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Visium HD Spatial Gene Expression Library, Human Breast Cancer (Fresh Frozen), Ultima Sequencing

HD Spatial Gene Expression dataset analyzed using Space Ranger 3.1.2

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Biomaterials

Fresh frozen human female breast cancer tissue (ductal carcinoma in situ; RIN: 7.7) was obtained from BioIVT.

Sample preparation

A 10 µm section was taken with a cryostat (Epredia CryoStar NX70). Tissue block preparation, sectioning, H&E staining, and imaging followed the Visium HD Fresh Frozen Tissue Preparation Handbook (CG000763).

Imaging

  • Image type: H&E
  • Microscope: Olympus VS200 Slide Scanner
  • Objective magnification: 20X
  • Numerical Aperture: 0.8
  • ScopeLED light source: VS200 LED, Olympus integrated bright field source
  • Camera: iDS VS-264C, Olympus scanner integrated camera
  • Exposure: 500 microseconds

Assay workflow

Probe hybridization, probe ligation, slide preparation, probe release, extension, and library construction followed the Visium HD Spatial Gene Expression Reagent Kits User Guide (CG000685).

  • Slide serial number: H1-649ZJJX
  • Area: A-1
  • Instrument: Visium CytAssist
  • Probe set: Visium Human Transcriptome Probe Set v2.0

Sequencing

Visium HD libraries were amplified to append Ultima-compatible sequences and pooled before sequencing. For additional information regarding making 10x libraries Ultima-compatible, please reach out to technical support at Ultima Genomics.

  • Indexing: Libraries were adapted for sequencing on the UG 100™ sequencing platform via conversion PCR using Ultima-specific (UG-tR1 and UG-srR2) indexing primers
  • Sequencing instrument: Ultima UG 100™
  • Sequencing configuration: sequenced via the UG 100 Solaris™ Flex workflow
  • Sequencing depth: 2 billion (downsampled)

Analysis

Space Ranger v3.1.2 was used to map reads to the reference, detect tissue, align the data to the microscope and CytAssist images, and output feature-barcode matrices for further analysis.

How to view data

To get started, download Loupe Browser v8.1 to explore the Loupe file, or read more about the other Space Ranger outputs.

This dataset is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. 10x citation guidelines available here.