SPanC-Lnc Manuscript data

This repository consists of the following directories under the main directory 'Manuscript_data'. cuTAR_counts: All the cuTAR count matrices associated with 10X visium and scRNA-seq samples along with the cuTAR coordinates (cuTARs.bed) Visium_spaceranger_outputs: Consists of outputs from 10X Visium spaceranger. This includes data derived from previously published data (Wu, Sunny Z et al., 2021; Vo, Tuan et al., 2025; Tran, M et al., 2022; Vo, Tuan et al., 2023; Raghubar, Arti M et al., 2023) STomics_Curio_data: The gene spatial anndata object files for the curio breast and melanoma samples acquired from Curio-Seeker (now Takara Bio USA). The uTAR object for breast and a the uTAR count matrix for melanoma are provided. The STomics gene + cuTAR data is also provided. Three samples (1 Melanoma + 2 Colorectal cancer samples were sequenced on a single chip) Xenium_processed_data: The Xenium gene + selected cuTARs for validation. Each cancer type is provided as a separate processed seurat object (.rds). Xenium_raw_data: The raw outputs from the Xenium experiment