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Sample GSM2087091 Query DataSets for GSM2087091
Status Public on Mar 08, 2018
Title two-weeks seedling plants_308D_MeDIPseq
Sample type SRA
 
Source name leaf_wildtype
Organism Oryza sativa
Characteristics development stage: seedling
tissue: leaf
genotype: WT
Growth protocol The genomic DNA samples were isolated from the shoots of the variety 308D and 307T3 grown in soil under 12-h-light/12-h-dark at 28°C in a greenhouse for 15 days.
Extracted molecule genomic DNA
Extraction protocol For each sample, about 20 individual plants were pooled and total genomic DNA was extracted using CTAB method. DNA samples were treated with RNase A and DNA was purified from the supernatant using chloroform.For each sample, about 20 individual plants were pooled and total genomic DNA was extracted using CTAB method. DNA samples were treated with RNase A and DNA was purified from the supernatant using chloroform. About 5 microgram of genomic DNA was sheared by sonication to fragments of 100-500 bp. Sonicated DNA was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina protocol. After agarose size-selection to remove unligated adapters, 2–5 μg of adaptor-ligated DNA was used for each immunoprecipitation using a mouse monoclonal anti-methylcytidine antibody, following performed by Magnetic Methylated DNA Immunoprecipitation kit (Diageno,Catalog No: mc-magme-048). MeDIP DNA was purified using Qiagen MinElute columns and eluted in 16 μl EB (Qiagen). Fifteen cycles of PCR were performed on 5 μl of the immunoprecipitated DNA using the single-end Illumina PCR primers. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis. Libraries were sequenced on the Hiseq2000 following the manufacturer's protocols.
libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Illumina HiSeq 2000
 
Data processing Illumina Casava1.8 software used for basecalling.
Low-quality reads and reads containg adaptor/primer were filtered. The filtered reads were mapped to rice reference genome using BOWTIE2 with default settings. The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis. Enriched regions of DNA methylation were identified using MACS14.
Genome_build: Os-Nipponbare-MSUv7.0
Supplementary_files_format_and_content: peak files. Columns contain the following: 1) Chromosome, 2) start peak position, 3) end peak position, and 4) number of reads.
 
Submission date Mar 13, 2016
Last update date May 15, 2019
Contact name yiwen Deng
E-mail(s) ywdeng@sibs.ac.cn
Phone 86-21-54924128
Organization name Shanghai Institute for Biological Sciences, Chinese Academy of Sciences
Department Institute of Plant Physiology and Ecology
Lab zuhua He
Street address 300 Fenglin Road
City Shanghai
State/province Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL13160
Series (2)
GSE78903 A Domestication-Selected Retrotransposon for Quenching Genomic Immunity in Rice
GSE79155 A Domestication-Selected Retrotransposon for Quenching Genomic Immunity in Rice [MeDIP-seq]
Relations
BioSample SAMN04549218
SRA SRX1630053

Supplementary file Size Download File type/resource
GSM2087091_peak_308D.tar.gz 284.3 Kb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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