|
| Status |
Public on Apr 20, 2018 |
| Title |
Cont.1h.2 |
| Sample type |
SRA |
| |
|
| Source name |
whole body tissue
|
| Organism |
Daphnia magna |
| Characteristics |
age: 5 day-old
Sex: female
strain: Xinb3
tissue: whole body
|
| Treatment protocol |
Animals were exposed to 1mg/L propranolol (Prop), 4mg/L propranolol (Prop3), 100 mg/L isoprenaline (Iso), and a mixture of the two: 1mg/L propranolol and 100 mg/L isoprenaline (IP)
|
| Growth protocol |
20 individuals of 5 days old D. magna were exposed to different 35 ml chemical solutions separately and were harvested at 1, 6, and 24 hours of exposure
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the body sample using the RNeasy kit and Qiashredder (Qiagen,Venlo, The Netherlands) following manufacturer’s protocol.
An Illumina mRNA sequencing library was made from 500 ng of total RNA using the 'Truseq stranded mRNA library prep kit' (Illumina, San Diego, CA, US)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
1 hour of exposure
|
| Data processing |
Adapter removal and dynamic trimming to achieve 99.9% base call accuracy was done with Trim Galore version 0.3.2.
Reads were alignmed using bowtie2 version 2.1.0 to the XinB3 transcriptome (BioProject PRJNA284518)
Aligned reads were processed to htseq resulting in read counts per gene
Read counts were normalized using a trimmed-mean of M-values in R using edgeR
A quasi-likelihood negative binomial generalized log-linear model was fitted to the data to determine differential expression. Benjamini-Hochberg method was applied to adjust for multiple testing
Genome_build: BioProject PRJNA284518
Supplementary_files_format_and_content: Matrix with normalized cpm values using edgeR per gene. Samples are listed by their title
|
| |
|
| Submission date |
Oct 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jana Asselman |
| E-mail(s) |
jana.asselman@ugent.be
|
| Phone |
+32 9 264 37 64
|
| Organization name |
Ghent University
|
| Lab |
Laboratory of Environmental Toxicology and Aquatic Ecology
|
| Street address |
Coupure Links 653 (Building F, 2nd floor)
|
| City |
Gent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL24022 |
| Series (1) |
| GSE104487 |
Effect of β-adrenergic receptor antagonist and agonist on cardiac structure and function and whole body gene expression in Daphnia magna |
|
| Relations |
| BioSample |
SAMN07728805 |
| SRA |
SRX3236763 |
