Spatial transcriptomic analysis of tumoural (PanCK+) and stromal (PanCK-) regions in TNBC tissue samples 
using an immunoncology  probe-based panel on the GeoMx™ Digital Spatial Profiler (DSP) 

This dataset was obtained by in-situ hybridisation of probes to a tissue microarray (TMA) of human 
triple-negative breast cancer (TNBC) tissue which was subsequently stained for Pan-cytokeratin (PanCK, Green)
and cluster of differentiation 45 (CD45, Magenta). In-situ probes were cleaved from the tissue using UV-light 
according to immunofluorescence staining. These probes were then hybridised to reporter code sets (nCounter 
Nanostring) and quantified on the MAX/FLAX nCounter system accoridng to manufacturer instruction (FOV 555).

The purpose of this dataset is to allow interrogation of the differential transcriptomic profiles of 
tumoural (PanCK+) and stromal (PanCK-) regions of TNBC disease to further investigate disease pathogenesis and 
spark hypothesis-driven research into potential new therapies and prognostic markers for patients with this 
subtype of disease.

These data can be used for further transcriptomic analysis as a validation dataset or discovery dataset to 
investigate different mRNA expression levels of genes of interest.

The data may be accessed via GeoMx Analysis Suite (avaliable at https://130.209.227.95/login) and/or visualised through importation into R Studio 
for comparative analysis.

Files included:
- Digital count files (dcc. files) from GeoMx nCounter (starting in 20210520_...)
- Raw data exported from GeoMx Analysis Suite (see TNBC-raw-data-GeoMx.xlsx)
- Normalised data exported from GeoMx Analysis Suite (performed using negative probe normalisation) (see TNBC-negprobe-normalised-data-all-GeoMx.xlsx)
- Immunofluorescence images (.tiff) of TNBC TMAs
 
All data has been anonymised for data protection purposes.