Adult Data

All the raw and curated data is provided for download below.

Raw sequence reads
Terabytes

Raw sequence data is deposited as .bam files in the sequence read archive under accession SRP135960, available at https://www.ncbi.nlm.nih.gov/sra/SRP135960.

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.
Expression values and metadata per cell
19 GB

Available as a single file L5_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.
Expression values and metadata per cluster
113 MB

Available as a single file L5_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.

Note: expression data is provided in Loom format. See loompy.org to learn how to work with Loom files from your favourite programming language.

Subsets of data are also available as loom files here:

Developmental Data

All the raw and curated data is provided for download below.

Raw sequence reads
Terabytes

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.
Expression values and metadata per cell
19 GB

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.
Expression values and metadata per cluster
113 MB

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.
HybISS spatial expression data (voxels)
12 MB

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.
HybISS spots data and anatomical annotation
180 MB

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.