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| Status |
Public on Dec 31, 2019 |
| Title |
S03-2 |
| Sample type |
SRA |
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| Source name |
Nippnbare
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| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cultivar: Nippnbare
bph feeding status: non-infested
tissue: Leaf sheath
development stage: Four-leaf stage
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| 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.
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| 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.
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| 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 Ion Total RNA-Seq Kit v2.0 (Thermo Fisher, code no. 4475936) according to the manufacturer’s instructions.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
HiSeq X Ten |
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| Data processing |
The clean reads were compared to GenBank (release 209.0) and Rfam (release 11.0) to move other types of RNA (rRNA, snRNA, snoRNA, tRNA). Also, the clean tags were aligned with rice genome. Those mapped to exons or introns were removed, and the tags mapped to repeat sequences were also removed.
The rest of the unique sequences were used to search against the miRBase database (release 21, http://www.mirbase.org/) for known rice miRNA identification.
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| Submission date |
Nov 28, 2018 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Bo Du |
| E-mail(s) |
bodu@whu.edu.cn
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| Organization name |
Wuhan University
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| Street address |
Luojiashan
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430072 |
| Country |
China |
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| Platform ID |
GPL23876 |
| Series (2) |
| GSE123079 |
A combined small RNA and transcriptome sequencing analysis illuminates the response of resistance to brown planthopper in rice [miRNA-seq] |
| GSE123148 |
A combined small RNA and transcriptome sequencing analysis illuminates the response of resistance to brown planthopper in rice |
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| Relations |
| BioSample |
SAMN10495058 |
| SRA |
SRX5075267 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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