Overview of working with baits

Baits are oligonucleotides that retrieve specific RNA species or genomic DNA fragments of interest for sequencing. The desired DNA or RNA molecules hybridize with the baits, and others do not. This forms the basis of a powerful selection method that lets you focus your sequencing efforts. The baits manufactured by Agilent are biotinylated RNA oligonucleotides. Currently, eArray supports a bait length of 120 nucleotides.

In eArray, a single bait is a nucleotide sequence that is associated with a unique Bait ID and species. Although the final product supplied by Agilent is a kit of biotinylated RNA oligonucleotides, Agilent first creates DNA oligonucleotides, and later transcribes these into RNA. Thus, bait sequences in eArray are specified in terms of DNA bases (A, C, G, T). Additional annotation can also be included with baits, such as the associated genomic interval, chromosomal location, gene symbols, and accession numbers. For the SureSelect Target Enrichment application type, bait sequences can be in either sense (+) or antisense (–) orientation, and libraries can contain baits in either or both orientations.

You can work with baits in several ways:

Search for baits – eArray lets you retrieve baits that already exist within eArray. With Search Your Baits, you can retrieve baits based on single or multiple search terms. You can search for baits based on a specific type of annotation or accession, or all types. In addition, you can limit the search by species, bait length, associated bait groups or libraries, and folder location within eArray.
Upload baits – You can prepare a file that contains bait data and upload it to your account in eArray. You can also create a new bait group based on the baits in the uploaded file.
Bait Tiling – This process creates baits that evenly cover specified genomic regions or transcript sequences of a given species. See Bait Tiling (SureSelect Target Enrichment) and Bait Tiling (SureSelect RNA Enrichment). You can customize the tiling process for specific sequencing technologies and protocols, as well as adjust the density of tiling. To help you define the genomic regions for Bait Tiling, eArray provides Interval Finder searches, which return the genomic intervals that are associated with annotation values that you specify, and Exon Interval Finder searches, which return exonic genomic intervals.

In the SureSelect Target Enrichment application type, for Agilent Catalog libraries, you can use Bait Tiling to add baits for additional genomic regions that are not otherwise represented. You first use the Bait Tiling wizard create a new custom library (a supplemental library) that contains the desired additional baits, and then create a combined library that contains the selected Agilent Catalog library (the base library) and the new supplemental library.