Data generated for the study 'Cell type-specific inference of differential expression in spatial transcriptomics' in which we develop Cell type-Specific Inference of Differential Expression (C-SIDE), a computational method for detecting cell type-specific differential expression in spatial transcriptomics data. This repository additionally contains data from previous studies analyzed in our paper.

Code used for processing this data and generating figures in the paper is contained at https://github.com/dmcable/spacexr/tree/master/AnalysisCSIDE

For a detailed description of each file including data type, technology, biological sample, replicate, and data source, please download and examine the readme.csv file.

Files in this repository contain newly generated Slide-seqV2 data on the mouse cerebellum and J20 hippocampus. In addition, this repository contains existing spatial transcriptomics datasets including Slide-seq tumor, Slide-seq testes, and MERFISH hypothalamus. For each dataset, a single cell RNA-seq reference from a prior study is included.

File types in this repository include:

• coords.csv: a matrix of spatial transcriptomics coordinates.
• counts.csv: spatial transcriptomics digital gene expression matrix.
• predictive_variable: the predictive variable used for predicting differential gene expression with C-SIDE.
• reference.rds: an RCTD Reference object used for assigning cell types in the RCTD step of C-SIDE.
• SpatialRNA.rds: an RCTD SpatialRNA object used for storing the spatial transcriptomics data to be used for C-SIDE.

Please see our Github (https://github.com/dmcable/spacexr) for instructions on running the C-SIDE algorithm on this data and others.