Agilent SureSelect DNA and Haloplex

[woodydon]

Dear all,

Does any have the experiences using targeted RNA from Agilent beads? I would like to know whether it is better than illumina's targeted RNA system. I guess illumina has better quality. How about Agilent's?

I don't really understand the difference between SureSelect DNA and Haloplex though...

Thanks!

Woody

[Bukowski]

I've used Agilent SureSelect, and Haloplex and done targeted RNA-Seq with SureSelect. I have not used the Illumina kit.

I have no issues with SureSelect at all, but we use it pretty much exclusively, the most common gripe is the complexity of the protocol and the number of steps involved. However the kits are generally extremely reliable.

SureSelect is a hybridisation capture. Haloplex is a hybrid - somewhere between pure hybridisation and an amplicon approach - it has aspects of both workflows. I don't like Haloplex, because the nature of the protocol means you have very uneven coverage of capture regions, and you can't de-duplicate the data owing to the amplification step although I have only used it for targeted DNA sequencing.

[woodydon]

Thank you for the quick and positive comments.

Indeed, the number of steps and complex protocol makes me wonder its reliability. Because it uses beads to capture RNAs. I am not sure how sufficient the approach works. Illumina's targeted RNA seems more simple and reliable in general. I have used neither of them, so I am not sure.

You mentioned that you are using SureSelect to capture RNAs. Did you use SureSelect and used MiSeq/HiSeq to do sequencing?

Thanks,
Woody

I've used Agilent SureSelect, and Haloplex and done targeted RNA-Seq with SureSelect. I have not used the Illumina kit.

I have no issues with SureSelect at all, but we use it pretty much exclusively, the most common gripe is the complexity of the protocol and the number of steps involved. However the kits are generally extremely reliable.

SureSelect is a hybridisation capture. Haloplex is a hybrid - somewhere between pure hybridisation and an amplicon approach - it has aspects of both workflows. I don't like Haloplex, because the nature of the protocol means you have very uneven coverage of capture regions, and you can't de-duplicate the data owing to the amplification step although I have only used it for targeted DNA sequencing.