Protein expression profiles from IBD and IBS-associated colonic biopsy FFPE sections using Nanostring GeoMx/DSP with differential segmentations for Mast Cell, Epithelial, sub-mucosal, and lymphocyte regions.
Description
The dataset contains results from Nanostring Digital Spatial Profiling (DSP, trade name is now GeoMx) experiments using colonic punch biopsy FFPE thin sections from IBD and IBS patients. The multiplex probe panel includes barcode-linked antibodies against 26 immune-oncology relevant proteins and 4 reference/normalization proteins. The IF labeling strategy included Pan-cytokeratin, Tryptase, and DAPI staining for epithelia, mast cells, and sub-mucosal tissues, respectively. 21 FFPE sections were used, representing 19 individuals. 14 pediatric samples included 8 IBD, 5 IBS, and 1 recurring abdominal pain diagnoses. 7 adult samples were studied - 2 normal tissue biopsies from a single healthy control, 3 X-linked Severe Combined Immuno Deficiency (XSCID) samples from 2 individuals, 1 graft-versus-host disease, and 1 eosinophilic gastroenteritis sample. 8 representative ROIs per slide were selected, with a 9th ROI selected representing a lymphoid aggregate where present. Each of the ROIs contained the three masks (PanCK/epithelia, Tryptase/Mast cell, Dapi/submucosa), and therefore generated 24 individual 30-plex protein expression profiles per slide, with a 25th lymphoid ROI per sample (when present). The data include: 1) Matrix of metadata with sample identifiers and clinical diagnoses (Excel file). 2) A PowerPoint for each sample showing an image of the full slide, images of each selected ROI and QC expression data. 3) An Excel file for each sample containing raw and normalized protein counts. Three normalization methods are reported: a) Normalization by nuclei count, b) Normalization by tissue area, c) Normalization by housekeeping proteins (Histone H3, Ribosomal protein S6). Analysis derived from these data have been published in two conference proceedings (see references below)