Questions & Answers

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  • Should the NeoPrep System be placed in a pre-PCR or post-PCR area?

    Illumina recommends locating the instrument in a post-PCR laboratory, because the final product collected from the instrument is amplified libraries.

  • Do I need a mouse and keyboard for the NeoPrep System?

    The NeoPrep System has a touch screen monitor with on-screen keyboard to enable on-instrument configuration and set-up using the software interface. A mouse and/or keyboard can be connected via the external USB ports if preferred. The system can also be customized to disable the on-screen keyboard and only use an external keyboard, however, these are not provided with the system. 

  • Is a wash required before starting a NeoPrep run?

    All library prep processes occur within the tightly controlled environment of the NeoPrep library card. The NeoPrep instrument is dry and performs no liquid handling. The library card is disposed of at the end of the run, therefore no washes are required. Routine maintenance procedures are included in the NeoPrep Library Prep System Guide.


  • How are NeoPrep library concentrations reported?

    Library concentrations are reported on the NeoPrep Control Software screen after the run is complete. In addition, the final report can be accessed using the Access Logs function on the Welcome Screen. The run report can also be saved to a network drive by specifying an alternate output folder location on the System Configuration screen. The information is also streamed to BaseSpace if run was set-up in BaseSpace Prep tab.

  • How long can NeoPrep libraries remain on the instrument?

    Libraries can remain at room temperature on a library card for up to 3 days after a run is complete.

  • What is a NeoPrep library concentration when normalization is performed by the instrument?

    The complete protocol on NeoPrep results in 10 µl of 10 nM library after the library droplet is collected from the library card, diluted in RSB, and then separated from the oil using the library separation tubes.

    This is true if library prep, or library prep and quantification, or library prep, quantification, and normalization are selected during run setup.

    The NeoPrep reported quantification and normalization values take into account the library dilution in RSB.


  • What is included in a NeoPrep library prep kit?

    To perform a run on the NeoPrep System, a single-use NeoPrep System library prep kit is required. Each kit contains the following for a single run:

    • Assay specific reagent plate and guide affixed on the reagent plate
    • Assay specific reagent tubes
    • Oil vial and funnel
    • Library card
    • Library card guide
    • Library separation tube strips

    For specific library prep kit contents and storage conditions, see the appropriate library prep reference guide.

  • How do I dispose of NeoPrep reagents and consumables?

    The used library card contains hazardous materials. Personal injury can occur through inhalation, ingestion, skin contact, and eye contact. Wear protective equipment, including eye protection, gloves, and a laboratory coat. Handle the used library card as chemical waste. Dispose of it in accordance with the governmental safety standards for your region. Refer to the safety data sheets (SDSs) for the consumables in the kit that you are using for detailed environmental, health, and safety information and dispose of according to your institution and other requirements. SDSs are available on the Illumina website at

  • Can I use index adapters that are not provided with NeoPrep library prep kits?

    Do not use adapters other than those provided in NeoPrep library prep kits. The adapters are especially formulated to work in the digital microfluidics environment.

  • What is the shelf life of NeoPrep library prep kit reagents?

    Guaranteed shelf life is 3 months from date of shipment.


  • How many libraries can I prepare per NeoPrep run?

    Up to 16 libraries can be prepared. If you run less than 16 libraries, it is recommended that the wells that do not have samples are the last ones in the row. RSB should be loaded into empty sample wells.

  • Can I use a sample sheet with the NeoPrep System?

    A sample sheet can be loaded during the Load Library Card step. If you are not using the default index adapter layout, create and edit a sample sheet to record information about your samples and indexes. Illumina recommends that you use IEM to create an appropriate sample sheet. For more information, see the Illumina Experiment Manager User Guide.

  • Does Illumina recommend pipettes and pipette tips to use with the NeoPrep System?

    Use the following required pipettes and tips. Other pipettes and tips are not supported and can result in reagents not dispensing properly and run failure.

    20 μl Volume:

      • Pipet-Lite XLS+ 8-channel LTS, 2 μl to 20 μl—Rainin, catalog # L8-20XLS+
      • One of the following 20 µl tips:
        • LTS tips 20 µl. Presterilized. Filter—Rainin, catalog # RT‑L10F
        • ART Barrier Pipette Tips 20 µl; 20 µl SoftFit-L—Fisher Scientific, catalog # 2749RI

    200 μl Volume:

      • Pipet-Lite XLS+ 8-channel LTS, 20 μl to 200 μl—Rainin, catalog # L8-200XLS+
      • One of the following 200 µl tips:
        • LTS tips 200 µl. Presterilized. Filter—Rainin, catalog # RT‑L200F
        • ART Barrier Pipette Tips 200 µl; 200 µl SoftFit-L—Fisher Scientific, catalog # 2769RI

  • Can I pre-load samples, reagents, and oil on the NeoPrep library card before placing it on the stage?

    No, load the library card when it is on the stage to avoid spilling oil or disturbing the contents after loading.

  • Is quantification and normalization optional on the NeoPrep System?

    Yes, you can select 3 types of workflows on NeoPrep:

    • library prep only
    • library prep and quantification
    • library prep, quantification, and normalization

    If you are not using the on board quantification, libraries can be quantified using a fluorometric quantification method that uses dsDNA binding dyes or qPCR. For more information, see the appropriate library prep reference guide.

  • Can I change the default number of PCR cycles and other parameters for the NeoPrep library prep process?

    Some options can be modified and the options vary by assay. For more information, see the appropriate library prep reference guide.

  • Does Illumina recommend checking final NeoPrep libraries on a Bioanalyzer ?

    A library quality check on a Bioanalyzer is optional. See the appropriate library prep reference guide for library trace examples.  

  • Do I have to remove the blue dye from a NeoPrep library before sequencing?

    A blue dye is used in NeoPrep library prep reagents to aid in loading and collection. It appears as a characteristic peak at 200–250 bp in a BioAnalyzer trace and is not indicative of issues with the final library. The blue dye has no impact on downstream sequencing.

    Fragment Analyzer does not show the blue dye peak in the trace due to dilution on that instrument.

  • What is the recommended loading concentration for sequencing NeoPrep libraries?

    NeoPrep libraries are ready for cluster generation. If you have performed quantification as part of the NeoPrep run, see the suggested clustering recommendations on the Requirements & Compatibility support page for the appropriate library prep kit.


  • Do I need a network connection for the NeoPrep System?

    In general no, because data from a run can be saved locally. However, the following operations require an internet connection:

    • Connection to BaseSpace
    • Receive and install software updates from the NeoPrep Control Software  interface.
    • Save run data from the instrument to a network drive.
    • Send instrument information to Illumina.

  • Can anti-virus software be installed on the NeoPrep System?

    Illumina recommends that you purchase and install an anti-virus software of your choice to protect the instrument control computer against viruses. For more information, see the NeoPrep Library Prep System Site Preparation Guide.