|
| Status |
Public on Mar 04, 2024 |
| Title |
BS-seq-WT-rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
ear
|
| Organism |
Zea mays |
| Characteristics |
tissue: ear
cell type: developing ear (<0.5 cm in length)
genotype: WT
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from the developing ear (<0.5 cm in length) with the traditional CTAB method.
Samples were fragmented and ligated with TruSeq-methylated adapters. Bisulfite conversion was performed on 500 ng of adaptor-ligated DNA using the MethylCode bisulfite conversion kit (Zymo Research, Orange, CA, USA). Converted DNA was amplified for 14 cycles.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequenced reads of each samples were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73.v4 whole genome and de duplicated using bismark. Calculated the sequencing conversion efficiency and methylation level of each sample based on the results generated from the previous step.
Merge the sequenced reads of same genotype and perform the same analysis as above, then calculate the differentially methylated regions based on the results generated.
Assembly: B73.v4
Supplementary files format and content: tab files, matrix, bw
|
| |
|
| Submission date |
May 08, 2023 |
| Last update date |
Mar 04, 2024 |
| Contact name |
Wang Zi |
| E-mail(s) |
wangz1994@cau.edu.cn
|
| Organization name |
China Agricultural University
|
| Department |
ational Maize Improvement Center of China
|
| Lab |
Yan He Lab
|
| Street address |
NO2 Yuanmingyuan West Road, Haidian
|
| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL25410 |
| Series (1) |
| GSE232004 |
Natural polymorphisms in ZMET2 encoding a DNA methyltransferase modulate the number of husk layers in maize |
|
| Relations |
| BioSample |
SAMN36026912 |
| SRA |
SRX20809083 |
