|
| Status |
Public on Jun 17, 2014 |
| Title |
Embryo DNA_MeDIP |
| Sample type |
SRA |
| |
|
| Source name |
Maize tissue
|
| Organism |
Zea mays |
| Characteristics |
cultivar: B73
tissue: Embryo
age: 14 days after self-pollination
chip antibody: anti-5-methylcytidine
antibody manufacturer: Diagenode
|
| Growth protocol |
Maize endosperm and embryos were collected from B73 ears 14 days after self-pollination (DAP).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA of two tissues was extracted by CTAB method,DNA was sheared using the Bioruptor sonicator, and Mehylated DNA were isolated with antibody.
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 |
preprocessing using fastx(version:0.0.13)
mapping B73 Maize genome using Bowtie2(version: 2.0.5) with default parameters
peak detection using MACS(version:1.4) with default parameters
Genome_build: B73 Maize Genome
Supplementary_files_format_and_content: Bed files generated using MACS;bed files contained the genomic sites information of peaks
|
| |
|
| Submission date |
Jun 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Xingjun Wang |
| E-mail(s) |
xingjunw@hotmail.com
|
| Organization name |
Shandong Academy of Agricultural Sciences
|
| Department |
Biotechnology Research Center
|
| Street address |
202#, Gongye Bei Road
|
| City |
Ji'nan |
| State/province |
Shandong |
| ZIP/Postal code |
250100 |
| Country |
China |
| |
|
| Platform ID |
GPL15463 |
| Series (1) |
| GSE58549 |
DNA Methylation Identifies Epigenetic Variation across Embryo and Endosperm in Maize (Zea may) |
|
| Relations |
| BioSample |
SAMN02863982 |
| SRA |
SRX603868 |
