|
Status |
Public on Mar 08, 2018 |
Title |
two-weeks seedling plants_308D_Bisulfite-seq |
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, 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 |
SAMN04549215 |
SRA |
SRX1630056 |