|
| Status |
Public on Jan 31, 2021 |
| Title |
B409_young_leaf_WGBS |
| Sample type |
SRA |
| |
|
| Source name |
B409 young leaf
|
| Organism |
Brassica napus |
| Characteristics |
cultivar: B409
age: young leaves from two-week seedlings
tissues: young leaf
|
| Treatment protocol |
Fresh samples are frozen using liquid nitrogen.
|
| Growth protocol |
Germinating seeds were obtained by placed on moist paper for 7 d at 22 °C. For roots and young leaves, the germinated seeds were grown in a phytotron with the day/night cycle set at 16 h/8 h and a temperature of 22 °C/18 °C. Roots were obtained 7 d after planting on moist filter paper, and young leaves were obtained from 2-week-old plants cultured hydroponically as described. Approximately 20-d-old seedlings were transplanted to the field and managed under normal agricultural conditions on the experimental farm of Huazhong Agricultural University, Wuhan, China. Flower buds and siliques were harvested.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using a DNeasy plant mini kit according to the manufacturer’s instructions (QIAGEN, 69104).
Bisulfite-treated DNA sequencing: Bisulfite conversion of DNA was conducted using the EZ DNA Methylation-GoldTM kit (ZYMO, D5005), and the bisulfite-treated DNA libraries were constructed using the Illumina TruSeq DNA sample prep kit, following the manufacturers’ instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with BatMeth2
The methylation level were calculated by BatMeth2
Genome_build: Download the genome from www.genoscope.cns.fr/brassicanapus
Supplementary_files_format_and_content: Show the echo site methylation level with detected
|
| |
|
| Submission date |
Jan 08, 2020 |
| Last update date |
Jan 31, 2021 |
| Contact name |
Guan Peng Peng |
| E-mail(s) |
[email protected]
|
| Organization name |
Huazhong Agricultural University
|
| Department |
college of informatics
|
| Street address |
shizishan street
|
| City |
WuHan |
| State/province |
HuBei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL26378 |
| Series (2) |
| GSE143285 |
Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [WGBS] |
| GSE143287 |
Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. |
|
| Relations |
| BioSample |
SAMN13761792 |
| SRA |
SRX7520639 |
