And as one the lab cried from the very depths of their souls: OH NOES!!!!!!1!!!!!!11!!!!!!

A new edict has come down from On High (that is, the Advisor).  From now on, complete sequences of every plasmid that is in our papers will be submitted as supplemental material.  Which means we need to have complete, annotated sequence files for every plasmid.

Advisor told me this little tidbit of news when I went in to see him with a few sample paragraphs of my Materials and Methods section which describes plasmid and strain construction.  Advisor had previously told me that he likes a very detailed M and M section.  So, I wanted to know if I had achieved the right amount of detail.  He told me that what I had would be fine because of this new rule had had just devised.  He further went on to tell me that this should not be much of an issue for me since he knows I have been making these sequence files all along, so I’ll just gather them up and if I email them to him he will convert them into genbank format.  He was not being sarcastic, the man honestly believes that I have annotated sequence files for every plasmid I have ever created (there are 62 of them, not that all of them will be in the paper only maybe a quarter of them).  I do have sequence files for most if not all.  But they are not annotated.  And if they are it’s in an obscure shorthand only understandable by me.

I casually mentioned this to a couple people in the lab and there were immediate cries of dismay.  And then I politely suggested to Advisor that he send an email detailing this exceptionally brilliant new planof his so people could start planning ahead.  Also, that I wasn’t going to spread the news because I didn’t want people to shoot the messenger.

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7 thoughts on “And as one the lab cried from the very depths of their souls: OH NOES!!!!!!1!!!!!!11!!!!!!

  1. Does you institution have a copy of VectorNTI? You can just import sequences and do virtual cloning, and then send them to him as .gb files.
    Minimal work, I promise. And you will look awesome to your labmates for telling them so.

  2. If you don’t have VectorNTI, you could try lablife, which is a free lab-by program frfrom Addgene. I have been using it to catalog my plasmids recently…if you enter the sequences, it finds all features, including gene inserts (if they have Pubmed entries). I haven’t tried any virtual cloning though…

  3. Because we must also deposit a copy of the sequence in a lab database, the program we use for our sequences is not up for discussion because The Almighty has decreed that we must use Highly Classified Super Top Secret Not Available Anywhere Else Program to document our plasmids. It does have virtual cloning, though. And is actually pretty easy to use.

  4. Every plasmid has to be entirely sequenced de novo? So you will be sequencing AmpR over and over and over in each of your plasmids?

    Or you just have to assemble the complete sequence from known pieces plus whatever novel shit is subcloned in?

    • The latter. I shudder to think what it would cost to sequence all of our plasmids in their entirety. It’s not that bad, really. It just feels like busywork. And, Advisor has been telling us all along he wants to have maps of every plasmid we make. It’s just now he has a way to make sure we comply. You should have seen the look of horror on people’s faces. You could almost hear them thinking, “Oh shit, I really should have been doing that all along like Advisor wanted me to.”

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