 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 26, 2018 |
| Title |
rice_RSV.rep2 (sRNA-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
Leaves
|
| Organism |
Oryza sativa |
| Characteristics |
infection: RSV
treatment time: 20d
tissue: Leaves
genome build: MSU7
|
| Treatment protocol |
4th instar nymphs of viruliferous planthoppers were transferred to fresh rice seedlings for RSV inoculation. After 24 h feeding, the planthoppers were removed and the inoculated seedlings were cultured at 25 ± 1°C with 16 h of light daily for 20 d until disease symptom appeared. Each rice seedling was fed by three viruliferous planthoppers, and three seedlings were used as a replicate. Meanwhile, healthy rice seedlings without inoculation were prepared and maintained at the same condition as the negative control. Leaves with typical disease symptoms from RSV-infected rice plants and leaves from healthy rice plants were collected at the same time and three biological replicates for each group were prepared for sequencing analysis
|
| Growth protocol |
The viruliferous and non-viruliferous small brown planthopper strains used in this work were derived from a rice field population in Hai'an, Jiangsu Province, China, and maintained in the laboratory for nearly nine years. The planthoppers were reared on 2 cm to 3 cm seedlings of rice (Oryza sativa Huangjinqing) in glass incubators, which were sealed with a nylon mesh, at 25 ± 1°C, 80% relative humidity, and 16 h of light per day. The planthoppers were transferred to fresh rice seedlings every 8 days to ensure sufficient nutrition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from rice plants or planthoppers by using the TRIzol Reagent (Invitrogen) according to manufacturer’s instructions. Approximately 100 mg rice leaves or 10 small brown planthoppers were ground in liquid nitrogen and mixed with 1 ml of TRIzol Reagent for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
rice_sRNAs_mock_vs_RSV.edgeR.txt
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
The adapter sequence was removed using cutadapt (v1.16) (Martin, 2011). Reads that are 18-30 nt in length and contain no ambiguous nucleotide (‘N’) were retained as clean reads, which were clustered into unique reads with an in-house python script.
For rice sRNAs datasets, clean reads were then mapped to the ncRNA reference (ftp://ftp.ensemblgenomes.org/pub/plants/release-31/fasta/oryza_sativa/ncrna/Oryza_sativa.IRGSP-1.0.31.ncrna.fa.gz) downloaded from ensemble database to remove reads mapped to known rice rRNA, tRNA, snRNAs using bowtie software (Langmead et al., 2009) with perfect match. For planthopper sRNAs datasets, cleans reads mapped to the rRNAs, tRNAs, snoRNAs, snRNAs resolved by our lab (Zhu et al., 2017) with perfect match were discarded.
The remaining sRNA reads were then mapped to the host genome (rice or planthopper genome, depending on the sample source) with perfect match or the RSV genome (MF287953-MF287956), allowing up to one mismatch. Only sRNAs reads with at least one mapping location were regarded as genuine sRNAs and retained for down-stream analyses
Genome_build: MSU7 for rice and in-house assmbly genome for planthopper (Zhu, J.J., Jiang, F., Wang, X.H., Yang, P.C., Bao, Y.Y., Zhao, W., Wang, W., Lu, H., Wang, Q.S., Cui, N., Li, J., Chen, X.F., Luo, L., Yu, J.T., Kang, L., and Cui, F. (2017). Genome sequence of the small brown planthopper, Laodelphax striatellus. Gigascience 6.)
Supplementary_files_format_and_content: Tab-delimited text file include RPM (Reads per Million) values
|
| |
|
| Submission date |
Apr 23, 2018 |
| Last update date |
Dec 26, 2018 |
| Contact name |
Liu Renyi |
| E-mail(s) |
ryliu@fafu.edu.cn
|
| Phone |
2157078228
|
| Organization name |
Fujian Agriculture and Forestry University
|
| Street address |
Shangxiadian Road 15, Fujian University of Agriculture and Forestry, Fuzhou, Fujian, P.R.China
|
| City |
Fuzhou |
| State/province |
Fujian Province |
| ZIP/Postal code |
350002 |
| Country |
China |
| |
|
| Platform ID |
GPL23013 |
| Series (2) |
| GSE113554 |
Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect [sRNA-Seq] |
| GSE113555 |
Rice stripe virus-derived siRNAs play different regulatory roles in host plant and vector insect |
|
| Relations |
| BioSample |
SAMN08971849 |
| SRA |
SRX3989082 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
