Tag Archives: FAIL

A note from the lab bench

Dear internet,

It is infuriating to discover you have slipped up somewhere and ended up with next to no DNA or RNA or whatever at the end of your prep.

It is even more frustrating when you had planned really well and done everything to the letter.

But the most frustrating thing of all must be to be certain you have done it all right, have it all go wrong anyway and then discover someone else in the lab already knows why. 

I have (had? *sadface*) some RNA. I DNA-ase treated it prior to using it in qPCR. It needed cleaning up.

In the previous incarnation of this experiment I cleaned up the RNA (Qiagen RNA MinElute) then DNA-ase treated it. (Turbo DNAfree, in case you’re interested).

Except that the more I thought about it the more I worried that I was leaving residual DNase behind. So this time around I used the Turbo DNA-ase and then cleaned it up using an RNease Mini Kit. Exactly like it says you should. And all of my beautiful RNA is… well not gone. But coming out at ~50ng / uL. FIFTY. What the actual hell?! The other way around I got nearer TWO THOUSAND!!

Now obviously a MinElute elutes into 14 uL not 30, so it’s only natural to expect the prep to be half as concentrated: let’s say it was a pretty rough prep that would have had 800, then I might expect 400. But fifty?! Absolutely gutted and so unbelievably cross with myself for throwing all 14 samples at it at once.

But the most annoying part of all? Another PhD student in the lab figured this out about 2 months ago. Turbo DNA free and Qiagen RNeasy mini just aren’t compatible with one another and as far as I can see nobody has ever made a note of this.

Yours grumpily,

Baking Biologist

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#summergoals: End of July evaluation

A few weeks ago I decided to get a handle on my summer by setting myself some goals (thanks to  Flora Poste for giving me the idea!) . I’m a very target driven person and also prone to floundering without a schedule (someone remind me why on earth I wanted to do a PhD?) The aim of the game was to make SMART goals (Specific, Measurable, Attainable, Relevant and Time-bound). In other words I set myself a whole bunch of tasks to be achieved; some big, some small; that would help my PhD in a noticeable way, and that were supposed to be complete by certain deadlines. The end of July was one of these deadlines.

My first recap of #summergoals was pretty successful. The end of July… less so.

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#summergoals: End of Week 1

At the end of last week I wrote a post about my #summergoals: aka the baking biologist’s attempt to be organised, and not have her life taken over by generic moping, procrastination, and political machinations. (Did I mention I’m an evil genius?)

As week 1 draws to a close, it seems sensible to establish how I’m doing so far (aka give myself a kick up the behind).

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My morning so far…

I’ve taken this off #Whatshouldwecallgradschool

The title is ‘When the -80 fails and I lose my samples’, which has happened to me, and was reacted to similarly to this. Today is less dramatic, but still requires a suitable amount of nerd angst. This is not helped by my having played squash for the first time ever, been suitably knackered this morning, and therefore turned off my alarm, gone back to sleep, and woken up at 8:40.

Le sigh.

#summergoals: How to survive July and August

At some stage yesterday, one of my Tweeps posted this article by Flora Poste about how to survive the summer without the structure of undergraduate teaching and other regular commitments to keep us in check. I think this is a topic I need to think about more, especially at the moment. I have a lot of … stuff … on my plate right now, and therefore not much lab work is getting done because I am easily distracted by a) moping about Alex, b) trying to fight fire in other quarters and c) faffing on the internet.  And I suffer from lab stage fright. The longer I go without doing things, the less gets done. And so now, after two weeks of moving house and giving a conference talk and … this week … I am getting to full on procrastinating-so-I-don’t-have-to-face-the-lab stage.

My friends and associates would have you believe that I am extraordinarily busy and organised. Little do they know that this is because I am incapable of getting anything done without structure. At school, university and in my first job I was superbly motivated and competent because I was busy all the time. As a PhD student I can regularly waste entire days achieving very little. At my best, I work incredibly efficiently by having every hour of the day scheduled: something that is very hard to do with a lab-based PhD!

So while my qPCR is running, and I am stuck here on a Friday afternoon while most of the lab skives off (PI is elsewhere today) here is my attempt to regulate myself for the next couple of weeks. The time scales are specific because I am really good at putting stuff off.

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qPCR standard curve FAIL

Several months ago I agreed to give a talk next Tuesday. At the time it seemed a given that by then I would have some beautiful qPCR data. And then my minus 80 freezer died, taking with it all of my vital tissue samples, which took a further 6 weeks to regrow before I could even think about RNA extractions and DNase treating and cDNA synthesis and qPCR.

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Dress to impress

Today, I wore a dress to work in the lab.

Maybe I was feeling slightly unhinged. Maybe I was inspired by the Science: It’s a Girl Thing video. (Maybe I am moving house on Friday and have packed 95% of my clothes, but not this dress because I thought it might be sunny at the weekend, and then I woke up late this morning and grabbed the nearest clothes).

Whatever the reason, today I learned a valuable lesson. If you dress inappropriately to work in the lab, the lab equipment will eat your clothes. 

(Note also the choice of unfashionable but practical footwear. I’m not completely stupid!)

Memo to self: no matter whether you’re just setting up PCR all day and it covers all of your skin, wearing a dress in the lab is never a great plan. Le sigh.