|
| Status |
Public on Apr 12, 2010 |
| Title |
Cymbidium Ringspot Virus (CymRSV)-derived siRNAs |
| Sample type |
SRA |
| |
|
| Source name |
Early systemic leaves of CymRSV-infected Nicotiana benthamiana
|
| Organisms |
Nicotiana benthamiana; Cymbidium ringspot virus |
| Characteristics |
tissue: early systemic leaves
treatment: CymRSV infection
|
| Growth protocol |
3 weeks old Nicotiana benthamiana plants grown in soil under normal growth conditions were used for virus infection. After infection with CymRSV, plants were grown in fitotrons under a 14 h light (50 E µm-2s-1) and 10 h dark regime at 21°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from early systemic leaves of Nicotiana benthamiana infected with CymRSV. The homogenized plant materials were resuspended in 600 \u03bcL of extraction buffer (0.1 M glycine-NaOH, pH 9.0, 100 mM NaCl, 10 mM EDTA, 2% SDS, and 1% sodium lauroylsarcosine) and mixed with an equal volume of phenol. The aqueous phase was treated with equal volumes of phenol and chloroform, precipitated with ethanol, and resuspended in sterile water and used in subsequent reactions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
CymRSV-derived small RNAs from early systemic leaves of Nicotiana benthamiana.
|
| Data processing |
Removed adaptors. Sequences without adapters were discarded. Small RNA sequences were mapped to the CymRSV genome (GenBank: X15511.1).
|
| |
|
| Submission date |
Jul 17, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Simon Moxon |
| E-mail(s) |
simonm@cmp.uea.ac.uk
|
| Organization name |
University of East Anglia
|
| Street address |
University of East Anglia
|
| City |
Norwich |
| State/province |
Norfolk |
| ZIP/Postal code |
NR4 7TJ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL10313 |
| Series (2) |
| GSE17162 |
Structural and Functional Analysis of Viral siRNAs using Solexa sequencing |
| GSE17278 |
Structural and Functional Analysis of Viral siRNAs |
|
| Relations |
| SRA |
SRX019044 |
| BioSample |
SAMN00011148 |
