Multiplex IHC Images (CD103 Panel), Bulk RNA-seq, and Single-nRNA/ATAC-seq Count Matrices from neoRhea Patients

These datasets originate from the NeoRHEA clinical trial, which investigates the effects of palbociclib combined with endocrine therapy in breast cancer patients. Samples were collected from patients at two timepoints: prior to treatment initiation (pre-treatment) and after treatment (post-treatment), allowing for multi-modal molecular and imaging analyses of treatment response. Multiplex immunohistochemistry data (Scans_mIHC.zip):Multiplex immunohistochemistry (mIHC) images from the CD103 panel acquired from 7 patients. The panel includes the following markers and fluorophore assignments: Opal 480 – KI67 Opal 520 – CD103 Opal 570 – CD39 Opal 620 – CD4 Opal 690 – CD8 Opal 790 – Cytokeratin (CK) Bulk RNA-seq data (cm_bulk_rna.RDS):Genes-by-samples expression matrix with 58,700 genes quantified from bulk RNA-seq data. The data was processed using Salmon for transcript quantification. The dataset includes expression profiles from 73 patients and 104 samples collected at two timepoints. Single-nuclei multi-omics data (seurat_sn_rna_atac.RDS):Seurat/Signac object integrating single-nuclei RNA and ATAC-seq data. The RNA assay includes 36,601 genes, and the ATAC assay contains 131,430 peaks. After quality control, 180,752 cells passed filters for both RNA and ATAC modalities. The data was aligned and preprocessed using the Cell Ranger ARC pipeline. Samples correspond to 37 patients and 63 samples.