIP-seq of WT(with 35S-SUC2 transgene) and proMBD7::gMBD7:4xMYC transgenic plants						
Comment[Submitted Name]	ChIP-seq of WT(with 35S-SUC2 transgene) and proMBD7::gMBD7:4xMYC transgenic plants
Experiment Description	In eukaryotes, heterochromatin is characterized by numerous epigenetic marks, including DNA methylation. Spreading of these marks into nearby active genes must be avoided in order to maintain appropriate gene expression. Here, we uncover Arabidopsis Methyl-CpG-Binding Domain 7 (MBD7) and Increased DNA Methylation 3 (IDM3) as anti-silencing factors that prevent transgene repression and genome-wide DNA hypermethylation. MBD7 preferentially binds to highly methylated, CG-dense regions associated with non-CG methylation and physically associates with other anti-silencing factors, including the histone acetyltransferase IDM1, IDM2, and IDM3. IDM1 and IDM2 were previously shown to facilitate active DNA demethylation by the 5-methylcytosine DNA glycosylase/lyase ROS1. Thus, MBD7 tethers the IDM proteins to methylated DNA, which enables the function of DNA demethylases that in turn establish chromatin boundaries and limit DNA methylation  Using ChIP-seq to study the genomic targeting principle of MBD7 protein Examination of MBD7 protein binding principle using ChIP-Seq. WT and proMBD7::gMBD7::4xMYC transgenic plants were used for ChIP-seq.						
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	Zhu	Lang	Lei	Wang	Tang	Miki	Zhu
Person First Name	Jian-Kang	Zhaobo	Mingguang	Xingang	Kai	Daisuke	Jian-Kang
Person Email	zhu132@purdue.edu						
Person Affiliation	Purdue University						
Person Address	Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Dr., West Lafayette, IN, USA						
Person Roles	submitter						
Protocol Name	P-GSE58789-3	P-GSE58789-2	P-GSE58789-1				
Protocol Description	The paired-end reads were mapped to the TAIR10 genome of Arabidopsis thaliana with bowtie2 (Langmead and Salzberg, 2012) allowing mapping of up to 10 different genomic sites with parameter M-bM-^@M-^\-k 10 --no-mixed --no-discordant -I 0 -X 1000M-bM-^@M-^] To remove potential PCR duplicates, rmdup from SAMtools (Li et al., 2009) was used featureCounts (Liao et al. 2014) was used to get the fragment numbers in the processed file with parameter -p -O Genome_build: TAIR10 Supplementary_files_format_and_content: TAIR10 genome was divided into 1-kb bins with an overlap of 500 bp and featureCounts (Liao et al. 2014) was used to get the fragment numbers in the each bin with parameter -p -O.	The ChIP-seq was performed as previously described (Wierzbicki et al., 2008). In brief, 3 g of 14-day-old seedlings was collected, placed in 35 ml of 1% formaldehyde PBS buffer, and then fixed by vacuum for 2 min followed by another 8 min. After glycine was added, samples were subjected to a vacuum for 5 min to stop the fixation. Samples were washed three times with sterile water and then ground into powder with liquid nitrogen. Nuclei were extracted with Honda buffer. The nuclei solution was sonicated to break genomic DNA into ~500-bp fragments. After centrifugation, supernatants were removed and used for immuno-precipitation. Dynabeads (Invitrogen, cat# 10003D) were used for pre-clearing and antibody binding. The antibodies were c-Myc Mouse Monoclonal Antibody (Invitrogen R950-25). The libraries were prepared using the NuGen Ovation Ultralow Library Systems and were sequenced in the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) with Illumina HiSeq2500.	Plants were grown at 23M-0C in a growth chamber with 16 h of light and 8 h of darkness on 1/2 MS medium with 1% glucose.				
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol	growth protocol				
Experimental Factor Name	genotype						
Experimental Factor Type	genotype						
Comment[SecondaryAccession]	GSE58789						
Comment[GEOReleaseDate]	2015-01-29						
Comment[ArrayExpressSubmissionDate]	2014-06-24						
Comment[GEOLastUpdateDate]	2015-01-29						
Comment[AEExperimentType]	ChIP-seq						
Comment[AdditionalFile:Data1]	GSE58789_MBD7_ChIP_featureCounts_results_pO.txt						
Comment[SecondaryAccession]	SRP043541						
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR1451409-SRR1451416						
SDRF File	E-GEOD-58789.sdrf.txt