image representing the current explore topic

Mouse Whole Cortex and Hippocampus 10x

This data set includes single-cell transcriptomes from multiple cortical areas and the hippocampal formation, including 1,093,785 total cells. Samples were collected from dissections of brain regions from ~8 week-old male and female mice, from pan-neuronal transgenic lines. 


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 443 MB .csv
Metadata about each cell. Each entry has an _order, _label, and _color column.
Gene expression matrix 63 GB .csv
Gene expression matrix provided as a csv
Taxonomy of clusters 1.5 MB .json
Serialized cluster hierarchy with all node information embedded.
Taxonomy metadata 1 MB .txt Metadata about the taxonomy.
Gene Expression by Cluster, median 45 MB .csv
Gene expression aggregated per cluster, calculated as medians.
Gene Expression by Cluster, trimmed means 57 MB .csv Gene expression aggregated per cell type, calculated as trimmed means (25%-75%).
2D coordinates 70 MB .csv
UMAP coordinates for each cell, as shown in the Transcriptomics Explorer


Explore & Analyze   Learn More   Protocols   Reference Genome Files