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Ovation® RNA-Seq System V2

Rapid and sensitive whole transcriptome RNA amplification process for preparing amplified cDNA from total RNA or poly(A) selected mRNA.
Overview
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Tab 01 / Overview
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Product News: User Guide Update

The look and feel of the user guide for Ovation RNA-Seq System V2 (M01206 v9) has been updated. The changes to the user guide are primarily in wording and organization to improve clarity. There are no changes to the protocol.

 

Selection guide

RNA-Seq sample preparation for complete transcriptome representation from picograms of total RNA

cDNA synthesis, also known as reverse transcription, generates complementary DNA (cDNA) from an RNA template. Synthesized cDNA is ready to be used for multiple downstream applications including RNA-Seq and archival storage for future analyses.

The Ovation RNA-Seq System V2 provides a rapid and sensitive whole transcriptome RNA amplification process for preparing amplified cDNA from total RNA or poly(A) selected mRNA. This kit provides high-quality cDNA samples from as little as 500 pg to 100 ng of total RNA in just four and a half hours.

This kit features our unique amplification technology (single primer isothermal amplification (SPIA)) which allows the ability to generate more molecules of cDNA compared to conventional reverse transcription methods. For challenging samples, it is important that the sequencing dataset appropriately captures the limited genomic information available in the biological samples. The SPIA cDNA amplification expands this limited information, improving the sensitivity of downstream applications like NGS, in particular for rare transcript detection. The product is particularly useful for the detection of rare transcripts, viruses, and unknown pathogens.

With over 900 publications and applications in multiple areas of life science studies, this technology has been proven to generate cDNA from many challenging samples including COVID-19 samples from nasal swabs.


Benefits of Ovation RNA-Seq System V2:


Low RNA input requirements:
  • Requires just 500 pg – 100 ng total RNA to provide RNA-Seq data from mRNA and non-polyadenylated transcripts

More complete transcriptome representation:
  • Provides enhanced depth of transcriptome coverage with no 5’/3’ positional bias

Fast, easy protocol based on proven technology:
  • Uses Tecan’s powerful SPIA® technology to produce double-stranded cDNA, ready for RNA-Seq library construction in four and a half hours without poly(A) selection or rRNA depletion

Applications

  • RNA Sequencing
  • Sample archiving




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Tab 02 / Highlights
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Simple, fast workflow that integrates seamlessly into multiple downstream workflows

  • Workflow completed in under 5 hours
  • Micrograms of DNA obtained for downstream applications such as RNA-Seq, microarrays and sample archiving


The cDNA produced by the Ovation® RNA-Seq System V2 may be used as input for Tecan’s Ovation® library systems or used with other library construction kits suitable for double-stranded cDNA samples.

Obtain reproducible sequencing results

  • High concordance seen with all sample input amounts
  • Proprietary combination of enzymes and primers allows for preferential priming of non-rRNA sequences with reduced number of reads from rRNA
Show more

Reproducibility of libraries from Ovation Library Systems

Concordance plots demonstrating reproducibility of the integrated workflow using Ovation® RNA-Seq System V2 with Tecan’s Ovation®  Rapid Library System with differing amounts of SPIA cDNA input to the library construction workflow. RPKM plots average R ≥ 0.9 for different library inputs.

Sequencing alignment metrics with MAQC samples

Data was generated using 2 ng of Total RNA from either Human Brain (MAQC B) or Universal Human Reference (MAQC A) input to the Ovation®  RNA-Seq System V2 followed by library construction using the Encore NGS Library System I. The resulting libraries were sequenced on the Illumina Genome Analyzer IIx with 40 bp single-read sequencing.

Obtain even exon coverage

  • Even distribution of sequencing reads across exons as shown with GAPDH and beta-actin transcripts
Show more

Even distribution of sequencing reads across exons as shown with beta-actin transcripts

Total RNA from Human Brain (MAQC B, 2 ng) was amplified using either the original Ovation®  RNA-Seq System or the Ovation® RNA-Seq System V2 and libraries constructed using the Encore®  NGS Multiplex System I. Single-read sequencing results were obtained using the Illumina Genome Analyzer IIx platform with 40 bp reads. Results depicted here are for Beta-Actin gene.

Improved exon read coverage as shown with GAPDH transcripts

Total RNA from Human Brain (MAQC B, 2.ng) was amplified using either the original Ovation® RNA-Seq System or the Ovation® RNA-Seq System V2 and libraries constructed using the Encore®  NGS Multiplex System I. Single-read sequencing results were obtained using the Illumina Genome Analyzer IIx platform with 40 bp reads. Results depicted here are for GAPDH gene.

Obtain high confidence in data for differential gene expression

  • Highly concordant results seen when compared to differential gene expression data from quantitative PCR
  • No significant compression of data as evidenced by the slope

 

Differences between Log2 transformed expression values for MAQC A and MAQC B samples, RNA-Seq data using 2 ng total RNA as input are plotted on the X axis, qPCR data are plotted on the Y axis. 659 TaqMan probes that uniquely map to the RefSeq annotations used in the RPKM calculations are represented. RPKM stands for Reads Per Kilobase of exon model per Million mapped reads. The RPKM measure of read density reflects the molar concentration of a transcript in the starting sample by normalizing for RNA length and for the total read number in the measurement.




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Tab 03 / Specifications
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Specifications

Specification

Specification/Description

Compatible Platform

Compatible Platform

Illumina HiSeq, MiSeq, NextSeq, MiniSeq

Starting Material

Starting Material

Total RNA

Input Amounts

Input Amounts

500 pg – 100 ng




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Tab 04 / Faq
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FAQ

Getting started

What materials are provided with the Ovation RNA‑Seq System V2?

The Ovation RNA‑Seq System V2 provides all necessary buffers, primers and enzymes for first strand synthesis, second strand synthesis and amplification. The kit also provides nuclease-free water and Beckman Coulter Agencourt Beads for second strand reaction cDNA purification. Beads are not provided for the final purification step.

What equipment is required or will be useful?

Required equipment includes a microcentrifuge, pipettes, vortexer, a thermal cycler, a spectrophotometer and a magnetic plate for 0.2 mL tubes, strips, or plates. An Agilent Bioanalyzer or Fragment Analyzer may also be useful for optional analytical tests. A system for fragmentation, such as a Covaris system, is required for use with most downstream library preparations.

What additional consumables does the user need?

For the SPIA cDNA purification step, we recommend using the QIAGEN MinElute Reaction Cleanup Kit. Refer to Appendix A in the User Guide other purification options.

Can Ovation RNA-Seq System V2 be used for qPCR, archiving and NGS?

Yes, Ovation RNA-Seq System V2 generates ds cDNA that can be used for all of these purposes. Resulting cDNA may be stored at -20C for at least six months following purification.

What library preparation kits are compatible with the ds-cDNA generated by RNA-Seq System V2?

Ovation RNA-Seq System V2 can be used with any ds-DNA library preparation kit.

Input recommendations

What methods do you recommend for RNA isolation?

We recommend a column-based method, including:

  • Norgen Biotek Total RNA Purification Kit
  • Zymo Research Quick-RNA™ Kits
  • Arcturus PicoPure® RNA Isolation Kit
  • Ambion PureLink® RNA Mini Kit
  • Qiagen RNeasy Kits

Organic methods such as TRIzol® Reagent should be subsequently followed with a column-based clean-up method.

Can I use TRIzol® or other phenol-chloroform based extractions for RNA isolation?

We do not recommend the use of TRIzol or similar methods as any carryover of organic solvents may inhibit downstream enzyme activity. If using TRIzol extracted RNA, we recommend using a column-based purification of the RNA prior to input into the kit.

Can I use carrier RNA during RNA isolation?

We do not recommend the use of carriers during RNA isolation. If a carrier is required, please contact Tecan NGS Technical Support for more information.

How much total RNA do I need for amplification?

The Ovation RNA‑Seq System V2 can be used with purified total RNA in the range of 500 pg to 100 ng. Input amounts outside this range may produce unsatisfactory and variable results.

Do I need to perform an rRNA depletion or poly(A) enrichment step before processing samples with the Ovation RNA‑Seq System V2?

rRNA depletion or Poly(A) enrichment is not required. The input range of 500 pg to 100 ng refers to total RNA.

Can I use poly(A) RNA as an alternative to total RNA?

Yes, if you are primarily interested in sequencing reads from mature coding transcripts then poly(A) RNA may be substituted for total RNA. Tecan has demonstrated that poly(A) RNA can be isolated from 5 to 500 ng of total RNA and used as input into the Ovation RNA-Seq System V2 protocol with good results. We recommend using at least 500 pg of isolated poly(A) RNA.

Can DNA be used as input for the Ovation RNA-Seq System V2?

No. The Ovation RNA-Seq System V2 is designed to amplify RNA, not DNA.

Do I need to use high-quality total RNA?

The Ovation RNA-Seq System V2 is designed to work with purified total RNA. When using purified total RNA, samples should be of high molecular weight with little or no evidence of degradation. While it is impossible to guarantee the highest levels of performance when using RNA of lower quality, this system should allow the successful analysis of somewhat degraded samples. With such samples, users may experience lower amplification yields and should plan to use relatively higher RNA inputs.

Do you recommend DNase treatment of purified total RNA samples?

Yes. When using purified total RNA samples, contaminating genomic DNA may amplify during the process. For this reason we recommend DNase treatment during RNA purification.

Can RNA from any organism be used in the Ovation RNA-Seq System V2?

The Ovation RNA-Seq System V2 has been optimized for use with mammalian samples. The system should work with most non-mammalian samples, however, you may observe a higher percentage of rRNA than is seen with mammalian samples.

General workflow

Can I perform fewer than 4 reactions at a time?

We recommend a minimum batch size of 4 reactions. Smaller batch sizes may result in difficulty pipetting small volumes and lead to poor performance.

How much overage is recommended when making reagent master mixes for each step?

A minimum amount of overage should be used in master mixes to ensure the full nominal number of reactions in the kit. The amount of overage needed depends on sample batch size, pipetting accuracy, and viscosity of reagents.

We have found that 10% extra volume in the master mixes in this kit is sufficient for most experiments.

How many rounds of amplification are performed with the Ovation RNA‑Seq System V2?

This System performs a single round of amplification and is not designed to support multiple rounds of amplification.

Do I have to use the DNA/RNA primers supplied with the kit?

Yes. The Ovation RNA‑Seq System V2 will not work properly with other primers.

Does the Ovation RNA-Seq V2 System deplete ribosomal RNA?

Tecan’s Ovation RNA-Seq System V2 does not selectively deplete ribosomal RNA. You may, however, observe a reduction in the amount of ribosomal RNA content with this system when used on mammalian samples.

Where can I safely stop in the protocol?

You may safely stop after the SPIA Amplification step or final SPIA cDNA Purification and store the cDNA at -20 °C.

What purification methods do you recommend?

For the final SPIA cDNA purification step we recommend using the QIAGEN MinElute Reaction Cleanup Kit. Alternative purification methods can be found in Appendix A of the User Guide.

SPRI bead purifications

What is the difference between RNAClean XP and AMPure XP SPRI beads? Can both be used interchangeably?

RNAClean XP beads are certified to be RNase and DNase free. We have tested both RNAClean XP and AMPure XP beads in our kits and observe no difference in performance between products.

What magnetic separation devices do you recommend for the SPRI bead purifications?

Due to the large number of commercially available magnets, we do not have a comprehensive list of compatible products. However, many magnets are compatible. As long as the magnet is strong enough to clear the solution of magnetic beads, it can be applied to the system. We have the following guidelines for selecting a magnetic separation device:

  1. Use a magnet designed for 0.2 mL tubes (PCR tubes), tube strips, or plates. Compared to magnets that are designed for 1.5 mL tubes, these minimize loss that can occur when samples are transferred from one tube to another.
  2. Prior to purchasing, check the manufacturer’s specifications for minimum and maximum volumes that can be effectively treated.
  3. Test the magnet with a mock purification to ensure the magnet will effectively clear the solution under the conditions in the Tecan workflow. This is also helpful to gain familiarity with the purification workflow.

How can I ensure maximum recovery of sample from the SPRI bead purification?

  1. Allow the SPRI beads to reach room temperature before use; cold beads result in lower yields.
  2. Ensure that the beads are fully resuspended in solution before adding to the sample.
  3. Always use fresh ethanol during the washing steps. When preparing the ethanol, measure out the ethanol and water separately to ensure the desired ethanol concentration is obtained.
  4. Mix the bead suspension and sample thoroughly to ensure maximum binding of the samples to the beads.

cDNA quantification and qualification

How do I measure my SPIA cDNA yield?

Refer to the Measuring SPIA cDNA Yield and Purity protocol on page 19 in the User Guide for guidance.

How much SPIA cDNA can I expect from a single reaction?

You should expect a minimum yield of 2.5 μg of SPIA cDNA from a starting input of 500 pg of good quality total RNA.

Is the cDNA yield dependent upon the quantity of total RNA input?

Yes, higher RNA inputs will produce higher yields. However, at inputs of above 100 ng, the yields may become variable without increasing.

Does the Ovation RNA‑Seq System V2 generate product in the absence of RNA input?

Due to the high sensitivity inherent in our amplification systems a non-specific product can be generated in the absence of input RNA. However, in the presence of even a very small amount of RNA the amplified cDNA has been demonstrated to be specific. To minimize the potential for carryover of non-specific amplification products into future reactions, we recommend using a low-input (i.e. 50-100 pg) rather than a no-input (i.e. negative) control.

Can I use an Agilent Bioanalyzer or Fragment Analyzer to evaluate the amplification products?

Yes. Refer to Appendix B of the User Guide for guidelines.

What size cDNA is generated by the Ovation RNA‑Seq System V2?

Figure 3 (page 27) in the User Guide shows a representative fragment distribution pattern obtained with 2 ng of high quality Universal Human Reference and human brain total RNA samples.

Can I use the final purified SPIA cDNA for qPCR analysis?

Yes. qPCR can be performed on the final SPIA cDNA before or after purification. Guidelines for qPCR analysis of SPIA cDNA can be found in Appendix D of the User Guide.




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Tab 05 / Literature
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Literature

Type
Title
No
User Guide
Ovation RNA-Seq System V2
M01206 V9
Quick Protocol
M01207 V3
Data Sheet
Ovation RNA-Seq System V2
400984 V1.1
Application Note
M01287 V1.2
Safety Data Sheet
Ovation RNA-Seq System V2
 
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