Design RNAseq project for PolyIC larval work

[AHuffmyer]

We have seen a difference in survival between offspring of PolyIC treated broodstock and control broodstock in lab trials. We would like to move forward with RNAseq (and maybe epigenetics?) analyses of these groups.

Here are the samples I have in hand stored in RNA/DNA shield and frozen at -80°C at FTR:

• n=12-15 per treatment at days 3, 8, and 14 post-fertilization of larval development
• n=15 per treatment of spat from 2 months post-fertilization
• n=15 per treatment of seed from 4 months post fertilization (will be collected next week)

Samples include replicate tanks/groups within each treatment (n=4-6 per replicate).

If we submit n=12 per treatment per time point, that would be a total of 120 samples.

Full metadata is available here: https://github.com/RobertsLab/polyIC-larvae/blob/main/data/rna-dna/sample_metadata.xlsx

If RNAseq costs ~$150 (previous Azenta cost with a discount), that would be minimum $18,000.

We need to decide what we would like to pursue for RNAseq.

Regardless of treatment effects, this would provide a nice developmental time series sampling that we do not currently have.

[AHuffmyer]

I can request an Azenta quote for the full set if we would like to see the expected cost.

[sr320]

go ahead and get a quote

[AHuffmyer]

I'm going to do a quote for mRNA seq - there is a promotion running for a discount currently.

[AHuffmyer]

Quote pending at Genewiz/Azenta