Just opening this as a reminder that the figure for abl1 needs to be updated to correct some mistakes with respect to the 'control' boundaries that we used.

We should add a link to this script to the README since we mention this in the manuscript.

We should create an Excel spreadsheet version of our expression data for use as Supplementary Information in the manuscript.

It would be great to have a nice overview cartoon figure, as well as some figures that illustrate various stages of this process (like representative multi-sequence alignments of PDB sequences to the canonical Uniprot sequence and plasmid source sequences).

@danielparton: I think you gave some talks containing material that could be reused for this purpose. Would you mind contributing your talks?

Some of the web pages @danielparton created are also great for the other figures, such as this alignment.

We should remember to update the author list when we update the bioRxiv manuscript.

It looks like the current manuscript has some major confusion over the numbers we report for expression yields.

The Caliper GX II yields are reported by the MacroLab in "ng/ul", which actually represents the number of nanograms of protein per microliter of sample loaded onto the Caliper. The sample comes from the eluted protein that came off the beads in the Nickel Buffer A incubation and wash (120 uL). Presumably, a few uL (how many) of this were loaded into the Caliper for quantification, and the final reported number is the concentration of this 120 uL eluate. The "ng/ul" number is not informative without reporting how many total uL of eluate we got from the culture volume, and how much that culture volume was.

The original culture volume was 900 uL, so Danny and I had been converting the ng/ul number to "ug/mL of bacterial culture" by multiplying by (eluate volume) / (culture volume). This is why the online table lists number 12 M3K5_HUMAN_D0 as 105 ng/ul but 12.6 mg/L expected scale-up: we appear to have calculated this as (105 ng/ul eulate) * (120 uL eluate) / (1000 uL culture) = 12.6 mg/mL culture (where you see we have erroneously assumed we had 1 mL culture instead of 0.9 mL culture). There seem to be some other issues with rounding in the online table from Danny as well----for ABL1_HUMAN_D0, the mg/L number 2.26 is truncated to 2.2 instead of being rounded to 2.3.

Can you guys fix the manuscript with this in mind? I'll check in my edits in just a few minutes, and then you can have a go at it. At minimum, we need to make sure we're talking about the right thing when we quote the yield or how many kinases expressed with a certain yield. Even better would be to draw a threshold of, say, 1 or 2 mg/L expected scale-up, since it isn't very reasonable to use this method for the kinases expressing way down at 0.27 mg/L (2 ng/ul eluate). That will drop the number of kinases we report as expressing, but will make it less embarrassing than suggesting people should use the kinase constructs that barely express.

Tagging @Lucelenie, @sonyahanson, @steven-albanese

"If you have made functional modifications to the commercial plasmids you obtained, MSKCC would generally consider these new, modified plasmids to be their IP. We always carry out the MTA with the legal office at the depositing institution (MSKCC if this is where your plasmids were made), as they have the final say over whether they would like to give Addgene permission to distribute. So if you are intending to deposit plasmids that are modified from the original ones you purchased, MSKCC is likely to give permission for this; if they are the unchanged commercial vectors we cannot accept these." -Addgene Outreach Scientist

We need to update the README.md with

• updated manifest
• updated list of contributors

We need to send the Src/Abl mutants through the CMO clearance process.

I forgot to write down the title we decided on. Could one of you add that?

Right now, the manuscript only mentions "coexpressed with either the truncated YopH164 for Tyr kinases" but doesn't give any information as to what "truncated YopH164" means.

Someone should contact Chris Jeans for clarification as to which construct exactly this corresponds to. We'll need to put in a few sentences about what sequence this corresponds to (e.g. YopH residues X-Y) and where that plasmid can be obtained.

Question for @danielparton : When was the Uniprot query run?

Human protein kinases were selected by querying the UniProt API for any human protein with a domain containing the string "protein kinase", and which was manually annotated and reviewed (i.e. a Swiss-Prot entry).
The query string used was:\\
{\tt taxonomy:"Homo sapiens (Human) [9606]" AND domain:"protein kinase" AND reviewed:yes}\\
Data was returned by the UniProt API in XML format and contained protein sequences and relevant PDB structures, along with many other types of genomic and functional information.

We have accidentally checked in an .ipynb_checkpoints/ directory (which should be deleted) and we don't have a README explaining what this is and how it was generated.

I've updated the online data table, though there are still plenty of other things to fix. We'll have to find a more sustainable way to keep all this data together and organized---things are currently scattered in random places across multiple repos right now, and it currently takes a huge amount of work to even figure out what we have and how to wrangle it whenever something minor (like the conversion factor) needs to be changed.

Just wanted to see if this is still a to do?

I guess the main thing is that the interactive table of kinase expression data and constructs is still in the kinome-data repo. It should be pretty easy to just make a gh-pages branch in this repo instead. Thoughts?

Is there anything else to wrangle?

We don't seem to have the two additional datasets we added to the paper (Abl construct boundary and Src/Abl mutation expression data) in this repo. We need to add this.

@Lucelenie : I left a hard copy of the manuscript with a bunch of edits to the protein expression methods section on your desk! I made what I thought were the most pressing edits, but I think that section could be rearranged a bit after we get it up on bioRxiv

Just a reminder!