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DV200 determination for FFPE RNA samples

DV200 Analysis with the Automated Electrophoresis Portfolio
Quickly determine the quality of your FFPE RNA samples with the Automated Electrophoresis Portfolio

The Automated Electrophoresis systems from Agilent utilize a quality metric, DV200, to address the unique QC challenges of FFPE RNA. The DV200 provides researchers with a tool to reliably classify degraded RNA by size and effectively parse samples suitable for NGS from unsuitable samples, conserving time and costs. Depending on the level of degradation and the DV200 score, researchers can modify their workflows to still enable the use of FFPE samples in downstream applications. For example, when a specific size is needed and the sample is slightly degraded, the shearing protocol can be adjusted to reach that size. Take advantage of automated evaluation of RNA samples using the DV200 quality metric with the Bioanalyzer, TapeStation, and Fragment Analyzer systems.

2100 Bioanalyzer system

If you are not using the 2100 Expert software revision B.02.10 or higher, please download the DV200 assay files:

Extract and store the DV200 RNA Nano.xsy or DV200 RNA Pico.xsy file in the 2100 Expert Software RNA assay folder:
c:\Program Files (x86)\Agilent\
2100bioanalyzer\2100expert\assays\RNA

To apply the DV200 calculation to an existing data file:

  1. Open the data file with the 2100 Expert Software
  2. Navigate to the Assay Properties tab
  3. Click Import Setpoints and select the appropriate .xsy file (DV200 RNA Nano or DV200 RNA Pico, dependent on the data file opened)

Assay parameters will be applied to the data file. Refer to the Technical Overview for more details.

Total RNA sample on the Bioanalyzer

TapeStation systems

Universal Mouse Reference on the Fragment Analyzer

The DV200 assays can be used with the TapeStation Analysis software A02.02 or higher.

  1. Open a data file with the TapeStation Analysis Software
  2. Click Regions
  3. Click Regions Settings
  4. Enter the lower (e.g. 200 nt) and upper limits (e.g. 10000 nt) of the region in the dialog box. Type DV200 as region comment.
  5. To apply the DV200 region to all samples in the active file, select This File. To apply the DV200 region to all files of the same assay as the active file, select Assay Files.

When DV200 regions are defined, the value is provided in the region table in the % of total column for each sample.

Refer to the Technical Overview for more details.

Fragment Analyzer systems

The DV200 calculation can be used with ProSize data analysis software. Download the DV200 calculation method/configuration files:

Store the method/configuration files for the RNA kit (15 nt) or the HS RNA kit (15 nt) in the Configuration folder of the ProSize data analysis software under:
C:\ProSize data analysis software\Configurations\33cm

To apply the DV200 calculation to an existing data file:

  1. Open Fragment Analyzer run in ProSize data analysis software
  2. Click “Option” Menu → Edit Configurations
  3. Click Smear Analysis → Enter start size (e.g. 200 nt) and end size (e.g. 10000 nt)
  4. Click Load → a second Advance Setting window will open
  5. Click “Load” → Open the Configurations file folder “33cm” (C:\ProSize data analysis software\
    Configurations\33cm)
  6. Select the desired Configuration file – Okay – Apply
  7. Click back on “Set individual parameters” Icon → Smear analysis tab → % total column

When DV200 regions are defined, the value is provided under the Smear analysis tab in the % of total column for each sample.

DV200 on the Fragment Analyzer

For Research Use Only. Not for use in diagnostic procedures.