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Mouse Whole Cortex and Hippocampus 10x

The raw updated data can be found here.

This data set includes single-cell transcriptomes from multiple cortical areas and the hippocampal formation, including 1.1M total cells. Samples were collected from dissections of brain regions from ~8 week-old male and female mice, from pan-neuronal transgenic lines. 

The research was funded by multiple grant awards from institutes under the National Institutes of Health (NIH), including award number R01EY023173 from The National Eye Institute, U01MH105982 from the National Institute of Mental Health and Eunice Kennedy Shriver National Institute of Child Health & Human Development, and U19MH114830 from the National Institute of Mental Health to H.Z.

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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 490 MB .csv
Metadata about each cell. Each entry has an _order, _label, and _color column.
2D coordinates 75 MB .csv
UMAP coordinates for each cell, as shown in the Transcriptomics Explorer
Link to Raw Data     Link to GEO archive, which includes both this 10x data as well as the related SMART-seq data used to create the cell types taxonomy


Gene Expression
File Size Type Description
Gene expression matrix (csv) 68 GB .csv
Gene expression matrix provided as a csv
Gene expression matrix (HDF5) 5.3 GB .hdf5 This HDF5 file contains the cell-by-gene expression matrix for cells, with introns and exons combined. 
Gene Expression by Cluster, median 47 MB .csv
Gene expression aggregated per cluster, calculated as medians.
Gene Expression by Cluster, trimmed means 59 MB .csv Gene expression aggregated per cell type, calculated as trimmed means (25%-75%).


Cell Types Taxonomy
File Size Type Description
Taxonomy of clusters (json) 1.5 MB .json
Serialized cluster hierarchy with all node information embedded.

Taxonomy of clusters (R)

800 KB .Rdata Serialized cluster hierarchy with all node information embedded.