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Visium HD 3' Gene Expression Library, Soybean Seed (Fresh Frozen)

HD 3’ Spatial Gene Expression dataset analyzed using Space Ranger 4.0.1

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Biomaterials

An soybean seed sample was obtained from Mountain Valley Seed Company.

  • ASIN: B08B31L21M

Sample preparation

The plant material was OCT-embedded and a 10 µm section was taken with a cryostat (Epredia CryoStar NX70) with set temperatures of -16° C (specimen) and -19° C (blade). Tissue preparation, sectioning, H&E staining, and imaging followed the Visium HD 3' Fresh Frozen Tissue Preparation Handbook (CG000804), with modifications for plant tissues described in this article. Tissues were sectioned onto SchottH slides.

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

Library preparation followed the Visium HD 3' Spatial Gene Expression User Guide (CG000805).

  • Slide serial number: H1-QPQGF92
  • Area: D1
  • Instrument: Visium CytAssist

Sequencing

  • Indexing: Dual index plate TT set A; sample index D6
  • Sequencing instrument: Illumina NovaSeq X+
  • Sequencing configuration: 43 bp read 1, 75 bp read 2, 10 bp i7 sample index, and 10 bp i5 sample index
  • Sequencing depth: 601.5 million read pairs

Analysis

Loupe Browser v9.0 was used to generate a manual alignment file (available for download under input files). Space Ranger v4.0.1 was used to map FASTQ files to the custom reference (Wm82), segment cells, and output feature-barcode matrices for further analysis.

Space Ranger's cell segmentation algorithm was not trained on plant data, and cell segmentation performance is impacted in this sample. For more information on running plant samples on Visium HD 3', see this article.

How to view data

To get started, download Loupe Browser v9.0 or later 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.