|
| Status |
Public on Jan 20, 2010 |
| Title |
CMV delta2b in rdr1 mutant of Arabidopsis thaliana |
| Sample type |
SRA |
| |
|
| Source name |
leaves of mutant Arabidopsis thaliana infected with CMVf-Δ2b
|
| Organisms |
Arabidopsis thaliana; Cucumber mosaic virus (strain FNY) |
| Characteristics |
a.thaliana genotype: rdr1 mutant
a.thaliana tissue: leaves
cmv genotype/variation: CMVf-Δ2b
cmv strain: FNY
collected time: 14 days after inoculation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNAs of 18- to 28-nt extracted by Trizol from the systemically infected leaves 14 days after inoculation with CMVf-Δ2b were purified from 15% denatured polyacrylamide gel. Purified small RNAs were directly ligated to the 3′-linker used for miRNA cloning (Integrated DNA Technology) by T4 RNA ligase 2Tr (New England Biolabs). The ligation products were purified and ligated to the 5′ Solexa linker (GUU CAG AGU UCU ACA GUC CGA CGA UC) by T4 RNA ligase I (New England Biolabs). The final ligation products were reverse transcribed using a primer targeting the 3′-linker (CTGTAGGCACCATCAAT OR CACTCGGGCACCAAGGA ) and the cDNA pool was amplified by PCR and sent for sequencing by the Solexa technology (Illumina). Duplicate libraries were constructed from two independent RNA samples from WT, rdr1, and rdr1 rdr2 rdr6 plants and sequenced by the Solexa platform in Illumina, Inc, and the University of California–Riverside Core Facility, respectively.
|
| |
|
| Library strategy |
OTHER |
| Library source |
viral RNA |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
total small RNAs in systemically infected leaves of A. thaliana
barcode: CGT
|
| Data processing |
All sequences containing perfect match 5' barcode (ATC/CGT/TAC) and at least 6 sucessive perfect-matched nucleotides of the 3' linker ( CTGTAGGCACCATCAAT / CACTCGGGCACCAAGGA) were kept for later analysis. The barcode and linker sequences were computationally removed by in-house perl script. All trimmed sequences in length of 17~30nt were aligned with CMV genome and the perfect matched reads were used for all further analysis.
|
| |
|
| Submission date |
Jan 20, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Qingfa Wu |
| E-mail(s) |
qingfawu@ucr.edu
|
| Phone |
1-951-827-2340
|
| Organization name |
UC Riverside
|
| Lab |
Shou-Wei Ding
|
| Street address |
900 University Ave
|
| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92507 |
| Country |
USA |
| |
|
| Platform ID |
GPL9951 |
| Series (1) |
| GSE19965 |
Virus-derived siRNAs in Arabidopsis thaliana |
|
| Relations |
| SRA |
SRX015846 |
| BioSample |
SAMN00007555 |
