Design for Longitudinal Sample Acquisition
I've discussed with my peers locally, but want to poll the depth and breadth of experience on the forums.
I am planning an experiment with six timepoints across seven weeks. The cells will be stained live, so staining will happen (from a frozen master mix) on each of the harvest days, then fixed and barcoded (intracellular pd barcode).
The two options:
1. Run each sample as quickly as possible post-staining+fixing (no more than a 1-2 nights in intercalator in the fridge). This would stretch acquisition dates across a two month period.
2. Cryopreserve stained+fixed sample until completion of the experiment, then run all the samples sequentially on the instrument within the shortest possible timeframe (1-3 days of acquisition). This would involve a freeze-thaw of fixed sample.
In the past I have performed both of these methods in various experiments, and haven't noticed any differences in normalization or variance between samples. I ask you all, then, which is the greater evil? A freeze-thaw cycle of stained/fixed cells, or spreading an acquisition out across two months?
I appreciate your perspectives!
~Riley