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Ion Xpress™ Barcode Adapters 1-96 Kit - FAQs

View additional product information for Ion Xpress™ Barcode Adapters 1-96 Kit - FAQs (4474517)

11 product FAQs found

Ion Xpress Plus Fragment Library Kit (Cat. No. 4471269) および Ion Plus Fragment Library Kit (Cat. No. 4471252) のユーザーガイドには、 low (50-100 ng) およびhigh (1 µg) DNA inputのプロトコルがありますが、どちらに従えばよいでしょうか?

DNA inputの量は、サンプルからどのくらいのDNA量が抽出できるのか、どのようなアプリケーションに興味があるのかによって決まります。例えば、多様性に富んだライブラリーを作製したい場合（脊椎動物のゲノムライブラリーなど）は、1 μg のDNA inputから始めていただき、超音波で断片化を行い（バイアスを軽減するため）、ライブラリー増幅を行わない（多様性を維持するため）ことをお勧めします。

input量の少ないプロトコル (50-100 ng)は、ampliconライブラリーなど多様性が少ないライブラリーやDNAの収量の少ないサンプルに使用します。100 ng以下のDNA inputの場合、最終的なライブラリー増幅が必要になる可能性があります。また、特定のアプリケーションはlow DNA inputには対応していなく、high DNA inputが必要となる（TargetSeq、ChIP-Seq、Mate-Pairedライブラリーなど)ことにご注意ください。

Do libraries constructed with the Ion Xpress Barcode adapters require balancing to help ensure equal representation on the Ion PGM or Proton instrument sequencing run?

No, the Ion Xpress Barcode adapters are designed with a 3 bp adapter sequence (GAT) at the 3' end of each barcode to help minimize adapter ligation bias. When pooling barcoded libraries, accurate library quantification is extremely important to help ensure even barcode representation on the sequencing run.

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

How many fragment or amplicon libraries can be made per barcode with the Ion Xpress Barcode Adapters kits?

The Ion Xpress Barcode Adapters kits are available as a set of 96 (Cat. No. 4474517) or in sets of 16 (Cat. Nos.4471250, 4474009, 4474518, 4474519, 4474520 or 4474521). Each barcode kit is sufficient for preparing ? 10 libraries per barcode (10 x 16 libraries or 10 x 96 libraries) for 100 ng input, or 2 libraries per barcode for 1 µg input.

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

How many samples can I multiplex on a single chip for sequencing on the Ion PGM or Proton System?

The number of samples that can be multiplexed in a single sequencing run depends on the capacity of the chip, the size of the library, and the required coverage. A table of approximate capacities based on the size of the library and chip can be found in the Ion Ampliseq Preparation User Guide (https://tools.thermofisher.com/content/sfs/manuals/MAN0006735_AmpliSeq_DNA_RNA_LibPrep_UG.pdf) within the section “Strategies for combining Ion Ampliseq libraries.”

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

What are the differences between the Tag Sequencing Barcode Set 1-24 (Cat. No. A31830) and the Ion Xpress Barcode Adapters (Cat. No. 4474517)?

The TAG Sequencing Barcode Set contains adapters designed for Oncomine workflows using AmpliSeq HD technology and they can be used only with those library kits. This type of chemistry uses a molecular tag in order to track polymerase errors and increase the assay sensitivity. The Ion Xpress Barcode Adapters are not an alternative of the TAG Sequencing Barcode Set and vice versa. The list of the barcodes set compatible with a library kit is specified in the library manual.

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

How many samples from the Oncomine Comprehensive Assay Plus, manual library preparation can I run on the Ion 550 Chip?

We recommend sequencing up to 5 DNA or RNA samples (4 samples and a non-template control (NTC)) on a single Ion 550 Chip.

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

What is included in the Oncomine Comprehensive Assay Plus, manual library preparation?

The Oncomine Comprehensive Assay Plus, manual library preparation (Cat. No. A46721) is designed to prepare barcoded sample libraries from DNA and RNA. The kit consists of Oncomine Comprehensive Assay Plus DNA (2-pool) (Part No. A45615), RNA Oncomine Comprehensive Assay v3M (2-pool) (Part No. A33637), and two kits of Ion AmpliSeq Library Kit Plus (Cat. No. 4488990). Sufficient reagents are provided to prepare libraries from 24 samples.

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

How much of each sample is needed for the Oncomine Comprehensive Assay Plus, manual library preparation?

10 ng of nucleic acid input per pool (20 ng of DNA and 20 ng of RNA) isolated from FFPE samples, including fine needle biopsies, is needed for the Oncomine Comprehensive Assay Plus, manual library preparation.

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

What types of sample is the Oncomine Comprehensive Assay Plus, manual library preparation compatible with?

The assay is optimized for use with formalin-fixed paraffin embedded (FFPE) samples.

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

What is the Oncomine Comprehensive Assay Plus, manual library preparation?

The Oncomine Comprehensive Assay Plus, manual library preparation (Cat. No. A46721) is a targeted, next-generation sequencing (NGS) assay that enables the detection of single nucleotide variants (SNVs), insertions and deletions (INDELs), copy number variations (CNVs), gene fusions, splice variants, tumor mutational burden (TMB), and microsatellite instability (MSI) across 500+ unique genes. This version of the assay is designed for manual library preparation, not for automated library preparation using the Ion Chef System.

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

I am planning to use the Oncomine BRCA Research Assay, Manual Library Preparation (Cat. No. A32840). Which other products would need I to order?

Here are the products you would need to order:

- Ion Xpress Barcode Adapters Kits
- Agencourt AMPure XP (Beckman Coulter Cat. No. A63880 or A63881)
- Ion Library Equalizer Kit (Cat. No. 4482298)