Dataset: Poseidon Data ccRCC Application
Description
This repository contains MALDI mass spectrometry imaging (MALDI-MSI) data acquired from a clear cell renal cell carcinoma (ccRCC) tissue section. The dataset comprises spatially resolved mass spectra of lipids, N-glycans, and tryptic peptides obtained from the same tissue section using a multi-omics imaging workflow. These complementary molecular layers enable the characterization of distinct histological regions, including healthy renal cortex, renal capsule, and tumor tissue. In particular: FinalMatrix_Coor.RDS contains pixel coordinates. FinalMatrix_Coor_reverseX.RDS contains the same coordinates flipped along the x-axis to match the orientation of the H&E-stained tissue image. FinalMatrix_Lipids.RDS, FinalMatrix_Glycans.RDS, and FinalMatrix_Peptides.RDS contain transformed molecular abundances for each pixel. Each row corresponds to a pixel and each column to an m/z value. list_ind_resolution_4123.RDS and list_ind_resolution_4123_cpp.RDS contain the indices of neighboring pixels for each pixel. The former uses 1-based indexing, whereas the latter uses 0-based indexing. These data were analyzed in the study “Multiomics Tissue Segmentation via Spatially-Informed Nested Biclustering Methods” by Francesco Denti, Cecilia Balocchi, Vanna Denti, and Giulia Capitoli, published in Biometrics. Preprint: https://fradenti.github.io/pdf/Poseidon.pdf Analysis code: https://github.com/Fradenti/poseidon-maldi
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Institutions
- University of Milano-BicoccaLombardy, Milan
Departments
Categories
Additional Metadata for University of Milano - Bicocca
| Language | English |
| Date the data was collected | 2021-11-30T23:00:00.000Z |
| ERC Keywords | LS1_2 Biochemistry, LS2_9 Proteomics, LS2_11 Glycomics/Lipidomics, LS2_14 Biostatistics |
| SSD Classification | BIO/10 - BIOCHIMICA, MED/01 - STATISTICA MEDICA |
| Geolocation | Italy |