|
| Status |
Public on Jan 04, 2017 |
| Title |
2J_YFV_cap_ntr2_lvp_96hrs_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
whole body
|
| Organism |
Aedes aegypti |
| Characteristics |
genotype/variation: recombinate SINV expressing a non-translatalbe version of YFV-capsid
|
| Treatment protocol |
Two day old mosquitoes were injected with 0.5 μl (106 pfu/ml) of recombinant SINV, and monitored daily for survival.
|
| Growth protocol |
Mosquito were reared in environmental chambers with a light cycle of 14:10 (day:night) and humidity of 80%.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with Tri RT (Molecular Research Center) from adult female mosquitoes 96 h after infection.
Small RNAs (18 to 35-nt) were recovered by PAGE separation, and libraries prepared with the Truseq small RNA sample prep kit (Illumina) according to the manufacturer's instructions.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
Randomly 25 million sequences were selected for analysis form each library using in house perl script
Mosquito ncRNAs were taken out using bowtie v12.7 (-q -t -p 8 -v 3 -k 1 -m 1)
Recombinat SINV viral small RNAs were removed using bowtie v12.7 (-q -t -p 8 -v 1 -k 1 -B 1 --best)
Mosquito miRNAs, Transposable elements, and endosiRNAs were removed using bowtie v12.7 (-q -t -p 8 -v 1 -k 1 -B 1 --best)
Individual counts for each small RNA class was totaled using in house perl scripts
Libraries were normalized using edgeR, using counts from viRNAs, miRNAs, TE, and endosiRNAs
Supplementary_files_format_and_content: Processed counts were pasted into excel spreadsheet
|
| |
|
| Submission date |
Apr 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Myles |
| E-mail(s) |
kmmyles@vt.edu
|
| Organization name |
Virginia Tech
|
| Street address |
Fralin Life Science Institute 360 West Campus Drive
|
| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24061 |
| Country |
USA |
| |
|
| Platform ID |
GPL21020 |
| Series (1) |
| GSE80691 |
The yellow fever virus capsid protein is a potent suppressor of RNA silencing that binds double stranded RNA. |
|
| Relations |
| BioSample |
SAMN04903474 |
| SRA |
SRX1728223 |
