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Visium HD Spatial Gene Expression Library, Human Pancreas (FFPE)

HD Spatial Gene Expression dataset analyzed using Space Ranger 4.0.1

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Biomaterials

A human female pancreas tissue block (FFPE) was obtained from Avaden Biosciences.

Sample preparation

A 5 µm section was taken from the FFPE tissue block with a microtome (Epredia HM355S). Sectioning, deparaffinization, H&E staining and imaging followed the Visium HD FFPE Tissue Preparation Handbook (CG000684).

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-HBNMBMC
  • Area: D1
  • Instrument: Visium CytAssist
  • Probe set: Visium Human Transcriptome Probe Set v2.0

Sequencing

  • Indexing: Dual index plate TS set A; sample index D2
  • Sequencing instrument: Illumina NovaSeq 6000
  • Sequencing configuration: 43 bp read 1, 50 bp read 2, 10 bp i7 sample index, and 10 bp i5 sample index
  • Sequencing depth: 428.4 M reads

Analysis

Space Ranger v4.0.1 was used to map FASTQ files to the reference, detect tissue, align the data to the microscope and CytAssist images, and output feature-barcode matrices for further analysis.

Note that the H&E image for this sample shows localized focus issues, and the performance of cell segmentation is impacted in these blurry areas. Users facing similar issues with their own samples may consider processing their H&E images through Space Ranger's segmentation pipeline (spaceranger segment) to evaluate performance before running the Visium HD assay.

How to view data

To get started, download Loupe Browser v9.0 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.