|
| Status |
Public on Dec 28, 2018 |
| Title |
210 days after bloom ncRNA seq repeat2 |
| Sample type |
SRA |
| |
|
| Source name |
fruits
|
| Organism |
Citrus sinensis |
| Characteristics |
cultivar: Newhall sweet orange (Citrus sinensis Osbeck)
development stage: 210 DAB
tissue: pericarp
|
| Growth protocol |
Newhall sweet orange (Citrus sinensis Osbeck) were all cultivated in a commercial orchard (Songyang, Zhejiang, China)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA (5µg) from each sample was used for separation of small RNA with 14~30nt in length on a 15% TBE-Urea Polyacrylamide Gel in XCell SureLock™ Mini-Cell (Thermo Fisher Scientific).
The small RNAs were recovered by ZR small-RNA PAGE Recovery Kit (Zymo Research, R1070). The enriched small RNAs were used for performing the library preparation with NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs, E7300L) according to the manufacturer’s instructions with different barcodes. Prepared libraries were assessed for quality by using NGS High-Sensitivity kit on the Fragment Analyzer (AATI) and for quantity by using Qubit 2.0 fluorometer (Thermo Fisher Scientific).
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Low-quality sequences (q < 20) and adapters were trimmed using trimmomatic.
Reads were mapped to Citrus sinensis(version2) using BWA 0.7.17-r1188
Genome_build: Citrus sinensis version 2 (http://citrus.hzau.edu.cn/orange/download/index.php)
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each read
|
| |
|
| Submission date |
Sep 17, 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) |
| GSE120025 |
Global increase in DNA Methylation during ripening of sweet orange [ncRNA-seq] |
| GSE120026 |
Global increase in DNA Methylation during ripening of sweet orange |
|
| Relations |
| BioSample |
SAMN10077435 |
| SRA |
SRX4702381 |
