SIGNAL-seq: Multimodal Single-cell Inter- and Intra-cellular Signalling Analysis

This repository contains the processed SIGNAL-seq multimodal scRNA-seq data that was generated in the BioRxiv pre-print - SIGNAL-seq: Multimodal Single-cell Inter- and Intra-cellular Signalling Analysis, 2024. The code used to generate the processed scRNA-seq RNA and ADT objects can be found along with further barcoding layout information can be found at the project github: https://github.com/TAPE-Lab/SIGNAL-seq. SIGNAL-seq protocols can be found at: http://tape-lab.com/resources Questions about data or protocols can be sent to: [e-mail] File Descriptions: ex0003_hela_rna_adata.h5ad - Figure 1 - HeLa spheroid data: An exported Scanpy anndata object of the RNA modality in .h5ad format. The X matrix is Log-normalised UMI count data. sample_id .obs metadata slot encodes the treatment. ex0003_hela_adt_adata.h5a - Figure 1 - HeLa spheroid data: An exported Scanpy anndata object of the ADT (protein/ptm) modality in .h5ad format. The X matrix is CLR UMI count data. sample_id .obs metadata slot encodes the treatment. ex0015_pdo_rna_adata.h5ad - Figure 2 - All PDO-CAF co-culture data: An exported Scanpy anndata object of the RNA modality in .h5ad format. The X matrix is Log-normalised UMI count data. sample_id .obs metadata slot encodes the treatment culture. cell_type .obs slot encodes cell type clustering annotation. cell_type_condition .obs slot encodes both cell type and treatment culture. ex0015_pdo_adt_adata.h5ad - Figure 2 - All PDO-CAF co-culture data: An exported Scanpy anndata object of the ADT (protein/ptm) modality in .h5ad format. The X matrix is CLR UMI count data. sample_id .obs metadata slot encodes the treatment culture. cell_type .obs slot encodes cell type clustering annotation. cell_type_condition .obs slot encodes both cell type and treatment culture. ex0015_epithelial_pdo_rna.h5ad - Figure 2 - Subset of PDO epithelial cells of RNA modality data. ex0015_epithelial_pdo_adt.h5ad - Figure 2 - Subset of PDO epithelial cells of ADT modality data.