What impacts Xenium Analyzer instrument run time?

• Transcript density: impacted by sample preparation (fresh frozen vs. FFPE), number of genes on the panel, tissue type, and disease state
• Tissue thickness
• Tissue area (up to 2.35 cm² per slide)
• Cell segmentation staining protocol (additional 2 cycles)
• Xenium Protein protocol and number of protein subpanels selected (additional 2-8 cycles)

The RNA quality, section thickness, expression profile, and the genes on the specific panel affect the detected transcript density. Fresh frozen tissue typically has higher RNA integrity and is sectioned to 10 µm thickness. On average, this results in a higher 2D density of detected transcripts compared to FFPE tissues.

The plots below show typical instrument run times for FFPE (left) and fresh frozen (right) samples. Data generation and analysis run time is estimated for:

• Assays: Xenium In Situ Gene Expression protocol ("Xenium v1"; blue points), Xenium Prime In Situ Gene Expression protocol ("Xenium Prime 5K"; green points), or Xenium In Situ Gene and Protein Expression protocol with all 27 protein markers ("Xenium Protein"; yellow points). All assays were performed with the Cell Segmentation Staining protocol.
• Software: Xenium Analyzer software v4.0 and the Xenium Onboard Analysis pipeline v4.0

Error bars indicate the 68% High Posterior Density Interval of run time across a broad range of samples used in testing. On the x-axis, tissue area is plotted per run (up to ~2.35 cm² x 2 Xenium Slides) to demonstrate the trend. On the y-axis, grid lines are shown in 6 hour increments.

^* The Xenium In Situ Gene and Protein Expression assay is only supported on FFPE tissues.

Registered users of a 10x Cloud-connected† Xenium Analyzer can monitor instrument status and run progress on the cloud.

When the run completes, the status will update from "Run in progress" to "Run complete":

Overview scan progress can be tracked when starting a new run:

In the event of a run error, click "Open Details" to send a message to the 10x Genomics Support team for assistance:

Instruments that are connected† and powered on with no run in progress will show "Instrument idle" status:

Instruments that are powered off or offline will show "Instrument not detected" status:

Please contact support@10xgenomics.com for help registering an instrument.

† Connected instruments are those that are powered on and meet the connectivity requirements detailed in Xenium Analyzer: Network Connectivity Guidelines (CG000645).