(In review)
Follow the Example Notebooks to visualize the data available below.
We use the FISHscale pipeline for unsupervised cell-free segmentation (m-states). We use the FISHspace software for plotting m-cells and further analysis. FISHspace software is based on stlearn with added plotting and processing functions.
For single-cell RNA sequencing data we used the Shoji tensor database and the cytograph-shoji pipeline.
For visualization and exploration of Molecules Spatial Coordinates we recommend using FISHscale. FISHscale visualizer is based upon Open3D, allowing for blazing fast visualization of datasets of millions of RNA molecules.
Complete spatial gene expression data can be downloaded at:
EEL gene expression matrix
Organoid expression matrix
Organoid scVI integrated expression matrix.
Spatial gene expression and accessory data files needed to reproduce the example notebook visualizations can be downloaded at:
EEL data for visualization (13 GB download, 57 GB uncompressed)
The raw single-cell RNA sequencing data for SL040 and SL057 are available at European Genome-phenome Archive under Accession number "EGAD50000001500". The dataset can also be browsed at CELLxGENE. The other samples (single-cell and bulk) are available at European Genome-phenome Archive under Accession number TBA. All samples can be accessed as h5ad-files at google cloud storage:
TruSeq Bulk GBO treated
Smartseq Xpress Bulk GBO control
Smartseq Xpress Bulk astrocytes
Patient SL040 scRNA-seq
Patient SL057 scRNA-seq
Patient KS920+KS924+KS925 scRNA-seq
Darmanis et al. Cell Rep. 2017 scRNA-seq