seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus
- Creators
- Shah, Sheel
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Lubeck, Eric
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Zhou, Wen
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Cai, Long
Abstract
We recently applied multiplexed seqFISH to profile expressions of hundreds of genes at the single-cell level in situ (Shah et al., 2016) and provided a map of spatial heterogeneity within each subregion, reconciling previously contradictory descriptions of CA1 at lower spatial resolutions. The accompanying Matters Arising paper from Cembrowski and Spruston questions the spatial organization described for CA1 and raise concerns that the results were determined only by high expression, non-barcoded genes. In response, we show that the same robust spatial structure is observed when only lower average abundance genes measured by barcoded seqFISH are used. In fact, many genes with low average abundance are informative of cell states because they can be expressed strongly in specific subpopulation of cells. Our discussion highlights the importance of single-cell in situ analysis in resolving cellular and spatial heterogeneities otherwise lost in population-averaged measurements. This Matters Arising Response paper addresses the Cembrowski and Spruston (2017) Matters Arising paper, published concurrently in this issue of Neuron.
Additional Information
© 2017 Elsevier Inc. Received 4 January 2017, Revised 20 April 2017, Accepted 2 May 2017, Available online 17 May 2017. Author Contributions: S.S. and L.C. performed the additional analysis. S.S., E.L., W.Z., and L.C. contributed in writing the paper. CONTACT FOR REAGENT AND RESOURCE SHARING: Further information and requests for resources and reagents should be directed to and will be fulfilled by the Lead Contact, Long Cai (lcai@caltech.edu). QUANTIFICATION AND STATISTICAL ANALYSIS: All clustering analyses are performed as described in Shah et al. (2016). Briefly, single-cell expression data are Z score normalized and hierarchical clustered. The cluster identity is then mapped onto the spatial images. In the analysis performed in this Matters Arising Response, we used only 100 genes that were measured by barcoded seqFISH and excluded the genes that were measured by non-barcoded seqFISH. DATA AND SOFTWARE AVAILABILITY: Single-cell seqFISH data were presented as supplementary tables in Shah et al. (2016). Analysis code is available upon requestAdditional details
- Eprint ID
- 77599
- Resolver ID
- CaltechAUTHORS:20170519-092429585
- Created
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2017-05-19Created from EPrint's datestamp field
- Updated
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2021-11-15Created from EPrint's last_modified field