{"action":"created","issue":{"url":"https://api.github.com/repos/choderalab/kinase-ecoli-expression-panel/issues/9","repository_url":"https://api.github.com/repos/choderalab/kinase-ecoli-expression-panel","labels_url":"https://api.github.com/repos/choderalab/kinase-ecoli-expression-panel/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/choderalab/kinase-ecoli-expression-panel/issues/9/comments","events_url":"https://api.github.com/repos/choderalab/kinase-ecoli-expression-panel/issues/9/events","html_url":"https://github.com/choderalab/kinase-ecoli-expression-panel/issues/9","id":130753144,"number":9,"title":"IMPORTANT: ug/mL vs ng/uL","user":{"login":"jchodera","id":3656088,"avatar_url":"https://avatars.githubusercontent.com/u/3656088?v=3","gravatar_id":"","url":"https://api.github.com/users/jchodera","html_url":"https://github.com/jchodera","followers_url":"https://api.github.com/users/jchodera/followers","following_url":"https://api.github.com/users/jchodera/following{/other_user}","gists_url":"https://api.github.com/users/jchodera/gists{/gist_id}","starred_url":"https://api.github.com/users/jchodera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jchodera/subscriptions","organizations_url":"https://api.github.com/users/jchodera/orgs","repos_url":"https://api.github.com/users/jchodera/repos","events_url":"https://api.github.com/users/jchodera/events{/privacy}","received_events_url":"https://api.github.com/users/jchodera/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":10,"created_at":"2016-02-02T17:24:54Z","updated_at":"2016-02-05T18:24:17Z","closed_at":null,"body":"It looks like the current manuscript has some major confusion over the numbers we report for expression yields.\r\n\r\nThe 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.\r\n\r\nThe 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](http://choderalab.github.io/kinome-data/kinase_constructs-addgene_hip_sgc.html) 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.\r\n\r\nCan 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.\r\n\r\nTagging @Lucelenie, @sonyahanson, @steven-albanese "},"comment":{"url":"https://api.github.com/repos/choderalab/kinase-ecoli-expression-panel/issues/comments/180483203","html_url":"https://github.com/choderalab/kinase-ecoli-expression-panel/issues/9#issuecomment-180483203","issue_url":"https://api.github.com/repos/choderalab/kinase-ecoli-expression-panel/issues/9","id":180483203,"user":{"login":"danielparton","id":4217946,"avatar_url":"https://avatars.githubusercontent.com/u/4217946?v=3","gravatar_id":"","url":"https://api.github.com/users/danielparton","html_url":"https://github.com/danielparton","followers_url":"https://api.github.com/users/danielparton/followers","following_url":"https://api.github.com/users/danielparton/following{/other_user}","gists_url":"https://api.github.com/users/danielparton/gists{/gist_id}","starred_url":"https://api.github.com/users/danielparton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/danielparton/subscriptions","organizations_url":"https://api.github.com/users/danielparton/orgs","repos_url":"https://api.github.com/users/danielparton/repos","events_url":"https://api.github.com/users/danielparton/events{/privacy}","received_events_url":"https://api.github.com/users/danielparton/received_events","type":"User","site_admin":false},"created_at":"2016-02-05T18:24:15Z","updated_at":"2016-02-05T18:24:15Z","body":"Just added a README.md\n\nhttps://github.com/choderalab/kinome-data/tree/gh-pages\n\nOn Fri, Feb 5, 2016 at 1:13 PM, Daniel Parton <danny.parton@gmail.com>\nwrote:\n\n> FYI, the code for the online table is stored here:\n> https://github.com/choderalab/kinome-data/tree/gh-pages\n>\n> It's just a static HTML page, generated by running this Python script:\n>\n> https://github.com/choderalab/kinome-data/blob/gh-pages/pythonscripts/gen-html-plasmids-addgene_hip_sgc.py\n> The input data filepaths are hard-coded, so you'll probably need to change\n> those. Relevant lines: 18 and 21\n>\n> If there are rounding errors in the table, that's probably some\n> misconfiguration of the DataTables js package.\n> The DataTables configuration is in this template file:\n>\n> https://github.com/choderalab/kinome-data/blob/gh-pages/app/templates/expression-construct-table.html\n>\n> Any problems, let me know.\n>\n> On Fri, Feb 5, 2016 at 12:33 PM, John Chodera <notifications@github.com>\n> wrote:\n>\n>> We should also update the online table once we get all these conversions\n>> sorted out.\n>>\n>> —\n>> Reply to this email directly or view it on GitHub\n>> <https://github.com/choderalab/kinase-ecoli-expression-panel/issues/9#issuecomment-180456998>\n>> .\n>>\n>\n>\n"}}