10x Genomics

Processing Samples Containing Infectious Agents
using the 10x Genomics Chromium Controller and Protocols

Last Modified on April 3, 2020

1. Will Recovery Agent (PN 220016) inactivate infectious agent/s in a sample?

We have not tested the impact of Recovery Agent on any infectious agents. Please contact your local biosafety officer for guidance.

2. Can Trizol be used as a substitute for Recovery Agent?

Trizol cannot be used as a substitute for Recovery Agent.

3. During GEM-RT Incubation, can the 85°C (step 2) be extended more than 5 min?

It is not recommended to extend step 2 at 85°C beyond 5 min as this can degrade the first strand cDNA and negatively impact library quality and complexity.

4. Can an additional temperature incubation step be included during GEM-RT Incubation?

The GEM-RT Incubation program maybe modified to include an additional 30 min incubation at 60°C, as outlined below. This modification to the protocol has not been tested by 10x Genomics and is not supported.

Step Temperature Time
1 53°C 00:45:00
Additional incubation
(not tested by 10x Genomics)
60°C 00:30:00
3 85°C 00:05:00
4 4°C Hold

5. Can the samples be treated with UV light, which is known to cross-link DNA? How would UV treatment affect RNA in the sample?

The impact of UV light on cells will vary based on the duration of exposure, intensity, and wavelength. The effects of UV exposure on cellular RNA has not been tested. Cell viability is known to be negatively affected resulting in higher background and failed runs: https://doi.org/10.1016/j.jphotobiol.2013.06.003.

6. If the Chromium Controller is placed in a biosafety cabinet, will the vibration from the hood/ biosafety cabinet affect Gel Bead-in-Emulsion (GEM) formation?

The vibration from the air flow at normal operating levels, defined by the cabinet manufacturer, will not impact the Chromium Controller performance.

7. How should the 10x Genomics gaskets and chips that have been used to run samples containing infectious agents be disposed?

We recommend discarding the used gaskets and chips according to applicable biosafety guidelines of your institution.

8. What is the cleaning procedure for the Chromium Controller under normal operation?

Follow the guidelines in the Chromium Controller Specifications document (CG00020) for cleaning the instrument, including the exterior surfaces, the door, and tray. See the knowledge base article here for more details: How do I clean my Chromium Controller?

9. How can the Chromium Controller be decontaminated?

We do not have recommendations for decontamination of the external or internal components of the instrument. Once contaminated the instrument cannot be decontaminated.

10. Can the Chromium Controller be moved between different BSL level labs?

Instruments should not be moved between laboratory areas with different biosafety certifications (e.g. from a BSL-3 or BSL-2 laboratory space to a BSL-1 space). Institutional and government guidelines should be consulted to verify regulations.


Contact your local Field Applications Scientist, or send an email to [email protected].