Example Visium datasets are available for download on the 10x datasets webpage. They cover a range of species, tissue types, products, and Space Ranger software versions.
Here, we provide a Visium HD 3' dataset that has a trimmed set of FASTQ files, and images edited to include only a corner of the tissue at low resolution, to reduce file size and compute time. This dataset is intended to demonstrate output file format changes introduced by new versions of the Space Ranger software on the CytAssist instrument. They can be used to test code dependencies on these output formats. Since these datasets are trimmed, they are not meant to be used to draw biological conclusions. File size and md5sum information are provided with the download link.
These datasets are licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. 10x citation guidelines available here.
| Species / tissue | Assay user guide | Download information |
|---|---|---|
| Mouse brain | Visium HD 3’ Spatial Gene Expression User Guide (CG000805) | 297 MB, 7cab710801d3776125a7aa5a792cd7e4 Download here |
Download with command line:
# Visium HD 3' Tiny Mouse Brain Dataset
curl -O https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_Tiny_3prime_Dataset/Visium_HD_Tiny_3prime_Dataset_outs.zip