|
| Status |
Public on Nov 05, 2015 |
| Title |
DENV infected Day 3 |
| Sample type |
SRA |
| |
|
| Source name |
Adult mosquitoes- 3 days post infection
|
| Organism |
Aedes aegypti |
| Characteristics |
tissue: Whole body
infection status: Blood fed/ DENV-2 (New Guinea strain) infected at 10^7 TCID50/mL
strain: Cairns
genotype: wild type
|
| Treatment protocol |
Ae. aegypti mosquitoes were fed with sheep blood containing DENV-2 (New Guinea strain) at 10^7 TCID50/mL.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from non-infected control and DENV-infected mosquitoes (1, 3, and 7 d after infection) by using Tri-Reagent following the manufacturer’s protocol (Molecular Research Center). RNA concentrations were measured by using a spectrophotometer, and integrity was ensured through analysis of RNA on a 1% (wt/vol) agarose gel and bioanalyzer.
Small RNA libraries were generated from both samples by using the Illumina Truseq Small RNA Preparation kit at LC Sciences. The purified cDNA libraries were sequenced on Illumina GAIIx, and raw sequence reads (36 nt) were obtained by using Illumina’s Sequencing Control Studio software version 2.8 followed by real-time sequencing image analysis and base-calling by Illumina’s Real-Time Analysis version 1.8.70 (LC Sciences).
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
CLC Genomic Workbench (version 7.0.4) was used to remove adapter sequences and reads with low quality score from datasets. To avoid any impurity in sequences we also discarded the reads without 3’ adapters and less than 16 nt in length after trimming.
FASTQ/A Collapser of FASTX-toolkit was used to produce copy number based sequence lists. The tab separated files with the read sequences and their counts were used as input file for further analysis.
miRanalyzer, a powerful web-based server for next generation sequencing analysis of miRNAs was used
To detect more potential variations, we allowed three possible mismatches in the mapping criteria and all length variation and even non-templated nucleotide additions collected as isomiRs
Genome_build: AaegL2 VectorBase
Supplementary_files_format_and_content: fasta files genrated by FASTQ Collapser and CSV file generated by miRanalyzer (IsomiRs Reads Count)
|
| |
|
| Submission date |
Jul 17, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Kayvan Etebari |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Queensland
|
| Department |
School of Biological Sciences
|
| Lab |
Insect host-pathogen Interaction
|
| Street address |
Building No 8
|
| City |
St Lucia |
| State/province |
QLD |
| ZIP/Postal code |
4072 |
| Country |
Australia |
| |
|
| Platform ID |
GPL11087 |
| Series (1) |
| GSE59516 |
Post-transcriptional microRNA modifications in the Dengue mosquito vector, Aedes aegypti |
|
| Relations |
| BioSample |
SAMN02921328 |
| SRA |
SRX655684 |
