|
| Status |
Public on Apr 25, 2020 |
| Title |
W161_young_leaf_DNAmeth |
| Sample type |
SRA |
| |
|
| Source name |
W161
|
| Organism |
Oryza sativa |
| Characteristics |
tissues: young leaf
age: young leaves from two-week old seedlings
cultivar: Y134
|
| Treatment protocol |
Fresh samples are frozen using liquid nitrogen.
|
| Growth protocol |
Germinating seeds were obtained by soaking dry seeds in water for 72 h at 37 °C. For roots and young leaves, the germinated seeds were grown in a phytotron with the day/night cycle set at 14 h/10 h and a temperature of 32 °C/28 °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 described34. 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. Mature leaves at the floral induction phase and young panicles 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 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 |
The sequence quality of the whole-genome bisulfite sequencing (WGBS) libraries was evaluated using FastQC, and the adapter sequences and low-quality reads were filtered using Trimmomatic
The cleaned reads were then mapped to the MH63/ZS97 reference genome using BatMeth
The uniquely mapped reads were used for further analysis. Individual cytosines with coverage of at least 3 were considered for methylation-level calling.
The DNA methylation level of each cytosine was obtained by dividing the depth of methylated reads by the total coverage of individual cytosines
Genome_build: MH63,MSU7.0
|
| |
|
| Submission date |
Dec 24, 2019 |
| Last update date |
Jul 08, 2020 |
| Contact name |
Liang Xie |
| E-mail(s) |
lxie@webmail.hzau.edu.cn
|
| Phone |
+8615827364128
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
No.1,Shizishan Street
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL24468 |
| Series (2) |
| GSE142568 |
Integrative analysis of reference epigenomes in rice [BiSulfite-seq] |
| GSE142570 |
Integrative analysis of reference epigenomes in rice |
|
| Relations |
| BioSample |
SAMN13676177 |
| SRA |
SRX7437775 |
