This data set includes single-cell transcriptomes from multiple cortical areas and the hippocampal formation, including 77K 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.
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
File
Size
Type
Description
28 MB
.csv
Metadata about each cell. Each entry has an _order, _label, and _ color column.
450 KB
.csv
Maps current sample ids (in metadata above) to sample ids released in October 2019.
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.
File
Size
Type
Description
Gene expression matrix (csv)
14 GB
.csv
This CSV contains one row for every cell in the dataset and one column for every gene sequenced. The values of the matrix represent counts (introns + exons) for that gene (column) for that cell (row).
Gene expression matrix (HDF5)
2.1 GB
.hdf5
This HDF5 file contains the cell-by-gene expression matrix for cells, with introns and exons combined.
Gene expression matrix (Seurat)
5.4 GB
.ss.rda
This Seurat object contains the cell-by-gene expression matrix, with introns and exons combined.
6.4 GB
.csv
This CSV contains one row for every cell in the dataset and one column for every gene sequenced. The values of the matrix represent intron counts for that gene (column) for that cell (row).
70 MB
.csv
Gene expression aggregated per cluster, calculated as medians.
88 MB
.csv
Gene expression aggregated per cluster, calculated as trimmed means.
File
Size
Type
Description
Taxonomy of clusters (.json)
1.5 MB
.json
Serialized cluster hierarchy with all node information embedded. JSON version.
327 KB
.Rdata
Serialized cluster hierarchy with all node information embedded.
