Oncomine™ Immune Response Research Assay - FAQs

查看更多产品信息 Oncomine™ Immune Response Research Assay - FAQs (A32881)

13 个常见问题解答

With the Oncomine Immune Response Research Assay, how many samples can I multiplex per run?

Multiplexing can be done with 1-4 samples on the PGM 318 or S5/S5XL 520 chips, or with 2-8 samples on the S5/S5XL 520 chip. This enables flexibility for small-to-large retrospective profiling studies.

Which RNA isolation method do you recommend for use with the Oncomine Immune Response Research Assay?

We recommend using the RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Cat. No. AM1975).

Can I automate the Oncomine Immune Response Research Assay workflow?

Yes, automated library and template preparation are enabled with the Ion Chef System.

Where can I find the User Guide for the Oncomine Immune Response Research Assay?

The User Guide can be found here (https://tools.thermofisher.com/content/sfs/manuals/MAN0015867_OncomineImmuneRespnseResrchAssay_UG.pdf).

What functional annotation groups are covered by the Oncomine Immune Response Research Assay?

The Oncomine Immune Response Research Assay content includes 395 genes across 36 functional annotation groups. These groups comprise genes associated with lymphocyte regulation, cytokine signaling, lymphocyte markers, checkpoint pathways, and tumor characterization.

How many genes are covered in the Oncomine Immune Response Research Assay?

The Oncomine Immune Response Research Assay covers 395 genes.

What is the minimum input amount of RNA for the Oncomine Immune Response Research Assay?

For the Oncomine Immune Response Research Assay, the minimum input amount of RNA is 10 ng.

Can I download graphs/visualizations from the Oncomine Immune Response Research Plugin or Transcriptome Analysis Console (TAC) software?

The visualizations/graphs from the Torrent Suite Software plugin can be saved as images by right-clicking on the image and saving the image to your selected folder. The TAC also provides similar export options for the graphs to be downloaded to your computer.

Why am I unable to visualize certain parts of the wikipathways in the Transcriptome Analysis Console (TAC) software?

The TAC currently does not provide pathway analysis for small panels such as the Oncomine Immune Response Research Assay.

What are the input files for the Transcriptome Analysis Console (TAC)?

The TAC needs expression data in .chp file format. The Oncomine Immune Response Research Plugin automatically generates these .chp formatted files. In addition, the TAC needs to be configured for analysis of the Oncomine Immune Response Research Assay data with these two files: the Transcripts Annotation file (https://s3.amazonaws.com/IonTorrent/usbupdate/TAC_4.0/Immune-response.transcript.csv) and TAC Analysis Parameters file (https://s3.amazonaws.com/IonTorrent/usbupdate/TAC_4.0/Immune-response.TAC_ARRAY_CONFIG). Your local support specialist can provide the bed file for the panel.

What outputs does the Oncomine Immune Response Research Plugin produce?

The plugin produces the following files:
-Summary report for all barcodes or samples processed in the same run
-Absolute read counts
-RPM data
-Expression data normalized by mean expression of housekeeping genes (scaled log2)
-CHP files derived from RPM
-CHP files derived from data normalized with housekeeping genes
-Background expression data from negative controls, genomic DNA, & H20

Is the Transcriptome Analysis Console (TAC) tool freely available?

Yes, the TAC tool is available for free. It can be downloaded from this link (https://downloads.thermofisher.com/TAC/TAC_4.0.2/TAC4x64.exe).

How do I get the Oncomine Immune Response Research Plugin?

The Oncomine Immune Response Research Plugin is available in the Torrent Suite Software (TSS) as an update to TSS v5.2.1.