Size selection: agarose gel / acrylamide gel

amazonic9 · 12-04-2012, 09:17 AM

Hello everybody,

Maybe I am going to ask something very basic, but I haven't found the answer on the internet (probably I did the wrong queries)...

Could anyone tell me why we usually make size selection in agarose gels for the majority of libraries, but the small RNA libraries have to be size selected on acrylamide gels? I thought it was a matter of size, but I've also seen acrylamide gel size selection when doing directional mRNA seq using the small RNA seq protocol from illumina.

Is there any particular reason for which one should use one type of gels or the others?

Thanks a lot in advance, and sorry if the question is a bit stupid.

amazonic9

cascoamarillo · 12-04-2012, 09:45 AM

Hi,
You are in part right; but don't ask me to size select my small RNA libraries on agarose gels cos I'm sure the resolution will be pretty bad in that case.

amazonic9 · 12-05-2012, 03:56 AM

Yes, that is what I thought, that it was a matter of size (small sizes). But as I have seen people doing selection on acrylamida gels at 300bp for example (with this directional mRNA protocol using small RNA kit), I was wondering if there's something I should take in account to distinguish when should I use one type of gels or the others.

I guess it should be ok to do the size selection from this directional RNA protocol on agarose gels.. resolution at those sizes is good.

Thanks for your answer!

amazonic9

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12-04-2012, 09:17 AM	#1
amazonic9 Member Location: Spain Join Date: Jan 2012 Posts: 10	Size selection: agarose gel / acrylamide gel Hello everybody, Maybe I am going to ask something very basic, but I haven't found the answer on the internet (probably I did the wrong queries)... Could anyone tell me why we usually make size selection in agarose gels for the majority of libraries, but the small RNA libraries have to be size selected on acrylamide gels? I thought it was a matter of size, but I've also seen acrylamide gel size selection when doing directional mRNA seq using the small RNA seq protocol from illumina. Is there any particular reason for which one should use one type of gels or the others? Thanks a lot in advance, and sorry if the question is a bit stupid. amazonic9

12-04-2012, 09:45 AM	#2
cascoamarillo Senior Member Location: MA Join Date: Oct 2010 Posts: 160	Hi, You are in part right; but don't ask me to size select my small RNA libraries on agarose gels cos I'm sure the resolution will be pretty bad in that case.

12-05-2012, 03:56 AM	#3
amazonic9 Member Location: Spain Join Date: Jan 2012 Posts: 10	Yes, that is what I thought, that it was a matter of size (small sizes). But as I have seen people doing selection on acrylamida gels at 300bp for example (with this directional mRNA protocol using small RNA kit), I was wondering if there's something I should take in account to distinguish when should I use one type of gels or the others. I guess it should be ok to do the size selection from this directional RNA protocol on agarose gels.. resolution at those sizes is good. Thanks for your answer! amazonic9