Longitudinal Multi-Omic Characterization of Patient Responses to Neoadjuvant HER2-Targeted Therapy

Additionally, imaging-based spatial transcriptomics was performed using the Xenium In Situ platform to map the spatial organization of the tumor microenvironment; note that the Xenium spatial data is exclusively available for the on-treatment time point. The dataset consists of the following: 1) RNA-seq/sequencing_batch/Sample.fastq.gz Folder containing raw paired-end FASTQ files from RNA-seq. Each tumor sample was multiplexed across sequencing sample/lane index combinations.

File names begin with the project-sample ID and include R1 or R2, denoting forward and reverse reads, respectively. 2) WES/sequencing_batch/Sample.fastq.gz Folder containing raw paired-end FASTQ files from RNA-seq. File names begin with the project-sample ID and include R1 or R2, denoting forward and reverse reads, respectively. 3) Xenium_5k Each subfolder contains the standardized, uncompressed output directory generated by the Xenium Ranger analysis pipeline for an individual tissue section.

The entire dataset is over 10,000 files and over 10TB in size.