Learn about SureSelect RNA Enrichment libraries

 

SureSelect RNA Enrichment libraries are collections of oligonucleotides that can be used to enrich specific RNA species in a pool of RNAs for sequencing. You use a library of oligonucleotide "baits" that are complementary to the RNAs of interest (target RNAs). The target RNAs hybridize well with the baits, but other RNAs do not, which forms the basis of a powerful selection method that lets you focus your sequencing efforts. The enrichment protocol also preserves the relative abundance of targeted RNAs.

When you order a SureSelect RNA Enrichment library from Agilent, the final product that you receive is a kit that contains a set of biotinylated RNA oligonucleotides. However, as part of the library manufacturing process, Agilent first creates DNA oligonucleotides, and then later transcribes them into RNA. Thus, when you create a SureSelect RNA Enrichment library in eArray, you specify bait sequences in terms of DNA bases (A, C, G, T).

With eArray, you can access existing baits and bait libraries or create custom libraries of baits. The SureSelect RNA Enrichment application type in eArray supports the Applied Biosystems SOLiD platform and the Illumina sequencing platform. Multiplexing, which lets you sequence multiple samples in the same sequencing reaction, is also supported.

To use eArray to create bait libraries, you must be an eArray registered user. When you log in to eArray, you set the Application Type to SureSelect RNA Enrichment, and the relevant tabs and commands appear. When you become a registered user, you also gain access to eArray's large, robust set of microarray and library creation tools for a variety of different application types.

Libraries, bait groups, and baits

In eArray, bait libraries contain one or more bait groups, and each bait group contains individual baits:

library_diagrm.gif

eArray stores individual baits as well as bait groups as separate entities, so you can use them as building blocks to make many different libraries.

For individual baits, you can use existing Agilent Catalog baits within eArray or your own baits. To put your own baits on eArray, you can upload them, and you can also use Bait Tiling, a method that creates baits that cover selected RNAs of interest, or the corresponding genomic regions, at even intervals. Currently, eArray supports a bait length of 120 nucleotides.

To organize baits into bait groups, you can select baits based on a Search Your Baits search. You can also create a bait group that contains baits that you upload or those that you create with the Bait Tiling tool. Baits and bait groups are separate entities—you can use a given individual bait in any number of bait groups.

Creating SureSelect RNA Enrichment libraries

One of the easiest ways to design bait libraries is to use one of eArray's built-in Library Wizards. Each wizard leads you step-by-step through the library creation process. As you complete a wizard, you can submit your newly-designed library to Agilent Manufacturing. To obtain the library, you can request a quote online through eArray. You can order the library from the Agilent Online Store or through your Agilent representative. eArray has several Library Wizards:

eArray also gives you other options for libraries:

As you create libraries, they go through several status changes. When a library has a status of Complete or Submitted, eArray assigns it a unique Enrichment Library ID (ELID).

If you require greater flexibility, or want to focus your attention on one aspect of the process at a time, eArray lets you do this, as well. See the following topics for more details:

Baits

Bait groups

Libraries and library sets

 

Guidance from Agilent

Agilent provides these recommendations for the creation of custom SureSelect RNA Enrichment bait libraries:

Collaborating with others

eArray makes it easy for you to work with others down the hall, or around the world. You can create collaborations with others, then work together to construct and submit bait libraries of mutual interest. You create a special collaboration workspace that has many of the same tools as your individual user workspace. See these topics for more details:

Collaborations

What are the roles in a collaboration

Create a collaboration

The SureSelect RNA Enrichment application type is available in collaborations. However, the Bait Tiling tool within the SureSelect RNA Enrichment application type is only available in your individual user workspace.