Computational pathology annotation enhances the resolution and interpretation of breast cancer spatial transcriptomics data

The samples in the dataset are connected to a study focusing on studying breast cancer intratumoral heterogeneity using spatial transcriptomic data and computational pathology. The dataset contains 14 samples from 3 patients (one triple negative breast cancer and two HER2-positive breast cancer). Multiple regions of the tumor were collected for analysis. Each sample is one tumor region from one of the patients.

Libraries for spatial transcriptomics were prepared using Visium spatial gene expression kits (10x genomics). Sequencing was performed using the Illumina NovaSeq 6000 platform at the National Genomics Infrastructure, SciLifeLab in Solna, Sweden.

The dataset contains 28 fastq files, compressed with GNUzip (gzip), from paired-end RNA sequencing (10X Visium spatial transcriptomics). The meta data is described in SND_metadata.xlsx file. The md5sum.txt file is provided for validation of data integrity. The total size of the dataset is approximately 300 GB.