Library prep can you get both mRNA and small RNAs in the same library?

willgordon · 07-14-2011, 03:38 PM

Hello,

I am new to RNA-Seq and we are looking to generate data for differential gene expression of both mRNA as well as small RNAs like miRNAs. From looking around most companies sell library prep kits for one or the other, is there any way to make a single prep that contains both? We have limited funds and it seems a waste to have to make separate libraries and perform separate runs.

Thanks

MrGuy · 07-14-2011, 11:52 PM

I know AB has a total RNA kit:

http://www.invitrogen.com/site/us/en...a-seq-kit.html

If it does the whole thing in one go, I have no idea as I haven't needed to do that.

Spider1374 · 07-19-2011, 06:29 PM

I don't know if there is a kit for both together. It seems like you would select against the bigger mRNA fragments if you had a PCR amplification step. And also, have higher adapter contamination issues.

You can always make libraries for each separately and have multiplexing bar-codes in them. The new TruSeq kits have them already built in. Then you can combine the samples after library generation and sequence them together.

Bioo Scientific · 07-20-2011, 09:00 AM

Hi Will,

You can use the NEXTflex Small RNA Seq kit for both small RNAs and directional mRNA work. I agree with the previous post that doing the library prep (mRNA and miRNA) separately is recommended otherwise you will flood your small RNAs with the more abundant mRNAs. You can do them separately (using the same kit) and barcode them (with up to 48 barcodes). Hope that helps.

Thanks.

pmiguel · 07-20-2011, 12:31 PM

Quote:

Originally Posted by MrGuy

I know AB has a total RNA kit:

http://www.invitrogen.com/site/us/en...a-seq-kit.html

If it does the whole thing in one go, I have no idea as I haven't needed to do that.

No it is pretty much an "either or", not "both" with the SOLiD RNA library kit.

--
Phillip

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07-14-2011, 03:38 PM	#1
willgordon Junior Member Location: SoCal Join Date: Jul 2011 Posts: 1	Library prep can you get both mRNA and small RNAs in the same library? Hello, I am new to RNA-Seq and we are looking to generate data for differential gene expression of both mRNA as well as small RNAs like miRNAs. From looking around most companies sell library prep kits for one or the other, is there any way to make a single prep that contains both? We have limited funds and it seems a waste to have to make separate libraries and perform separate runs. Thanks Last edited by willgordon; 07-14-2011 at 05:31 PM.

07-14-2011, 11:52 PM	#2
MrGuy Member Location: earth Join Date: Mar 2009 Posts: 68	I know AB has a total RNA kit: http://www.invitrogen.com/site/us/en...a-seq-kit.html If it does the whole thing in one go, I have no idea as I haven't needed to do that.

07-19-2011, 06:29 PM	#3
Spider1374 Junior Member Location: LA Join Date: Apr 2011 Posts: 1	I don't know if there is a kit for both together. It seems like you would select against the bigger mRNA fragments if you had a PCR amplification step. And also, have higher adapter contamination issues. You can always make libraries for each separately and have multiplexing bar-codes in them. The new TruSeq kits have them already built in. Then you can combine the samples after library generation and sequence them together.

07-20-2011, 09:00 AM	#4
Bioo Scientific Registered Vendor Location: Austin, Tx Join Date: Oct 2009 Posts: 99	Hi Will, You can use the NEXTflex Small RNA Seq kit for both small RNAs and directional mRNA work. I agree with the previous post that doing the library prep (mRNA and miRNA) separately is recommended otherwise you will flood your small RNAs with the more abundant mRNAs. You can do them separately (using the same kit) and barcode them (with up to 48 barcodes). Hope that helps. Thanks.