|
| Status |
Public on Aug 13, 2021 |
| Title |
1-dodecyl chloride-3-methylimidazolium_rep3 - C12mimCl_R3 |
| Sample type |
SRA |
| |
|
| Source name |
Whole-body
|
| Organism |
Daphnia magna |
| Characteristics |
development stage: 48 hours
tissue: whole-body
treatment: EC20 of 1-dodecyl chloride-3-methylimidazolium
number of organisms: pool of 90 individuals
|
| Treatment protocol |
Each replicate contained a total of 120 neonates in 500 mL of test solution, and the exposure lasted for exactly 48 h with no food addition.
|
| Growth protocol |
Dedicated bulk cultures were established for a synchronised yield of the 3rd brood neonates needed (1440), all strictly ageing less than 10 h old. These neonates were then randomly assigned to 12 glass vessels comprising 3 replicates for each of the four treatments, i.e. control (blank ASTM medium) and EC20 of [Chol]Cl, [C2mim]Cl and [C12mim]Cl.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After exposure, active organisms were randomly collected from each replicate into RNAlater® for further storage at -80 °C. Pools of 90 individuals collected from each replicate were used for extraction. Organisms were homogenized with a disposable pestle before RNA extraction with the RNeasy kit and Qiashredder by Qiagen (Venlo, Netherlands) following the manufacturer's protocol.
The library construction of cDNA molecules was carried out using the Kapa Stranded mRNA Library Preparation Kit (Kapa Biosystems) and the generated DNA fragments were sequenced in an lllumina HiSeq 4000 platform, using 150 bp paired-end sequencing reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were trimmed with Trimmomatic (version 0.39)
Cleaned reads were mapped against the reference transcriptome of D. magna using the STAR aligner (version 2.7.3a)
HTseq-count in the intersection-nonempty mode was used for reads counting
Genome_build: Reference transcriptome of D. magna from Orsini et al. 2016: Orsini L, Gilbert D, Podicheti R, et al (2016) Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors. Sci Data 3:. doi: 10.1038/sdata.2016.30
Supplementary_files_format_and_content: Reads counting text files
|
| |
|
| Submission date |
Aug 24, 2020 |
| Last update date |
Aug 13, 2021 |
| Contact name |
Guilherme de Abreu Jeremias |
| E-mail(s) |
jeremias@ua.pt, gabreujeremias@gmail.com
|
| Organization name |
University of Aveiro
|
| Department |
Biology Department
|
| Street address |
Campus Universitário de Santiago
|
| City |
Aveiro |
| ZIP/Postal code |
3810-193 |
| Country |
Portugal |
| |
|
| Platform ID |
GPL24325 |
| Series (1) |
| GSE156769 |
Transcriptional toxicity of imidazolium- and cholinium-based ionic liquids |
|
| Relations |
| BioSample |
SAMN15894648 |
| SRA |
SRX8999045 |
