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Sample GSM2087090 Query DataSets for GSM2087090
Status Public on Mar 08, 2018
Title two-weeks seedling plants_307T3_Bisulfite-seq
Sample type SRA
 
Source name leaf_Resui retrotransposition insertion line 307T3 (three copies)
Organism Oryza sativa
Characteristics development stage: seedling
tissue: leaf
genotype: WT-3 copies
Growth protocol The genomic DNA samples were isolated from the shoots of the variety 308D, 307T1 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. About 5 microgram of genomic DNA was sheared by sonication to fragments of 100-500 bp, and the adapters were ligated following the Illumina protocol. The library was then treated twice with sodium bisulfite (which converts unmethylated Cs to Us) using the Qiagen EpiTect kit, and amplified by 18 cycles of PCR using PfuTurboCx DNA polymerase (Stratagene), The PCR product was purified with AMpure XP beads to obtain the final library DNA. BS-seq libraries were sequenced using an Illumina HiSeq 2000.
libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
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 (pseudomolecules/MSUv7.0 ) by software BSMAP, allowing up to 2 mismatches and retaining only uniquely-mapping, only the unique mapping were retained for further analysis.
Genome_build: Os-Nipponbare-MSUv7.0
Supplementary_files_format_and_content: tar archives of text files with methylation status data
 
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
GSE79154 A Domestication-Selected Retrotransposon for Quenching Genomic Immunity in Rice [Bisulfite-seq]
Relations
BioSample SAMN04549217
SRA SRX1630058

Supplementary file Size Download File type/resource
GSM2087090_307T3.tar.gz 1.4 Gb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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