Visium HD Spatial Gene Expression Libraries, Post-Xenium, Human Lung Cancer (FFPE)
HD Spatial Gene Expression dataset analyzed using Space Ranger 3.0.0
Learn about Visium analysis
Overview
These datasets are provided as part of the Post-Xenium In Situ Applications: Immunofluorescence, H&E, Visium v2, and Visium HD Technical Note (CG000709, Rev C). Visium HD post-Xenium workflow samples were compared to controls (samples only processed through the Visium HD workflow) using 5 µm (FFPE) serial sections.
The corresponding Xenium experiments are available here.
Biomaterials
A human lung tissue sample (FFPE) with adenocarcinoma was obtained from Avaden Biosciences.
Sample preparation
A 5 µm section was taken 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).
| Sample | Slide Serial Number | Area |
|---|---|---|
| Experiment 1, HD only (control) | H1-9QZXXNP | A-1 |
| Experiment 1, post-Xenium v1 | H1-9QZXXNP | D-1 |
| Experiment 2, HD only (control) | H1-84QJZFR | D-1 |
| Experiment 2, post-Xenium Prime 5K | H1-JGHRVB7 | D-1 |
- Instrument: Visium CytAssist
- Probe set: Visium Human Transcriptome Probe Set v2.0
Sequencing
- Indexing: Dual index plate TS set A
- 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
| Sample | Sequencing Depth | Sample Index |
|---|---|---|
| Experiment 1, HD only (control) | 395.7 million read pairs | C8 |
| Experiment 1, post-Xenium v1 | 374.1 million read pairs | D8 |
| Experiment 2, HD only (control) | 298.7 million read pairs | H2 |
| Experiment 2, post-Xenium Prime 5K | 300.9 million read pairs | B8 |
Analysis
Space Ranger v3.0.0 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. For Experiment 2, Loupe Browser v8.0 was used for manual alignment.
How to view data
To get started, download Loupe Browser v8.0 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 license.