|
| Status |
Public on Dec 31, 2019 |
| Title |
R-early-1 |
| Sample type |
SRA |
| |
|
| Source name |
BPH6-transgenic line
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: Leaf sheath
development stage: Four-leaf stage
cultivar: BPH6-transgenic line
bph feeding status: early feeding stage (6-24h)
|
| Treatment protocol |
At the four-leaf stage, the seedlings were infested with eight second-instar BPH per plant from 0 to 72 hours, and divided into non-infested control (0), early feeding stage including 6, 12 and 24 hours, and late feeding stage including 48, 60 and 72 hours. All treatments, each with three biological replicates, with each biological replicate having 15 seedlings per rice line used for analysis.
|
| Growth protocol |
BPH6-transgenic line and Nipponbare were sown in plastic cups (9 cm in diameter and 15 cm in height), with 15 plants per cup in a greenhouse, which was controlled to have 30 ± 2 °C/14 h light (07:00–21:00) and 28 ± 2 °C/10 h dark (21:00–07:00) cycles.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from infested and mock the leaf sheathes using a RNAiso Plus kit (TaKaRa, code no. 9109) according to the manufacturer’s instructions.
The cDNA libraries were constructed for each sample using the NEBNext® Ultra™ directional RNA library prep kit (NEB, code no. E7420S) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
The clean reads were then aligned to rice genome (TIGR7) using the Hisat2.
HTseq was used to get gene counts and RPKM method was used to determine the gene expression.
Supplementary_files_format_and_content: Excel file with RPKM
|
| |
|
| Submission date |
Nov 27, 2018 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Bo Du |
| E-mail(s) |
bodu@whu.edu.cn
|
| Organization name |
Wuhan University
|
| Street address |
Luojiashan
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430072 |
| Country |
China |
| |
|
| Platform ID |
GPL23876 |
| Series (2) |
| GSE122993 |
A combined small RNA and transcriptome sequencing analysis illuminates the response of resistance to brown planthopper in rice [RNA-seq] |
| GSE123148 |
A combined small RNA and transcriptome sequencing analysis illuminates the response of resistance to brown planthopper in rice |
|
| Relations |
| BioSample |
SAMN10485214 |
| SRA |
SRX5065833 |
