|
| Status |
Public on Feb 15, 2024 |
| Title |
BS-cvip |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
treatment: hypermethylation
|
| Treatment protocol |
For zebularine treatment, an inhibitor of DNA methyltransferase leading to a global reduction of DNA methylation, 100 of 5-d-old rice seedlings were treated with 80 µM zebularine (Sigma-Aldrich Z4775) dissolved in DMSO or DMSO only (as control) for another five days. The zebularine-treated or untreated seedlings were collected and kept at -80℃ until used. For genomic DNA with M.CviP I (M0227S, NEB) treatment, a type of CpG Methyltransferase resulting in a global increase CG methylation in the eukaryotic genomes. 4 μg of purified rice genomic DNA was incubated with 8 units of M.CviP I with an addition of 640 μM SAM (S-adenosyl-methionine) at 37℃ for 1 h in a total of 20 μl reaction system. After inactivation of the enzyme activity with incubation at 65℃ for 20 min, M.CviP I treated DNA was recovered by using phenol/chloroform extraction followed by pre-cold alcohol precipitation.
|
| Growth protocol |
After pre-germination at room temperature (RT) for three days, uniformly germinated Nipponbare (Oryza sativa L., Japonica) rice seeds were put on the nutrient soil and grew in a greenhouse at 28-30℃ and a 14h/10h light-dark cycle. Two-week old seedlings were harvested and stored at -80℃ until used.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The fine powder was used for nuclei preparation and genomic DNA extraction following the procedures as described previously
5 µg of M. Cvip I-/zebularine-treated genomic DNA and CK were used for bisulfite treatment followed by library preparation and sequencing, which was conducted by Berry Genomics company (Beijing)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
hyper_DMR.txt.gz
|
| Data processing |
BS-seq data were trimmed by using Fastp to remove the adapter sequences, then mapped to the rice reference genome (MSU7.0) by using Bismark
The methylated cytosines were counted from total uniquely mapped reads using the Bismark methylation extractor script.
Differential methylation regions (DMRs), including hyper and hypo DMRs, were identified by using intersect and dmr function of CGmapTools with the cutoffs: P-value < 0.01 and ΔmC ≥ 0.1.
Supplementary files format and content: txt files containing information of hyper and hypo DMRs respectively
|
| |
|
| Submission date |
Jun 12, 2023 |
| Last update date |
Feb 15, 2024 |
| Contact name |
Xing Ma |
| E-mail(s) |
2020101156@stu.njau.edu.cn
|
| Organization name |
Nanjing Agricultural University
|
| Street address |
No.1 Weigang, Nanjing, Jiangsu 210095, P. R. China
|
| City |
Nanjing |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL27860 |
| Series (2) |
| GSE234750 |
Differential impacts of DNA methylation on pH dependent i-motifs formation in rice [Bisulfite-seq] |
| GSE234752 |
Differential impacts of DNA methylation on pH dependent i-motifs formation in rice |
|
| Relations |
| BioSample |
SAMN35717470 |
| SRA |
SRX20662394 |
