All the raw and curated data is provided for download below.
Raw sequence data is deposited as .bam files in the sequence read archive under accession PRJNA637987, available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA637987/.
Useful if you want to reanalyze everything from scratch. Note that these .bam files are output files from the cellranger pipeline; The original cellular index is available in the CR tag and the UMI in the UR tag.Available as a single file dev_all.loom, with one cell per column and one gene per row. Metadata is available as row and column attributes.
Suitable for exploring single cells.Available as a single file dev_all.agg.loom, with one cluster per column and one gene per row. Metadata is available as row and column attributes.
Suitable for exploring cell types.Available as a single HDF5 file mousedev_hybiss.h5, containing two HDF5 Datasets, "hybiss" and "genes". "hybiss" has shape (section, x, y, gene) = (25, 200, 150, 119) and contains RNA counts per voxel for each of the 119 genes. "genes" is a vector of length 119 containing the names of the genes.
Suitable for exploring spatial gene expression.Available as a single Python pickle file spots.pkl, containing two dictionaries, "spots" (x, y, gene, section) and "polygons" (named anatomy polygons per section).
Suitable for exploring spatial gene expression.Note: expression data is provided in Loom format. See loompy.org to learn how to work with Loom files from your favourite programming language.