We have now performed experiments in HT29 and HepG2 cells to test mitigation/synthetic lethality between…
Week 1 update: getting started
A frantic week kicked off on Sunday, March 22 when we had our first Google Hangouts group call pitching and brainstorming ideas. In the week that has followed, our lab has accomplished a dizzying array of tasks of all kinds to get projects off the ground, culminating in our first data! It has taken a truly amazing amount of persistence and cooperation to get to where we are now. Here are some notes that attest to the wide range of tasks that needed to be accomplished even just to get started:
· We started a group Slack account on Monday and a lab Twitter account on Friday. Already, Slack has now become an invaluable way to communicate as a group, and we hope Twitter will serve likewise for communicating with the broader community.
· We ordered remdesivir (MedChemExpress), hydroxychloroquine (Selleck), an RNA-seq kit (Lexogen), two batches of genome-wide CRISPR lentiviral library (Addgene), and Illumina Nextseq kits, all while the lab was officially closed. We tried to order remdesivir from Selleck but they were out until at least next week, so Sam and Miha frantically called several other companies before finding MedChemExpress, where we got the last vial they had. Addgene said they wouldn’t ship virus to us until Minsun pleaded with them to make an exception (we even offered to pick it up directly from their Kendall Square lab). Joyce has had to specially handle every order to make sure the companies are open and follow through. We are grateful that the NRB loading dock is still operational.
· Anticipating needing a larger amount of remdesivir, Heysol put a call into Gilead asking whether they might be able to provide us with an aliquot. They are clearly quite busy, and it took dogged effort to even get in touch. We’ll see if they do provide us with any, but our recent toxicity titration has suggested we may need much less than we thought we might (good for our ability to perform the proposed experiments, not necessarily a good sign for the safety of the drug as it is showing toxicity at doses as low as 5 uM in certain cell lines).
· Through efforts from many in the lab (among those not named already, Minja and Larissa), we have cobbled together actionable protocols for a number of initial experiments we started this week including drug toxicity titration on four cell lines we had in LN2 (HepG2 and PLC/PRF/5 liver lines, HCT116 and HT29 intestinal lines) and lentiviral titrations.
· Mia has taken a crash course in understanding the bizarre mechanisms of coronavirus RdRP transcription, getting to the point of designing fluorescent assay constructs for us to begin cloning. We’re still looking for SARS-CoV2 genomic RNA/cDNA to use as a template for cloning.
· Ersin just spent >2 hours feeding 128 tubes to the FACS analyzer because the only one that is available to us at present does not have 96-well plate capabilities.
· We submitted a COVID-related grant on Tuesday through a massive group effort.
· We submitted a request to allow others to come to lab to perform the research we have been setting up since currently, only a skeleton crew has been keeping the in-lab experiments afloat.
· All the while, we have been working hard on data analysis for all of our other non-COVID-related research projects.
I am really curious what next week has in store!