Frequently Asked Questions

NuGEN Illumina Protocol

Q1. What is the Illumina Solution?
The NuGEN Illumina Solution consists of a protocol described in an Application Note. The protocol describes the cDNA labeling method, lists the specific materials and reagents required, and provides source and order information. The technical report includes results from the validation of this protocol using Ovation and WT-Ovation-generated cDNA on the Illumina BeadArray platform.

Q2. What is the workflow for using the Illumina Solution?
The workflow consists of the following steps:

  • Define Sample type: Based on sample characteristics, choose one of NuGEN's amplification system products.
  • Amplify RNA: Obtain the appropriate amplification system and amplify RNA to yield amplified cDNA.
  • Label cDNA: Using the detailed protocol in Illumina Solution Application Note #2, label the amplified cDNA and proceed with hybridization to the Illumina whole genome expression arrays.

Q3. Which NuGEN amplification systems can I use with this protocol?
The NuGEN Illumina labeling protocol can be used with the Ovation™ RNA Amplification System V2 (Cat. #3100), the WT-Ovation™ Pico System (Cat. #3300), or the WT-Ovation™ FFPE System (Cat. #3400).

Q4. What sample types can I use with this protocol?
The sample type and characteristics primarily defines which amplification system is best to use. For example, for FFPE RNA the WT-Ovation FFPE System should be used while for whole blood RNA the Ovation WB solution is optimal. For typical small samples (above 500 pg) or compromised and partially degraded RNA samples the WT-Ovation™ Pico System is the standard amplification approach.

Q5. Does NuGEN support this protocol? Who do I call if I have questions or problems?
The labeling protocol is supported by NuGEN. In case of questions and problems you may contact the NuGEN Technical Support team.

Q6. Can I use alternate sources of reagents other than those specified in the technical report?
We have tested and validated the protocol using only the reagents and sources listed in the Application Note #2. If other reagents are used, NuGEN may not be able to support this protocol.

Q7. Are the Illumina hybridization and wash conditions different with this protocol?
The hybridization temperature is reduced to 48 degrees, but all the other conditions are exactly as outlined by Illumina for the BeadArrays.

Q8. Are the data analysis approaches different with this protocol?
No, we recommend you follow all data analysis procedures outlined by Illumina for BeadArrays.