3D in situ sequencing

Project leader

Funding source

Swedish Research Council - Vetenskapsrådet (VR)

Project Details

Start date: 01/01/2016
End date: 31/12/2017
Funding: 1800000 SEK


Though the throughput of single cell sequencing is impressive and provides a very sensitive sampling of the transcriptional output of all genes in a cell, current and foreseeable technology only provides a very sparse sampling of tissues. Typically, in the order of thousand cells can be characterized per cubic centimeter tissue that commonly contains in the order of a billion cells, and due to sample bias in cell isolation the method does not reveal even the relative abundance of cell types. In order to monitor entire transcriptional programs in all cells in their native location within tissues, a technology is needed that enables in situ single-cell molecular profiling with a sensitivity to cover the whole “cellome” of tissues: 3D in situ sequencing. In this project we aim to develop such a 3D technology, and we are going to base it on our recently developed 2D in situ sequencing method. The mouse brain is an ideal candidate to establish 3D sequencing technology since it exhibits high heterogeneity on a cellular level, and its general organization is well characterized, e.g. through projects such as the Allen Brain Atlas (http://www.brain-map.org). Moreover, single-cell transcriptome data sets are increasingly becoming available and developments in whole-volume imaging technologies are driven by neuroscience questions. In this project, we will develop 3D sequencing technology and as a proof-of-concept apply it on mouse brain specimens to create a 3D map of cell-types.

Last updated on 2017-12-10 at 11:47