Parameter
Instructions/Details
Library Category
(Read-only) eArray supports RNA Capture libraries, which retrieve specific RNA species from a pool of RNAs.
Design Options
Design Job Name
Type a name to identify this Bait Tiling job.
Sequencing Technology
From the list, select the type of sequencing instrument that you will use.
Sequencing Protocol
Select the desired protocol. In the list, eArray shows the protocol(s) that are available for your selected sequencing technology.
Bait Length
(Read-only) eArray supports a bait length of 120 nucleotides.
Bait Tiling Frequency
Select the desired tiling frequency. This parameter controls the density of tiling. Agilent recommends that you use a Bait Tiling frequency of 2x.
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1x – eArray tiles baits end-to-end over the target in a single layer.
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2x – eArray overlaps baits by 50% as it tiles each target. Two baits cover each base in each target.
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3x – eArray overlaps baits as it tiles each target so that three baits cover each base in each target.
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4x – eArray overlaps baits as it tiles each target so that four baits cover each base in each target.
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10x – eArray overlaps baits as it tiles each target so that ten baits cover each base in each target.
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Note: The exact density of tiling may differ slightly from that indicated above at the extreme 5' and 3' ends of each target.
Keep only unique baits
By default, if the Bait Tiling process produces two or more baits that have the same sequence, eArray includes only one copy of the bait when you create a bait group from the Bait Tiling results. To include all copies of such baits, clear this option.
Target Details
Target Type
Select one of these options:
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Transcript Targets – Tiles baits either to the transcript sequences in an uploaded file, or to the sequences that are associated with uploaded GenBank accessions. If you select this option, the items described below in Upload Options and Transcriptome Details appear.
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Genomic Intervals – Tiles baits to specific genomic intervals in a species that you enter or upload. If you select this option, the items described below in Genome Build and Genomic Intervals appear.
Species
Select the species that is associated with the target sequences.
(Upload Options)
(Available if you select Transcript Targets in Target Type) Select one of these options:
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Upload in FASTA Format – Lets you upload a FASTA format file that contains the base sequences of the transcripts to be tiled. The file must be a text file (*.txt) in zip format. Each transcript can be up to 120 kb in length, and the total targeted sequence length can be up to 5 Mb.
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Upload as GenBank Accessions – Lets you upload a *.txt file that contains GenBank accession values, one per line. The transcripts associated with these accessions can each be up to 120 kb in length, and the total targeted sequence length can be up to 5 Mb.
In either case, follow these steps to upload the file:
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Next to the desired option, click Browse.
A Choose File dialog box appears. -
Select the desired file, then click Open.
The name of the file appears in the previous dialog box, in File Name. -
Click Upload File.
eArray uploads the selected file.
Genome Build
(Read-only, appears if you select Genomic Intervals in Target Type) Shows the currently available genome build in eArray for the selected species.
Genomic Intervals
(Available if you select Genomic Intervals in Target Type) Type the desired target genomic intervals in the box. Use the format chrX:<start>-<end>. Example: chr21:1000000-1500000). Separate multiple intervals with pipe "|" characters. Each interval can be up to 120 kb in length, and the total targeted sequence length can be up to 5 Mb.
Alternatively, you can upload a list of intervals. Create the list as a *.txt file with one interval per line. End each line with a new line character — that is, in a word processor, press Enter at the end of each line. Then follow these steps:
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Next to the Genomic Target Intervals box, click Upload.
A dialog box appears. -
Click Browse.
A Choose File dialog box appears. -
Select the desired file, then click Open.
The location of the file appears in the appropriate box. -
Click Upload File.
eArray uploads the list of intervals, and displays them in pipe-separated format in the Genomic Target Intervals box.
Transcriptome Details
Transcriptome Options
(Available if you select Transcript Targets in Target Type) eArray uses the transcriptome file as a similarity database to identify potential cross-hybridization problems.
Select one of these options:
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Select Agilent-Provided Transcriptome (by Species) – Uses one of Agilent's available species transcriptome databases. If a transcriptome is available for your species of interest, select this option. These databases have been specifically constructed for use in bait design. Select the desired species from the list.
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Upload Transcriptome File – Uses a FASTA format transcriptome file that you upload as the similarity database. If you select this option, click Browse. Select the desired transcriptome file, then click Open. The location of the file appears in the box. eArray requires a compressed (*.zip format) version of the file.