DNA-sekvenseringsbaserad mikroskopi för ultramultiplexerad, optikfri, 3D-avbildning av proteiner och gener

Tidsperiod: 2021-01-01 till 2024-12-31

Projektledare: Ian Hoffecker

Finansiär: Vetenskapsrådet

Bidragstyp: Bidrag för anställning eller stipendier

Budget: 3 600 000 SEK

Last year marked the emergence of DNA sequencing-based microscopy: methods to produce optics-free microscopic images by encoding spatial information in DNA sequence format prior to recovering that information with next generation sequencing. Among these new methods is my approach, published last year in PNAS, which enables 2D image generation by sequencing strands formed from a network of interlinked DNA pixels or polymerase colonies (polonies). Though promising, it has the limitation of requiring diffusive transfer of molecules-of-interest to a DNA chip. I propose to build off of this with my recently developed extension: “N-dimensional Adjacency Reconstruction” (NDAR) capable of producing 3D images from polony networks - an experimentally minor adjustment that would enable one to achieve microscopic imaging with unprecedented multiplicity of targets and isotropic 3D resolution. I propose to expand NDAR’s theoretical and computational foundations and develop the experimental pipeline to image multiple proteins and RNA in multicellular samples, and finally apply NDAR to construct a detailed atlas of a model system: transcriptional regulation in the developing nematode embryo. This grant would enable me to relocate to Uppsala University as an independent investigator where I will establish the first European DNA sequencing-based microscopy node and cultivate my role as one of the field’s founders.