Transcriptomic cell types in the mouse brain: SMART-seq cells
nemo:std-k8xgfw7 · Short name: zeng_sc_SSv4_proj
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"Our goal is to create a high-quality atlas of cell types in the mouse brain using large scale single cell transcriptomic analysis across the entire mouse brain. Transgenic or viral strategies were used to label specific cell populations in the brain with fluorescent reporters. Sample collection was biased to enable sampling of as many cell types as possible and reduce redundant cell type collection. Most of the cells in this dataset were collected using broad Cre-driver lines that labeled all neurons (Snap25-IRES2-Cre), all Glutamatergic cells (Slc17a7-IRES2-Cre), or all GABAergic cells (Slc32a1-IRES-Cre or Gad2-IRES-Cre). Cells from primary visual cortex (VISp) and anterior lateral motor cortex (ALM, a subset of secondary motor cortex, MOs) were collected from a broad set of transgenic driver and reporter combinations in addition to the broad lines specified above. Fine dissections of brain regions and cortical layers were performed and tracked throughout sample processing. Specimens were dissected from both hemispheres in both male and female mice. Fluorescence activated s+J10orting of cells was performed based on expression or absence of fluorescent reporter labels to isolate individual cells into separate tubes. Isolated cells were processed for single cell RNA sequencing using SMARTer v4. This method enables tracking of dissection location and high gene detection per cell to identify fine differences in gene expression and highly selective marker genes. This dataset will survey all major regions of the mouse brain. Publication: Tasic, B. et al. Nature 563, 72;78 (2018)."
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