|
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.
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|
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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.
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|
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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 |