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View additional product information for Ion AmpliSeq™ Transcriptome Mouse Gene Expression Panel, Chef-Ready Kit - FAQs (A36412)
16 product FAQs found
The Ion AmpliSeq RNA ERCC Companion Panel provides enough reagents to perform 96 manual reactions or 48 automated reactions.
To view data from the Ion AmpliSeq RNA ERCC Companion Panel, Torrent Suite Software version 5.10 or later is required and Version 5.10.0.3 or later of the ERCC_Analysis plugin for Torrent Suite Software is required.
We do not recommend using the Ion AmpliSeq RNA ERCC Companion Panel with FFPE samples or with any panels besides human and mouse Ion AmpliSeq transcriptome gene expression panels.
We recommend adding 1 µL of the Ion Ampliseq RNA ERCC Companion Panel per manual target amplification reaction and 8 µL per primer pool for an automated target amplification reaction on the Ion Chef Instrument.
The Ion AmpliSeq ERCC Companion Panel is compatible with Ion AmpliSeq Transcriptome Human Gene Expression Kit and Ion AmpliSeq Transcriptome Mouse Gene Expression Kit (not recommended for use with FFPE samples or panels outside of Ion AmpliSeq Human or Mouse Transcriptome kits). With the addition of the Ion AmpliSeq RNA ERCC Companion panel to your Ion AmpliSeq RNA panel, dynamic range and sensitivity can be similarly evaluated in Ion AmpliSeq RNA libraries that are prepared from RNA samples containing the ERCC RNA Spike-In Mix
The Ion AmpliSeq RNA ERCC Companion Panel consists of 10 primer pairs targeting 10 transcripts from the ERCC RNA Spike-In Mix representing a 13log2 dynamic range. Chosen for general GC balance and amenability for linear amplification (TaqMan qPCR), the selected ERCC targets produce R2 > 0.9 under normal experimental conditions.
The Ion AmpliSeq RNA ERCC Companion Panel is compatible with both manual and chef-ready versions of human and mouse Ion AmpliSeq transcriptome gene expression kits:
- Ion AmpliSeq Transcriptome Human Gene Expression Kit (Cat. No. A26325, A26326, or A26327)
- Ion AmpliSeq Transcriptome Mouse Gene Expression Kit (Cat. No. A36553, A36554, or A36555)
- Ion AmpliSeq Transcriptome Human Gene Expression Panel, Chef-Ready Kit (Cat. No. A31446)
- Ion AmpliSeq Transcriptome Mouse Gene Expression Panel, Chef-Ready Kit (Cat. No. A36412)
The TAC needs expression data in .chp file format. The ampliseqRNA analysis Plugin automatically generates these .chp formatted files. In addition, the TAC needs to be configured for analysis of the Ion AmpliSeq Transcriptome Mouse Gene Expression data with these two files: the Transcripts Annotation file (https://s3.amazonaws.com/IonTorrent/usbupdate/TAC_4.0/AmpliSeq_Mouse_Transcriptome_V1_Designed.transcript.csv) and TAC Analysis Parameters file (https://s3.amazonaws.com/IonTorrent/usbupdate/TAC_4.0/AmpliSeq_Mouse_Transcriptome_V1_Designed.TAC_ARRAY_CONFIG). Your local support specialist can provide the bed file for the panel.
We recommend multiplexing up to 8 samples with this kit when using the Ion Proton system, or the S5 system with the 540 Chip.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
The Ion Xpress barcode kit is recommended for libraries with multiple samples.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
As a starting point, we recommend 5,000 reads per amplicon for an Ion AmpliSeq RNA library targeting from 1-200 genes. The actual sequencing depth required depends on the expression levels of the gene targets in your sample RNA so the sequencing depth can be scaled up or down if needed.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
The Ion AmpliSeq Mouse Transcriptome Panel requires at least 10 ng of RNA input, including FFPE samples.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
We recommend using MagMAX-96 Total RNA Isolation Kit (Cat. No. AM1830), PureLink RNA Mini kit (Cat. No. 12183018A), or PureLink RNA Micro Scale Kit (Cat. No. 12183016) for total RNA isolation from cells or tissues. For FFPE tissue, we recommend RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Cat. No. AM1975). For best results, treat the RNA with DNase prior to library generation.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
The Ion AmpliSeq Transcriptome Mouse Gene Expression Kit can be used with as little as 10 ng of total RNA from challenging samples such as FFPE tissue, or other samples with degraded RNA.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
The TAC currently does not provide pathway analysis for small panels such as the Oncomine Immune Response Research Assay.
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).