|
| Status |
Public on Dec 28, 2018 |
| Title |
120 days after bloom rna-seq repeat1 |
| Sample type |
SRA |
| |
|
| Source name |
fruits
|
| Organism |
Citrus sinensis |
| Characteristics |
tissue: pericarp
developmental stage: 120 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 |
total RNA |
| Extraction protocol |
Total RNAs were extracted using the TRIzol (Invitrogen) method, and RNase-free Dnase (Qiagen) was used to remove contaminating DNA before RNA-seq.
Total RNAs were sent to Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) for library preparation and sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Low-quality sequences (q < 20) and adapters were trimmed using trimmomatic.
Reads were mapped to Citrus sinensis(version 2) from the Citrus Genome Database using STAR(020201)
Differetial gene expresssion was analysed by DESeq
wiggle files were normalized to reads per million of mapped reads
Genome_build: citrus sinensis (version 2)
|
| |
|
| 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) |
| GSE108930 |
Global increase in DNA Methylation during ripening of sweet orange [RNA-seq] |
| GSE120026 |
Global increase in DNA Methylation during ripening of sweet orange |
|
| Relations |
| BioSample |
SAMN08330581 |
| SRA |
SRX3542428 |
