Question

What is loaded in the first lane of electrophoresis gel?

Answer 1

Typically you load the "marker" or the "standard" - this is your reference to determine the sizes of your own bands.

It would look something like this: http://www.vectorlabs.com/data/descriptions/images/descr_7671_MWdna.jpg

Answer 2

Hmm, I try to leave the first and last lanes empty to avoid edge effects. Of all things, I wouldn't put my ladder there - as it's the reference for all the other samples, it would skew the entire analysis...

Answer 3

Ah @blues - thanks for the correction. Do you mind explaining what causes the "edge effect"?

Answer 4

@kma230 The edges of the gel are cooler than the center of the gel. Affects the rate at which samples migrate for a variety of thermodynamic and structural reasons. In general, cooler migrates slower. The edge effect is also called "smiling" because affected gels look like this:



Where the two lanes on the edges show edge effects and the two lanes in the middle don't.

It's one of those details they don't talk about in school but expect you to know in a real lab.

Answer 5

The bands in this drawing are all supposed to be the same molecular weight.

Answer 6

Thanks! Are there any textbooks or such that cover lab knowledge like this? Or is it more so something you pick up as you go?

Answer 7

@kma230

There are no textbooks that I know of - and I think a good solid "Intro to Molecular Analysis" is well and truly needed - but quite a molecular analysis and lab techniques courses publish their lab manuals online.

I never got beyond year two of college so I have no personal experience with what they teach. The B.Sc and M.Sc. grads I see coming out of those programs into the real world tend to be very thin on their wet skills - they have too little depth over too broad a sampling of techniques, like butter scraped over too much bread.

You can get the rudiments by reading upper level undergraduate and grad level lab manuals online.

Beyond that, you can get surprisingly solid by reading the protocols for the various procedures from the companies which sell the kits. I'd have to say reading five qRT-PCR protocols from BioRad, Invitrogen, etc and figuring out how they're similar and different and why has been how I really started to feel grounded in the lab. Often times you will find gems like edge effects buried in the footnotes and side notes of the professional literature.

If you have not yet discovered Bionet, do so:

http://www.bio.net/

It is OpenStudy for practical scientists. For talk of wet lab stuff you might want to follow http://www.bio.net/bionet/mm/methods/, but all the forums on there are wonderful according to your interest. (And yes, I am one of the frequent answerers on there too, though no medals).

Lastly, much of it is live and learn. When you get out into the real lab (I assume, possibly incorrectly, that you are a college student), some of the older career lab techs and lab managers have been in those labs for more than your age and mine combined. They have seen it all, done it all and have much to teach.

And if in your searchings you find a good text on lab techniques, please let me know about it.

Answer 8

Considering this question is on my exam and not an actual experiment is it okay to say
marker or ladder?

Answer 9

That's a lot of awesome advice, @blues. Thanks so much! I'm actually still in high school; unfortunately it's been a bit difficult finding professors willing to take on students my age, but I look forward to getting to do research as an undergrad.

What do you think of http://openwetware.org/wiki/Main_Page if you use it? Is it reliable?

@Aka_966 I think it's very important to know the actual answer, which is what blues gave. I feel the textbook answer would probably be the marker or ladder(?), and for the sake of completing an assignment, I assume it would suffice - but if this were an open-ended question...it wouldn't hurt to give the actual answer and demonstrate some extra knowledge :P