Anyone here know how to interpret really shitty smears on electrophoresis

Contaminants maybe. Gels can also be obnoxious to read from time to time as well. Maybe they werent run long enough.

>>8771623
I get that there may have been contamination, but the smears begin and end within specific regions so I'm sure I can still use them to genotype people
I need to do that

Alright here's another question

If someone was heterozygous, you'd expect either two bands, a band and a smear, or two smears right? If there's only one big smear that appears to be completely uniform, does that mean the individual is homozygous for one of the two alleles?

>>8771621
Pretty sure I remember the guy telling us that upper smears imply that it is a soloLTR, even if there is presence in the pre-integrational site location. So the last one on ur pic could be homozygote for LTR. But then again I'm just starting the write-up, so I'll know more after I read up on the instructions.

>>8771621
interesting
i have never worked in a lab with that sort of thing, but have had to deal with such gels at an exam

i think the last one is homozygous LTR
the ones below the PIS boundary are both hetero for no LTR, the first two are heterozygous

>>8771662
You go to reddit uni too? Nice
I feel like there's gotta be a pre-integration site in the DNA somewhere if the smear begins or ends exactly where you'd expect the pre-integration site. Otherwise if the individual is homozygous for the solo-LTR, what are the chances of getting a longer DNA fragment to stop just at that line? The gel doesn't know how long the fragment would be without the solo-LTR.

>>8771665
Thanks
For the second one below the boundary though, I meant to show how it starts just at the boundary. Is that insignificant then? And did you mean homozygous for no LTR?

Why is it that the first two have the same genotype but look different? I was wondering if it's possible that the second one is just homozygous for solo-LTR because the smear could be very faint and travelling all the way down from the expected LTR band height (since it begins above PIS)

And what makes you think that about the last one? Does the fact that it ends at the PIS just mean it's above the boundary and therefore no PIS alleles are present?

>>8771682
>And did you mean homozygous for no LTR?
yes

the last one is closer to the LTR mark, so they didn't travel a lot, meaning the repeat is there, so by the same criterion as when judging the two that traveled farther than the PIS boundary(meaning they don't have a repeat)

the two heteros could be different because different retroviruses? they do tend to change a lot so what's to say you don't have more than 1 endogenous type with different number of long terminal repeats - this probably wouldn't explain getting a smear on an individual sample though

i am used to seeing very clean gels and am just shooting in the dark, but i hope i gave you some ideas, even if what i'm saying is incorrect as i'm not 100% sure i'm reading it correctly

>>8771710
Thanks that makes sense for the last 3

And sorry, I didn't give enough context for the experiment I guess. These are all integration sites for the same retrovirus. Although we looked at several different integration sites with different lengths, all the solo-LTR lengths are the same.
The picture I drew is just to illustrate what it would look like in the case of one single integration site.

Sometimes the same integration site had a smear and a band, sometimes just the smear so I didn't get it

File: Screen Shot 2017-03-23 at 19.49.38.png (203KB, 708x760px) Image search: [Google]

203KB, 708x760px

The band at around 650bp - just a homozygote for pre-integration site with a long smear behind it? I mean if it was a heterozygote, surely the solo-LTR DNA would smear somewhere beyond the boundary by chance

>>8771911
that would be my guess. The band on lane 3 is a primer dimer despite the smear that goes up to 650bp, right?

>>8772046
I didn't think of that, I assumed it was a smear that went past the PIS so possibly indicating a heterozygote

The primer dimers are generally just bands at the very bottom, never seen them smear or smudge
But then I've never been sure about anything

>>8772248
nvm, you're probably right that it's heterozygote. I was slightly concerned because there is no bright band for the preintegration site, just an upwards smear that overlaps with the hypothetical preintegration site location and expands beyond.