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Visium CytAssist, Mouse Embryo, 11 mm Capture Area (FFPE)

Spatial Gene Expression dataset analyzed using Space Ranger 2.1.0

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10x Genomics obtained FFPE Mouse Embryo tissue blocks from Avaden Biosciences. The tissue was sectioned as described in Visium CytAssist Spatial Gene Expression for FFPE – Tissue Preparation Guide Demonstrated Protocol CG000518. Tissue sections of 5 µm was placed on a standard glass slide, and H&E-stained following deparaffinization. Sections were coverslipped with 85% glycerol, imaged, decoverslipped, followed by dehydration & decrosslinking (Demonstrated Protocol CG000520). The glass slide with the tissue section was processed with the Visium CytAssist instrument to transfer analytes to a Visium CytAssist Spatial Gene Expression slide (11 mm Capture Area). The probe extension and library construction steps follow the standard Visium for FFPE workflow outside of the instrument.

The H&E image was acquired using an Olympus VS200 Slide Scanning Microscope with the following settings:

  • Olympus Objective magnification: 20x UPLXAPO Objective
  • Numerical Aperture: 0.8
  • ScopeLED light source: Xcite Novum
  • Camera: VS-264C
  • Exposure: 410 µs

Libraries were prepared following the Visium CytAssist Spatial Gene Expression Reagent Kits for FFPE User Guide (CG000495).

  • Sequencing instrument: Illumina NovaSeq, flow cell HNT5WDSX3 (lane 1-4)
  • Sequencing configuration: 28bp read 1 (16bp Visium spatial barcode, 12bp UMI), 90bp read 2 (transcript), 10bp i7 sample barcode and 10bp i5 sample barcode
  • Dual-Index set: SI-TS-D6
  • Slide: V52Y09-019
  • Area: B

This dataset is licensed under the Creative Commons Attribution license.