Question: What is the expected dropout rate for spatial barcoded squares within the Visium HD capture area?
Answer: Visium HD slides undergo a rigorous manufacturing process and extensive quality controls. These procedures include ensuring that >99% of the spatial barcoded squares within each capture area are present and functional. We are always working on continuous improvement of our production processes, and our intention and expectation is to exceed our specifications.
The details of our manufacturing processes and QC methods are proprietary, and therefore, we cannot share additional information.
Localized low UMI recovery can also be attributed to issues experienced during the assay workflow such as debris on the Visium and/or Tissue slide(s), damage to the Visium slide capture area, or bubble formation introduced during the probe release step. It is important to follow the order and timing of steps as outlined in the Tissue Preparation Handbook (CG000684) and Library Construction User Guide (CG000685).
To avoid localized low UMI recovery, the following best practices should be followed:
- Work in a clean environment.
- Utilize lint-free wipes where indicated.
- Ensure that the glass slides used for tissue placement are within the recommended dimensions.
- Avoid placing cassette gaskets face-down on work surfaces.
- Inspect the Visium HD Slide for particulate after performing the Visium HD Slide Preparation Wash Step (3.1). Repeat wash if particulate is present before continuing.
- Dispense and remove reagents along the side of the cassette wells without touching the slide surface or tissue sections.
- Verify the Tissue Slide frosted areas are not within the dashed zone on the CytAssist Tissue Slide Stage.
- Ensure the Visium HD Slide capture areas are dry before adding Perm Enzyme B to Probe Release Mix.
- Carefully aspirate the Probe Release Mix and inspect the pipette tip to ensure no bubbles are present before dispensing.
- Slowly dispense the Probe Release Mix using a fresh pipette tip for each spacer well. Avoid pushing the plunger past the first stop.
Product: Visium HD