Entering edit mode
9 weeks ago
Jane
•
0
Hello everyone,
I plan to conduct a transcriptomic study on juvenile Daphnia magna exposed to different chemicals. I.e, I will expose D. magna to chemical A, B and C, and a control condition (without adding chemicals). Each exposure experiment will include three biological replicates per condition. After the exposure, I will pool all individuals within each biological replicate to create a single RNA sample for sequencing. I will repeat this entire exposure experiment twice to obtain three independent biological replicates per condition. Given this experimental design, would this approach be considered appropriate for transcriptomic analysis? Is this pooling technique correct? I intend to make sure the result is also reproducible.
Why do you pool the replication from one day? Is it to have enough RNA? That already could be your replication, but performing such exposures on different days is just as valid but might create some batch effects.
Yes, to have enough RNA and reproducibility of the result. The batch effect is one thing that concerns me. Should it happen, is it possible to cancel out the outlier? I am super new to transcriptomic and R.