Visium HD 3' Gene Expression Library, Human + Mouse Xenograft (Fresh Frozen)

Biomaterials

A human/mouse xenograft was obtained from HeraBioLabs.

• Sex: male
• Mouse strain: NSG
• Human: HCT-116 Colorectal Cancer cell line

Sample preparation

A 10 µm section was taken with a cryostat (Epredia CryoStar NX70). Tissue preparation, sectioning, H&E staining, and imaging followed the Visium HD 3' Fresh Frozen Tissue Preparation Handbook (CG000804).

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-GZVTJZF
• Area: A1
• Instrument: Visium CytAssist

Sequencing

• Indexing: Dual index plate TT set A; sample index A1
• Sequencing instrument: Illumina NovaSeq 6000
• Sequencing configuration: 43 bp read 1, 75 bp read 2, 10 bp i7 sample index, and 10 bp i5 sample index
• Sequencing depth: 243.1 million read pairs

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, segment cells, and output feature-barcode matrices for further analysis.

Note that a warning is displayed in the web_summary.html for "Low Fraction of Reads Confidently Mapped to Transcriptome GRCm39". This is acceptable in a xenograft sample where the major tissue of interest is human, and this warning does not indicate an issue with the sample.

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.