|
| Status |
Public on Jun 21, 2022 |
| Title |
Nip-pa-R1 Bs-seq |
| Sample type |
SRA |
| |
|
| Source name |
young panicle
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: japonica
tissue: panicle
genotype: control
|
| Growth protocol |
RIce plants grown in soil in Hannan province
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was extrated using CTAB method.
Genomic DNA was sonicated and then end-repaired with End repair Enzyme Mix. The blunt-ended DNA were treated with Klenow fragment and dATP to yield a proruding3-"A" and cytosine-methylated adaptors from Illumina were ligated according to manufacture's instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ck Bs-seq
ck_methy.txt.gz
|
| Data processing |
Low-quality sequences(q<20) and adapters were trimmed using trimmomatic.
Reads were mapped to MSU7.0 using MSMAP 2.87 with parameters -g 1
methratio.py pathon script of BSMAP was used to extrac methylation ratios from BSMAP results with parameters -z and -r
Genome_build: MSU 7.0
Supplementary_files_format_and_content: tdf, methy.txt.gz
|
| |
|
| Submission date |
Mar 23, 2018 |
| Last update date |
Jun 21, 2022 |
| Contact name |
Lili Wang |
| E-mail(s) |
2014201023@njau.edu.cn
|
| Organization name |
Nanjing Agricultural University
|
| Street address |
Weigang No.1
|
| City |
Nanjing |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL23013 |
| Series (2) |
| GSE112258 |
Reinforcement of DNA methylation in CHH context through RNA-directed DNA methylation ensures sexual reproduction in rice [BS-Seq] |
| GSE112259 |
Reinforcement of DNA methylation in CHH context through RNA-directed DNA methylation ensures sexual reproduction in rice |
|
| Relations |
| BioSample |
SAMN08783748 |
| SRA |
SRX3837328 |
