|
| Status |
Public on Apr 22, 2020 |
| Title |
EtOH-rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Sua 4.0 cells
|
| Organism |
Anopheles gambiae |
| Characteristics |
cell line: Sua 4.0
treatment: control
|
| Treatment protocol |
Mosquito cell lines were exposed to 10% ethanol (control) or 20-hydroxyecdysone (20E) in 10% ethanol for 24 hrs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Following cell treatments, cells were incubated for 24 hours before control- and 20E-treated cell samples were isolated. RNA was isolated using TRIzol reagent and evaluated for quality using an Agilent 2100 Bioanalyzer. Samples were sent to the DNA Facility at Iowa State University for library construction and stranded mRNA-Seq. Gene expression analysis was performed the Genome Informatics Facility at Iowa State University.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Mosquito cell lines were exposed to 10% ethanol (control).
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were quality checked with fastqc, mapped to Agam 4.7 whole genome using STAR v2.5.2b.
FeatureCounts from subread was used to estimate read counts for genes.
Genome_build: AgamP4.7
Supplementary_files_format_and_content: counts_genes_EtOH_20E.txt: Tab-delimited text file includes raw counts for each Sample.
|
| |
|
| Submission date |
Jun 25, 2018 |
| Last update date |
Apr 22, 2020 |
| Contact name |
Andrew J Severin |
| E-mail(s) |
[email protected]
|
| Phone |
5152941320
|
| Organization name |
Iowa State University
|
| Department |
Office of Biotechnology
|
| Lab |
448 Bessey Hall (Genome Informatics Facility)
|
| Street address |
2200 Osborn Drive
|
| City |
Ames |
| State/province |
IA |
| ZIP/Postal code |
50014 |
| Country |
USA |
| |
|
| Platform ID |
GPL25232 |
| Series (1) |
| GSE116252 |
Influence of 20E on mosquito gene expression |
|
| Relations |
| BioSample |
SAMN09484318 |
| SRA |
SRX4297676 |
