10x Visium Spatial Transcriptomics Dataset: Kidney (3) and Lung (5) Cancer with Tertiary Lymphoid Structures

The kidney and lung cancer dataset with tertiary lymphoid structures (TLS) consists of 5 μm thick FFPE sections from kidney (3) and lung (5) tumors obtained from the Institute of Pathology at the University Hospital of Zurich, mounted onto Visium slides with the Human Probe Set v1. The samples were stained with hematoxylin and eosin (H&E) and subsequently processed for sequencing following the manufacturer's recommendations. After library preparation, the samples were sequenced on an Illumina NovaSeq 6000 and preprocessed using Space Ranger v2.1.0. Patient analyses were conducted in accordance with the Declaration of Helsinki. Ethical approval for performing research on anonymized, archival patient material was obtained from the Cantonal Ethics Commission of Zurich (BASEC Nr. 2022-01854 and BASEC Nr. 2024-01428). Spatial transcriptomics sequencing was performed at the Functional Genomics Center Zurich (FGCZ) of University of Zurich and ETH Zurich. The Visium spots were annotated in the corresponding H&E images by expert researchers (K.S. and S.D.) and included manual annotations with the following labels: TLS, Immune, Tumor, Normal, and Unassigned. Data samples include KC[1-3] indicating kidney cancer and LC[1-5] indicating lung cancer. K.N performed the manual fiducial alignment and tissue detection on the high-resolution images using Loupe Browser 8.0.0 and preprocesseed the AnnData objects.

Data summary:

1) 10x_Visium contains the Space Ranger v2.1.0 output (raw matrix, filtered matrix and spatial information including scaled images).

2) h5ad contains preprocessed AnnData objects along with the manual annotations.

3) tif_slides contains the high-resolution images along with aligned spot coordinates.

Folder structure: 

├── 10x_Visium
│   ├── KC1
│   │   ├── filtered_feature_bc_matrix
│   │   ├── raw_feature_bc_matrix
│   │   └── spatial
│   ├── KC2
│   │   ├── filtered_feature_bc_matrix
│   │   ├── raw_feature_bc_matrix
│   │   └── spatial
│   ├── KC3
│   │   ├── filtered_feature_bc_matrix
│   │   ├── raw_feature_bc_matrix
│   │   └── spatial
│   ├── LC1
│   │   ├── filtered_feature_bc_matrix
│   │   ├── raw_feature_bc_matrix
│   │   └── spatial
│   ├── LC2
│   │   ├── filtered_feature_bc_matrix
│   │   ├── raw_feature_bc_matrix
│   │   └── spatial
│   ├── LC3
│   │   ├── filtered_feature_bc_matrix
│   │   ├── raw_feature_bc_matrix
│   │   └── spatial
│   ├── LC4
│   │   ├── filtered_feature_bc_matrix
│   │   ├── raw_feature_bc_matrix
│   │   └── spatial
│   └── LC5
│       ├── filtered_feature_bc_matrix
│       ├── raw_feature_bc_matrix
│       └── spatial
├── h5ad_preprocessed
└── tif_slides