|
| Status |
Public on Sep 01, 2015 |
| Title |
93-11-6D embryo |
| Sample type |
SRA |
| |
|
| Source name |
Oryza sativa embryo
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: embryo
developmental stage: 6 DAP
cultivar: 93-11
|
| Treatment protocol |
Embryo of 3,6,9 days after pollination (DAP) and endosperm of 2,3,6,9 DAP were manually selected under the dissecting scope. Selected embryo and endosperm were transferred to the eppendorf tube, rinsed with ethanol and placed on ice in the 100% ethanol.
|
| Growth protocol |
Rice variety Zhonghua11 (Oryza sativa spp. Japonica) and 93-11 (Oryza sativa spp. indica) were cultivated in a phytotron with a light (12h, 28℃)/dark(12h, 22℃) cycle.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from the embryo and endosperm of rice seeds. Methylated DNA was isolated with anti 5-mc antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hiseq2000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
MeDIP-seq reads were aligned to the japonica genome (version 7.0, http://rice.plantbiology.msu.edu/) 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: the japonica genome (version 7.0, http://rice.plantbiology.msu.edu/)
Supplementary_files_format_and_content: peak files
|
| |
|
| Submission date |
May 15, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
yijing zhang |
| E-mail(s) |
zhangyijing@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Department |
Biochemistry
|
| Lab |
Functional Epigenomics Group
|
| Street address |
2005 Songhu Road
|
| City |
shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL13160 |
| Series (1) |
| GSE57706 |
Genome-wide maps of DNA methylation state in rice embryo and endosperm |
|
| Relations |
| BioSample |
SAMN02780940 |
| SRA |
SRX543543 |
