|
| Status |
Public on Jun 29, 2023 |
| Title |
Copper-exposed female biol rep 2 [AORF-1-11] |
| Sample type |
SRA |
| |
|
| Source name |
entire adults
|
| Organism |
Eurytemora affinis |
| Characteristics |
tissue: entire adults
Sex: female
exposure time: 72h
developmental stage: adult
treatment: Cu 25 µg/L
|
| Treatment protocol |
Copepods were exposed 72h to 25 µg/L of copper by balneation (15°C, 15 psu, acidified water 0,2%). Water (15°C, 15 psu) for the control condition was also acidified (0,02%)
|
| Growth protocol |
Copepods were kept under optimal conditions (i.e. 15°C, 15 psu, 18h/6h light-dark cycle) in laboratory prior to exposure
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the Quick-RNA Tissue/Insect Microprep Kit (Zymo Research, Mülhauser, Germany) following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using Universal Plus™ mRNA-Seq library preparation kit with NuQuant® (Tecan) following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Cu-F
|
| Data processing |
Reads quality score (Phread score above 30) was accecced with FastQC
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (Bolger, A. et al. 2014)
Trimmed sequence reads were aligned against the Eurytemora affinis genome GCA_000591075.2 Eaff_2.0 using STAR (Dobin, A. et al. 2012)
Read count extraction was performed using FeatureCounts (Liao, Y. et al. 2013)
Read count normalization and the differential analysis was perfomed using DESeq2 R package
Assembly: Eaff_2.0
Supplementary files format and content: Tab-delimited text files matrix with gene counts for each samples
|
| |
|
| Submission date |
Sep 02, 2022 |
| Last update date |
Jun 29, 2023 |
| Contact name |
Caroline Arcanjo |
| E-mail(s) |
arcanjo.caroline@hotmail.fr
|
| Organization name |
UMR-I02 SEBIO
|
| Street address |
25, rue Philippe Lebon
|
| City |
Le Havre |
| ZIP/Postal code |
76063 |
| Country |
France |
| |
|
| Platform ID |
GPL30085 |
| Series (1) |
| GSE212602 |
Decoupled responses of the copepod Eurytemora affinis transcriptome and its microbiota to dissolved copper exposure |
|
| Relations |
| BioSample |
SAMN30648341 |
| SRA |
SRX17408511 |
