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Mouse Whole Cortex and Hippocampus SMART-seq

This data set includes single-cell transcriptomes from multiple cortical areas and the hippocampal formation, including 76,533 total cells. Samples were collected from dissections of brain regions from ~8 week-old male and female mice, primarily from pan-GABAergic, pan-glutamatergic, and pan-neuronal transgenic lines, with the addition of more specific transgenic lines and some retrogradely-labeled cells in VISp and ALM.


File Size Type Description
Readme 12 KB .txt
Read-me file with additional information about the other files in this directory
Table of cell metadata 28 MB .csv
Metadata about each cell. Each entry has an _order, _label, and _color column.
Gene expression matrix 7.1 GB .csv
Gene expression matrices provided as an HDF5 file with column-indexed sparse matrices. Exon and intron counts are stored separately. 
See "readme.txt" for data access instructions.
Taxonomy of clusters 1.5 MB .json
Serialized cluster hierarchy with all node information embedded.
Taxonomy information 1 KB .txt
Metadata about the taxonomy.
Gene Expression by Cluster, median 82 MB .csv
Gene expression aggregated per cluster, calculated as medians.
Gene Expression by Cluster, trimmed means 88 MB .csv Gene expression aggregated per cluster, calculated as trimmed means.
2D coordinates 3 MB .csv
UMAP coordinates for each cell, as shown in the Transcriptomics Explorer
Sample ID mapping 450 KB .csv Maps current sample ids (in metadata above) to sample ids released in October 2019.


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