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Experiment Design - New Drugs #76
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To answer @gwaygenomics clarification questions: Clarification Questions
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cool 😎
I think I am missing the connection of drug dose to sequencing... can you clarify? Also, if our observations are leaning us towards the identification of a "drug tolerance" signature, then dose information is how we support it. Although this question is directly related to the scope and target of the journal. Here is how I see the paper: Paper with dose for one drug (bortezomib) and without dose for two drugs
Paper with dose for three drugs
SummaryI think we have a nice story either way we go. I think including dose information might be a bit more compelling, but, again, only if it does not add too much additional work.
Gotcha! I thought that the original question was, "should we also include WT clones on this plate that we already made previously". The answer to that is yes, please! Is that the question? Or, is the question, "should we perform a new round of selection to get WT clones, grow them up, and then add to new plates"? The answer to that is, yes, please, if it is not too much trouble and would delay us too much. |
Thanks for the feedback @gwaygenomics! If we were to generate new wild type clones, then @ayberman and I would be delayed several weeks. Instead, could we use 4 wild type clones that we generated previously (batch 3) but haven't been thoroughly characterized yet (not used in batches 4-7)? |
Thanks for this note!
I think that is perfectly reasonable 💯 |
@mekelley and @ayberman are getting ready to ramp up data collection. Specifically, we will collect Cell Painting data from 7 resistant clones and a wildtype parental line undergoing two drug treatments and a DMSO negative control. The drugs are ixazomib (proteasome inhibitor) and CB-5083 (p97 inhibitor). The cells will be treated for four hours.
Clarification Questions
Wildtype Clonal Line Discussion
In my opinion, we definitely should try to mirror the same clonal selection procedure for the wildtype parental line to acquire a wildtype clonal line. Our approach in identifying morphology features of resistance mechanisms will be skewed by clonal selection signal. In other words, we're likely to obscure the resistance signals by also isolating the clonal selection signals.
I view the wild-type parental line as a really great validation resource. We should see a lot of heterogeneity in these samples, and could validate some resistance signatures we find by comparing wildtype clones and other resistant clones.
If we use the same clonal selection procedure for selecting resistant cells to the new drugs, then I think using the same WT clones for batches 4-7 (see #40) is sufficient.
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