|
| Status |
Public on Feb 28, 2022 |
| Title |
Adult T1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole body
|
| Organism |
Anopheles gambiae |
| Characteristics |
common name: African malaria mosquito
exposure condition: Control Adult
devlopmental stage: 4-day old non-blood fed adult females
tissue: Whole body
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from four pools of 20 individuals sampled for each life stage (larvae or adult females) and condition (treated with pesticide mixture or not). RNA extractions were performed using Trizol (Life Technologies) according to manufacturer's instructions.
RNAseq libraries were prepared from 150 ng total RNA using the NEBNext® Ultra ™ II Directional mRNA Library Preparation Kit for Illumina (New England Biolabs) following manufacturer's instructions. Libraries were quantified using the Qubit DNA BR assay (Thermofisher Scientific) and quality checked using Bioanalyzer DNA 1000 assay (Agilent). Libraries were sequenced in multiplex as single 75 bp reads on a NextSeq 500 sequencer (Illumina) by Helixio (Clermont-Ferrand, France). After unplexing and quality check using FastQC, reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
After unplexing and quality check using FastQC, reads were then filtered based on their length, pairing and quality using Trimmomatic (v0.32.1)
Cleaned reads were mapped to the AgamP4 assembly annotated with the AgamP4.12 gene set using HISAT2 (Kim et al., 2015).
The Cufflinks (v0.0.7) tool was applied to aligned reads to enumerate for each library the number of short reads overlapping annotated genes.
Cuffmerge (v0.0.6) was used to merge multiple transcriptome assemblies from each sample. Gene transcription levels were computed from aligned reads and compared statistically using the Cuffdiff (v0.0.7) tool (Trapnell et al., 2012) implemented in a Galaxy pipeline (http://galaxyproject.org).
Gene transcription levels were computed from aligned reads and compared statistically using the Cuffdiff (v0.0.7) tool (Trapnell et al., 2012) implemented in a Galaxy pipeline (http://galaxyproject.org).
Genome_build: AgamP4
Supplementary_files_format_and_content: Cufflink files
|
| |
|
| Submission date |
Nov 22, 2021 |
| Last update date |
Mar 01, 2022 |
| Contact name |
Stéphane REYNAUD |
| E-mail(s) |
stephane.reynaud@univ-grenoble-alpes.fr
|
| Phone |
04 76 51 46 80
|
| Organization name |
Grenoble-Alpes University
|
| Lab |
Laboratory of alpine ecology
|
| Street address |
2233 rue de la piscine
|
| City |
Saint Martin d'Hères |
| ZIP/Postal code |
38400 |
| Country |
France |
| |
|
| Platform ID |
GPL22033 |
| Series (1) |
| GSE189345 |
Exposure of Anopheles gambiae larvae to a sub-lethal dose of an agrochemical mixture induces tolerance to Fludora® Fusion and to its neonicotinoid component in adults |
|
| Relations |
| BioSample |
SAMN23390430 |
| SRA |
SRX13197189 |
