|
| Status |
Public on Sep 01, 2017 |
| Title |
RI-1 mRNA |
| Sample type |
SRA |
| |
|
| Source name |
leaf cells
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: Infected leaf cells
|
| Treatment protocol |
Rice seedlings at the three-leaf stage were inoculated by viruliferous small brown planthoppers
|
| Growth protocol |
Small brown planthoppers (Laodelphax striatellus) were raised on rice plants (cv. Wuyujing 3) in a growth room
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue samples were stored at -80°C prior to use, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by fastx_toolkit-0.0.13.2, then mapped to whole genome using SOAP with parameters: maximum number of mismatches allowed = 2bp， number of valid alignments per read pair (-k) = 40
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) were calculated.
Genome_build: http://rice.plantbiology.msu.edu/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Oct 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Heng-Mu Zhang |
| E-mail(s) |
[email protected]
|
| Phone |
86-571-86416056
|
| Organization name |
Zhejiang Academy of Agricultural Sciences
|
| Department |
Institute of Virology and Biotechnology
|
| Lab |
State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control
|
| Street address |
198 Shiqiao Road
|
| City |
Hangzhou |
| ZIP/Postal code |
310021 |
| Country |
China |
| |
|
| Platform ID |
GPL21087 |
| Series (2) |
| GSE74497 |
Integrative analysis of microRNAome and transcriptome elucidates the response of susceptible rice plants to rice stripe virus RSV (RNA-Seq) |
| GSE74499 |
Integrative analysis of microRNAome and transcriptome elucidates the response of susceptible rice plants to rice stripe virus RSV |
|
| Relations |
| BioSample |
SAMN04226117 |
| SRA |
SRX1399003 |
