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.
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.|