|
| Status |
Public on Jun 03, 2024 |
| Title |
Aedes aegypti, Dengue-infected, Day1, Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Higgs
|
| Organism |
Aedes aegypti |
| Characteristics |
strain: Higgs
treatment: Dengue infection
time: Day 1
|
| Treatment protocol |
The female mosquitoes at 7 to 14 days post eclosion were used for the experiments. The mice were tail-vein injected with DENV TW-2015 or PBS as naïve infection. After 3-4 days, the female mosquitoes were feed with DENV- or naïve- infected mice.
After taking the blood meal, the mosquitoes were supplied with 10% sucrose until whole body harvesting for RNA-seq.
|
| Growth protocol |
The mosquitoes were kept in 75%–80% humidity at 28℃ and were given 10% sucrose. Light and dark periods were 12:12 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNA extraction kit (ZYMO Research, catalog E1011-A). Five ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Agilent's SureSelect Strand-Specific RNA Library Preparation Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The bcl2fastq conversion software v2.20 was used to convert BCL files from all Illumina sequencing platforms into FASTQ reads.
Sequence reads were trimmed for adaptor sequence/low-quality sequence with Trimmomatic v0.36 with a sliding-window approach (parameter: Q20)
Trimmed sequence reads were aligned to AaegL5.0 using HISAT2
Cuffdiff (cufflinks v2.2.1) with genome bias detection/correction and Welgene Biotech's in-house pipeline were used to perform differential expression analysis.
Assembly: AaegL5.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jan 13, 2023 |
| Last update date |
Jun 03, 2024 |
| Contact name |
Yu-Ning Huang |
| E-mail(s) |
[email protected]
|
| Organization name |
National Taiwan University
|
| Department |
Biochemistry and molecular biology
|
| Street address |
No.1 Jen Ai road section 1
|
| City |
Taipei |
| ZIP/Postal code |
100 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL28657 |
| Series (1) |
| GSE222893 |
Investigating the factors that regulate dengue virus infection in Aedes aegypti female mosquitoes with Aedes aegypti transcriptomic analysis |
|
| Relations |
| BioSample |
SAMN32733583 |
| SRA |
SRX19032237 |
