|
| Status |
Public on Apr 10, 2020 |
| Title |
CLD-rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Approximately 5 day old adult female An. gambiae abdominal carcass tissues (internal organs removed).
|
| Organism |
Anopheles gambiae |
| Characteristics |
strain: Keele
developmental stage: Approximately 5 day old adult female An. gambiae abdominal carcass tissues (internal organs removed).
Sex: female
condition: injected with clodronate liposomes (experimental) one day prior to malaria parasite challenge.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Following treatment with liposomes, mosquitoes were challenged with P. berghei. ~24hrs post-infection, mosquitoes were dissected to remove digestive and reproductive organs, then the remaining abdomen was processed for RNA isolation. Samples were prepared from ~15 mosquitoes and processed in TRIzol reagent. RNA was 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 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were qulaity 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: tab-delimited text files include raw counts for each Sample ...
|
| |
|
| Submission date |
Jun 22, 2018 |
| Last update date |
Apr 10, 2020 |
| Contact name |
Andrew J Severin |
| E-mail(s) |
severin@iastate.edu
|
| 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) |
| GSE116156 |
Effects of hemocyte ablation on fat body gene expression |
|
| Relations |
| BioSample |
SAMN09470101 |
| SRA |
SRX4283371 |
