|
| Status |
Public on Dec 28, 2018 |
| Title |
90 days after bloom bsseq repeat1 |
| Sample type |
SRA |
| |
|
| Source name |
fruits
|
| Organism |
Citrus sinensis |
| Characteristics |
tissue: pericarp
development stage: 90 DAB
cultivar: Newhall sweet orange (Citrus sinensis Osbeck)
|
| Growth protocol |
Newhall sweet orange (Citrus sinensis Osbeck) were all cultivated in a commercial orchard (Songyang, Zhejiang, China)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from fruits and sent to Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
treated with bisulfite
|
| Data processing |
Low-quality sequences (q < 20) and adapters were trimmed using trimmomatic.
Reads were mapped to Citrus sinensis (version2) from the Citrus Genome Database using BSMAP 2.87
methratio.py python script of BSMAP was used to extract metylation ratios from BSMAP results with parameters -z and -r
two replicates were merged to generate wiggle files
Genome_build: Citrus sinensis (version 2)
Supplementary_files_format_and_content: Methylation ratio in bigwig files
|
| |
|
| Submission date |
Jan 09, 2018 |
| Last update date |
Dec 28, 2018 |
| Contact name |
Huang Huan |
| E-mail(s) |
ahuanghuan@163.com
|
| Organization name |
Chinese Academy of Sciences
|
| Department |
Shanghai Center for Plant Stress Biology
|
| Street address |
No. 3888 Chenhua Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL21082 |
| Series (2) |
| GSE108931 |
Global increase in DNA Methylation during ripening of sweet orange [BS-seq] |
| GSE120026 |
Global increase in DNA Methylation during ripening of sweet orange |
|
| Relations |
| BioSample |
SAMN08330598 |
| SRA |
SRX3542440 |
