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本数据集配套支撑的研究论文为：Umeh Garcia 等人发表于2024年的《空间分析揭示乳腺癌脑转移中脑模拟与适应的等效性衍生分子特征》。 本研究针对乳腺癌脑转移（Breast Cancer Brain Metastases, BCBM）开展的相关数据采集与处理工作涵盖以下内容： 1. 奈斯特林（Nanostring）GeoMx数字空间分析（Digital Spatial Profiling, DSP）：针对149例独立患者的235个组织芯进行采样，共获得473个感兴趣区域（Area Of Interest, AOI）转录组图谱，经质量控制过滤后保留450个图谱，包含技术重复样本。 2. 组织芯样本涵盖乳腺癌脑转移灶（含毗邻正常脑组织）、原发性浸润性乳腺癌组织以及正常（非癌性）脑组织。 3. 对450个感兴趣区域内的18677个RNA转录本（基于全转录组探针组）完成分析。 4. 本研究引入等效表达指数（Equivalent Expression Index, EEI）这一高特异性与高精度算法，可识别具有统计学显著性的等效表达基因（Equivalently-Expressed Genes, EEGs）。 本次上传的数据包含以下内容： - DCC计数文件 - 实验记录单（LabWorksheet）/注释文件，包含生物标本的元数据信息 - 探针试剂盒配置（Probe Kit Configuration, PKC）文件 - 计数矩阵 - 处理后的原始数据框（感兴趣区域×基因矩阵） - 经Q3标准化处理的数据框（感兴趣区域×基因矩阵） - GeoMx DSP扫描图像：包含感兴趣区域的高分辨率DSP玻片PNG图像 - PNG文件名与实验记录单/注释文件中的“扫描名称”列一一对应 - 等效表达指数（EEI）文件夹，内含： - LICENSE（许可证文件） - EEI README.md - Equivalent_Expression_Index.Rmd - Inputs：用于演示的示例输入文件 - Outputs：用于演示的示例输出文件