Ion 510™ & Ion 520™ & Ion 530™ Kit – Chef (2 sequencing runs per initialization) - FAQs

View additional product information for Ion 510™ & Ion 520™ & Ion 530™ Kit – Chef (2 sequencing runs per initialization) - FAQs (A34461)

18 product FAQs found

Why did my Ion Chef Instrument stop during a run?

- The instrument may have encountered an error. We recommend recording the error shown on the instrument display, then tapping OK. For further assistance, contact Technical Support at techsupport@thermofisher.com.
- A consumable may have been improperly loaded. We recommend ensuring that all consumables are correctly loaded. For instructions, see the user guide for your templating kit. For further assistance, contact Technical Support at techsupport@thermofisher.com.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

Why is the door of the Ion Chef Instrument not opening?

- An obstruction may be present on or around the door mechanism. We recommend removing the obstruction blocking the door, then resuming normal instrument operation.
- The instument may be experiencing a hardware or software error. We recommend contacting Technical Support at techsupport@thermofisher.com.C8

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

Why does the Ion Chef Instrument not display the home screen when powered on?

Multiple causes are possible. We recommend powering off the instrument, waiting for 30 secs and then powering on the instrument. If you continue to experience the issue, contact Technical Support at techsupport@thermofisher.com.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

What control do you recommend using with the Oncomine TCR Beta-LR Assay?

We recommend using T Cell Leukemia (Jurkat) Total RNA (Cat. No. AM7858) as a control. T cell Leukemia (Jurkat) Total RNA is derived from a cell line consisting of a single T cell clonotype. Running the Oncomine TCR Beta-LR Assay on Jurkat Total RNA should enable detection of a single clonotype.

Are there any BED files for the Oncomine TCR Beta-LR Assay?

Unlike other AmpliSeq panels, there are no BED files and no reference is needed. All downstream analysis takes place in Ion Reporter Software.

Can I quantitate the Oncomine TCR Beta-LR Assay library with the Ion Library Equalizer Kit?

We have tested the Ion Library Equalizer Kit with this kit for library quantitation and it does function, but manually balancing library input into the Ion Chef instrument is preferred.

What version of Torrent Suite Software and Ion Reporter Software can be used with the Oncomine TCR Beta-LR Assay?

Torrent Suite Software 5.6 and Ion Reporter Software 5.6 are needed to generate reports. In Torrent Suite Software 5.6, two Planned Run templates are provided for use with the Oncomine TCR Beta-LR Assay.

Can I run the Oncomine TCR Beta-LR Assay on the Ion PGM System?

The Oncomine TCR Beta-LR Assay has been developed and verified for use on the Ion GeneStudio S5 Series System. The assay can be used with the Ion PGM System, however, this instrument configuration is not supported.

What are the components of the Oncomine TCR Beta-LR Assay?

Here are the components of the Oncomine TCR Beta-LR Assay:

- Oncomine TCR Beta‑LR Panel
- Ion AmpliSeq Library Kit Plus
- Ion Select Barcode Adapters

What is the concentration of the primer pool in the Oncomine TCR Beta-LR Assay?

The primer pool is at 5X concentration.

What are the amplicon read lengths in the Oncomine TCR Beta-LR Assay?

The Oncomine TCR Beta-LR Assay enables long-read RNA sequencing (up to 400 bp amplicon length) for complete characterization of the T cell receptor Beta (TCR Beta) chain, including all three complementarity-determining regions (CDR1, 2, and 3) of the variable gene. This enables allele-specific interrogation of TCR Beta to potentially predict drug-mediated adverse events.

How many primer pools does the Oncomine TCR Beta-LR Assay kit contain?

The primers are provided as a single pool.

With the Oncomine TCR Beta-LR Assay, how many samples can I multiplex on each chip?

Up to 16 samples can be multiplexed on an Ion 530 chip, up to 4 samples can be multiplexed on an Ion 520 chip, and up to 4 samples can be multiplexed on an Ion 318 chip.

What research sample types are compatible with the Oncomine TCR Beta-LR Assay?

A variety of research sample types including fresh-frozen tissue, whole blood, and sorted T cells are compatible with the Oncomine TCR Beta-LR Assay.

Why are immunologists and immuno-oncologists interested in T cell repertoire sequencing research?

T cell repertoire sequencing helps:

- To characterize diversity and study features of T lymphocytes in blood and infiltrated tumors
- To study variable gene polymorphisms implicated in autoimmune disease or immune-mediated adverse events
- To study the production and function of therapeutic or engineered T cells

How many samples can I analyze with the Oncomine TCR Beta-LR Assay?

This kit is good for 24 samples.

What does the Oncomine TCR Beta-LR Assay measure?

The Oncomine TCR Beta-LR Assay is an RNA-based next-generation sequencing (NGS) research assay that enables the characterization of the T cell receptor Beta (TCR Beta) sequences including all three complementarity-determining regions (CDR1, 2, and 3) of the variable gene. The assay measures T cell repertoire diversity as well as clonal expansion, and allows for identification of allele-specific polymorphisms.

How many runs per initialization can I perform on the Ion S5 and Ion S5 XL Systems, when using in conjunction with the Ion Chef?

You can perform one or two runs per initialization depending on the kit you have:

- Ion 510 & Ion 520 & Ion 530 Kit - Chef (1 sequencing run per initialization), Cat. No. A34019)

- Ion 510 & Ion 520 & Ion 530 Kit - Chef (2 sequencing runs per initialization), Cat. No. A34461)

- Ion 540 Kit - Chef (1 sequencing run per initialization), Cat. No. A27759

- Ion 540 Kit - Chef (2 sequencing runs per initialization), Cat. No. A30011

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.