Spatial Profiling Reveals Equivalence-Derived Molecular Signatures of Brain Mimicry and Adaptation in Breast Cancer Brain Metastases

This collection of data accompanies the study: Umeh Garcia et al. Spatial Profiling Reveals Equivalence-Derived Molecular Signatures of Brain Mimicry and Adaptation in Breast Cancer Brain Metastases. (2024). 

Data collected and processed as a part of this study of breast cancer brain metastases (BCBM) include: 

Nanostring GeoMx Digitial Spatial Profiling collected from 149 unique patients, across 235 tissue tissue cores, generating 473 Area Of Interest (AOI) transcriptome profiles (reduced to 450 after quality control filtering), including technical replicates.

Tissue cores from BCBM (including adjacent normal brain), primary invasive breast cancers, and normal (non-cancer) brain

Analysis of 18,677 RNAs (whole transcriptome atlas probe set) in 450 areas of interest (AOIs)

Introduction the “Equivalent Expression Index” a highly specific and accurate algorithm that identifies statistically significant "Equivalently-Expressed Genes" (EEGs)

Uploaded data include: 

DCC count files

LabWorksheet / Annotation file including biospecimen metadata information

Probe Kit Configuration (PKC) file

Count Matrices

Processed raw data frame (AOI x gene matrix)

Processed Q3 normalized data frame (AOI x gene matrix)

GeoMx DSP Scan Images: high resolution PNGs of DSP slides (w/ AOIs)

PNG file names correspond to "scan name" column in Lab Worksheet / Annotation file

Equivalence Expression Index (EEI) Folder containing: 

LICENSE

EEI README.md

Equivalent_Expression_Index.Rmd

Inputs - example files for demo

Outputs - example files for demo