Abstract:
:Identifying the spatial organization of tissues at cellular resolution from single-cell gene expression profiles is essential to understanding biological systems. Using an in situ 3D multiplexed imaging method, seqFISH, we identify unique transcriptional states by quantifying and clustering up to 249 genes in 16,958 cells to examine whether the hippocampus is organized into transcriptionally distinct subregions. We identified distinct layers in the dentate gyrus corresponding to the granule cell layer and the subgranular zone and, contrary to previous reports, discovered that distinct subregions within the CA1 and CA3 are composed of unique combinations of cells in different transcriptional states. In addition, we found that the dorsal CA1 is relatively homogeneous at the single cell level, while ventral CA1 is highly heterogeneous. These structures and patterns are observed using different mice and different sets of genes. Together, these results demonstrate the power of seqFISH in transcriptional profiling of complex tissues.
journal_name
Neuronjournal_title
Neuronauthors
Shah S,Lubeck E,Zhou W,Cai Ldoi
10.1016/j.neuron.2016.10.001subject
Has Abstractpub_date
2016-10-19 00:00:00pages
342-357issue
2eissn
0896-6273issn
1097-4199pii
S0896-6273(16)30702-4journal_volume
92pub_type
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