Add a Target Using Chromosome Coordinates

Select the Coordinate tab.

In the Chromosome drop-down box, select a chromosome of interest.

In the Chromosome free text fields, enter a coordinate or range of coordinates.

For example, to get UTRs for PIK3R1, enter Chr 5 : 67,522,462 - 67,597,649

Select a Targeting Option:

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CDS Only—Limits probe design to the coding sequence only. If a different targeting option is selected, probes are designed from derived CDS coordinates, as defined in the specified reference genome. DesignStudio can automatically target CDS within a defined region of interest. This option differs from Exon Only by excluding untranslated regions (UTRs) with the exons.

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[Optional] To include untranslated regions, select the 3ʹ UTR and the 5ʹ UTR checkboxes.

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Exon Only—Limits probe design to the exons within the target region only. When targeting a gene by exons, all exons (and no introns) are provided, where the 5’ and the 3’ exons include UTRs. Probes are designed from derived exon coordinates, as defined in the reference genome selected. DesignStudio can automatically target exons within a defined region of interest. The DesignStudio exon boundaries are identical to the UCSC hg19 build. Use the Coordinate tab to add a coordinate not included in the reference coordinates. See Add a Target Using Chromosome Coordinates

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Full Region—Targets probes across the entire region, from start to stop, in introns, exons, and intergenic regions.

Select a Probe Spacing to control the center-to-center spacing of the enrichment probes within the region of interest:

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Standard—230 bp

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Intermediate—180 bp

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Dense—120 bp

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Adjacent—80 bp

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Overlapping—60 bp

[Optional] Enter a label in the Label field.

Add multiple labels by separating them with a comma. You can use labels to filter and select targets.

Select Add Target.

The target is added to the table below the Add Targets panel.

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Add a Target Using Chromosome Coordinates