Mouse Whole Cortex and Hippocampus SMART-seq
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.
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General
| 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. |
| 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. |
| 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) | 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. |
| Introns only | 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). |
| Exons only | 6.9 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 exon counts for that gene (column) for that cell (row). |
| Gene Expression grouped by Cluster, median | 70 MB | .csv |
Gene expression aggregated per cluster, calculated as medians. |
| Gene Expression grouped by Cluster, trimmed means | 88 MB | .csv | Gene expression aggregated per cluster, calculated as trimmed means. |
Cell Types Taxonomy
| 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. |
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