Add a Target by Gene Name

1. Select the Gene tab.
2. In the Gene Name field, begin entering a gene name, and then select it from the drop-down list.
3. Select a Targeting Option:
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.
[Optional] To include untranslated regions, select the 3ʹ UTR and the 5ʹ UTR checkboxes.
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
Full Region—Targets probes across the entire region, from start to stop, in introns, exons, and intergenic regions.
[Optional] In the Up and Down fields, enter the number of additional bases to add to both ends of the gene to capture flanking regulatory regions.
4. Select a Probe Spacing to control the center-to-center spacing of the enrichment probes within the region of interest:
Standard—230 bp
Intermediate—180 bp
Dense—120 bp
Adjacent—80 bp
Overlapping—60 bp
5. [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.

6. Select Add Gene.

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