READ ME File For 'Dataset supporting the University of Southampton Doctoral Thesis "Investigating fibroblast heterogeneity in head and neck squamous cell carcinoma"'

Dataset DOI: 10.5258/SOTON/D3247 

ReadMe Author: Benjamin Jenkins, University of Southampton ORCID ID https://orcid.org/0000-0002-7588-0044

This dataset supports the thesis entitled 'Investigating fibroblast heterogeneity in head and neck squamous cell carcinoma'
AWARDED BY: University of Southampton
DATE OF AWARD: 2025

DESCRIPTION OF THE DATA
This data includes single cell RNA-Sequencing data (10x 3' v3) and spatial transcriptomics data (10x Visium V2 Cytassist). The scRNA-Seq and spatial datasets consist of 10 patients with oropharyngeal squamous cell carcinoma. 

.RDS files are provided which can be easily opened in the R environment (readRDS).

This dataset contains:

HNSCC_Visium_data.tar - SpaceRanger output files for each sample generated using 10x Visium V2 Cytassist. This data can be read into Seurat (in the R environment) using Load10X_Spatial().

metadata_final_UoSdata.csv - .csv file containing metadata for 10x Visium V2 Cytassist dataset.

HNSCC_VisiumSpatialGeneExpressionDataset.RDS - Seurat object with processed 10x Visium V2 Cytassist data, including cell type deconvolution results in metadata (Robust cell type deconvolution and SpatialDWLS. 

HNSCC_scRNASeq_EPGdataset.RDS - Seurat object containing 10x 3' v3 scRNA-Seq data for 10 patients, including 10 oropharyngeal squamous cell carcinoma and 7 matched normal mucosa. 

Licence:
Creative Commons Attribution CC-BY

Date that the file was created: APRIL, 2025