|
| Status |
Public on Aug 22, 2016 |
| Title |
TY1S_21dpi |
| Sample type |
SRA |
| |
|
| Source name |
TYLCV infected leaves
|
| Organism |
Solanum lycopersicum |
| Characteristics |
host variety: FL505
inoculum: TYLCV
inoculation method: Agrobacterium-mediated inoculation
time: 21 days post-inoculation
tissue: leaf
|
| Treatment protocol |
Tomato 'Moneymaker' and ‘FL505’at 6~8 leaf stages (5-week-old) were agroinoculated with infectious clones of the pBinPLUS-SH2-1.4A which contain TYLCV-[CN:SH2] (AM282874) as described previously (Zhang H et al., 2009). The two samples were called as ‘MMS’ and ‘TY1S’, respectively. Mock-inoculations was performed by inoculating plants with Agrobacterium tumefaciens strain GV3101 containing pBinPLUS, that samples were called ‘MMC’ and ‘TY1C’, respectively.
|
| Growth protocol |
Inoculated plants and controls were kept in an insect-free chamber at 25~27℃ with a 16 h/day light.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol and DNA was removed with DNase I (Takara, JAPAN) treatment.
small RNA library: After total RNA isolation, low molecular weight RNAs (LMW) were isolated as described Hafner et al., 2008.By polyacrylamide gel electrophoresis, the sRNAs were purified and ligated to 5’ and 3’ RNA adapter. A reverse transcription reaction followed by low cycle PCR was performed to obtain sufficient product for Solexa sequencing. PCR products were collected by gel purification and analysis based on Solexa high-throughput sequencing takes the SBS-sequencing by synthesis.
degradome library: The tomato degradome library was constructed as previously described German et al., 2009. In this study, we utilizing identical copy of samples which proposed for sRNA deep sequencing to identify degradome by parallel analysis of RNA ends (PARE) in high-throughput sequencing. The degradome data of MMC and TY1C were marked as MMCD and TY1CD, respectively; in addition, we balanced mix DNA of 21dpi and 30dpi samples of MMS or TY1S, and marked MMCD and TY1CD, respectively.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
small RNA
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
The data is processed by the following steps: 1) Getting rid of low quality reads; 2) Getting rid of reads with 5' primer contaminants; 3) Getting rid of reads without 3' primer; 4) Getting rid of reads without the insert tag; 5) Getting rid of reads with poly A; 6) Getting rid of reads shorter than 18nt; 7) Summarize the length distribution of the clean reads.
Supplementary_files_format_and_content: The .fa files report the host plant sRNAs (from MMC and TY1C samples only) and virus sRNAs (from MMS and TY1S samples). 't0xxxxxx' is a custom ID number for unique sequence filter from .fq files.
|
| |
|
| Submission date |
Aug 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Miao Bai |
| E-mail(s) |
baimiao2010@gmail.com
|
| Organization name |
Hunan Agricultural University
|
| Street address |
Hunan Agricultural University, No. 1 Nongda Road, Furong
|
| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410128 |
| Country |
China |
| |
|
| Platform ID |
GPL16345 |
| Series (1) |
| GSE50085 |
Characterization and function of Tomato yellow leaf curl virus-derived small RNAs generated in the tolerant and susceptible tomato varieties using deep sequencing |
|
| Relations |
| BioSample |
SAMN02324533 |
| SRA |
SRX337928 |
