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#gel electrophoresis

Results!  The lane closest to the edge of the gel is a DNA ladder (or DNA standard).  Next to it is the solution we created in which we ligated the plasmid and kanamycin resistance gene.  And next to that is an unligated control solution containing the separated plasmids and kanamycin genes.

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spent 7 hours in the lab today (after getting up at 5 a.m. to do schoolwork, and 5 hours of classes 9a-2p) for an experiment which didn’t work :/ Took bacteria I transformed, miniprepped for dna, checked to make sure I /got/ dna, restriction digested them, and then checked that in a western blot. I must’ve messed up the protocol somewhere between the restriction digestion and imaging tho, bc I saw my ladder but no bands. Which sucks. a lot.

But I’m also happy/proud of myself, bc I spent basically a full work day in the lab, and took something start to finish. I’ll need to redo it, but the experience itself was totally worth it - I’m growing more independent by leaps and bounds, I asked my fellow undergrad only 1 tiny clarification in the 7 hours I was working.

Tomorrow’s another day, and hopefully a more productive one.

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Literally everyday I’m in the lab, and I’m finishing up the last thing I need to do so I can leave (usually running a gel) some ridiculous thing happens causing me to start all over, or jerry rig something and hope the gel runs properly and no one notices. Like today, I’m clamping the positive node on, and it’s putting up a fight, so naturally the whole thing tips over, spilling all the buffer, my DNA comes out of their wells. 😒

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just filled wells in Lab Dad’s gel electrophoresis!! He said I had rlly good lab hands + pipetting skills, especially for how little time I’ve been there (a week!!)

I’m just really excited, this is all I wanna do and everyone’s so nice and I’m learning so much.

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“and the little babies are like falling into the ground” –Steve

In the next step of this scientific journey with my independent study with the DMPI, we performed gel electrophoresis. Gel electrophoresis is a method used to separate the mixtures of DNA, RNA, or proteins based on their size. Specifically, we used this method to determine whether or not the process of amplifying a sequence in our bisulfite-converted DNA sample was done correctly. The gel electrophoresis would have to show us strong, colored bands to indicate that we have a good sample to work with before we put it into the Pyro Mark Q24 machine. Unfortunately, we did not see the strong bands that we desired, but the issue was because the sample of unconverted DNA was already questionable from the beginning. My savvy mentor, Stephen Siecinski, suspected this issue knowing that the sample was old, so now he needs to get a hold of a better sample for us next time. Despite our unfortunate results, it was interesting to perform gel electrophoresis for the first time. I learned the basic process of making the gel itself, using the lab equipment that utilizes the gel, and understanding what the image of the gel with the colored bands tell about the sample. The quote above was when Steve explained how size determines how fast a band moves through the gel. The bigger the sample the slower it travels; the smaller the sample, the more quickly it moves through the gel. In addition to this post, I will follow up with an in-depth process of how we made and used the gels and images we took of the colored bands.


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