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Publication Number MAN0010907 - Ion AmpliSeq Designer 7.4: Getting Started (5.9 MB PDF download)
To make RNA Gene Fusions panels with a combination of Gene Fusion and Gene Expression Assays (GEX), follow the steps below.
Important: | For successful panels, you must have at least 12 GEX assays per panel. We provide 12 default GEX assays for each panel that you may accept or replace with targets of your choice. For panels requiring two pools, the GEX assays will be split between the two pools. |
If you are already on Ampliseq.com working in another application, click the “home” icon in the navigation bar to return to the main page:
Select RNA Gene Fusion designs (multi-pool) button, in application type.
Note: Human (RefSeq/Ensembl) is the only genome permitted with this panel type.
Repeat step 4 a-c to add additional targets.
Ion AmpliSeq Designer uploads the targets and checks them. Once complete, a status message appears at the top of the screen: either “Target saved successfully” in green text, or “# duplicate fusions ignored” in red text.
Now add your gene expression assays. Every pool is required to have 12 gene expression assays, and we have pre-selected them to get you started. If you want to pick your own gene expression assays, delete the proposed ones and add your own gene expression targets by gene symbol or RefSeq transcript accession.
At the top of the screen, enter valid gene symbols (preferably an HGNC-approved symbol) or valid RNA RefSeq accession numbers as in the example below and click Add target.
Alternatively, you can upload your own gene expression assays. Please click Input Specification link in the software user interface for more details and a CSV template for creating your own list of genes or RefSeq Accession numbers.
Note: If you would like to restore the pre-populated gene expression assays, click the Restore pre-populated genes button and they will be restored.
Confirm your submission.
Note: You can submit a second submission if required.
Acknowledgement of the submission appears at the top of the screen and is also sent to you via email.
When your fusion results are ready, you will receive an email instructing you to review the results in Ion AmpliSeq Designer.
Note: You may need to check your Spam folder and move the email to your Inbox and therefore enable its links.