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Spatial Omics Initiative

Goal

Our goal is to bring together researchers from different disciplines across the University of Illinois to enable breakthroughs in genomic biology by developing new ways to embed omics data in space.

See the links above for tutorials, data examples, and additional resources to get started.

Contact

Please contact us at spatial@igb.illinois.edu if you are interested in taking part.

Overview

Spatial omics is an approach to biology research that combines

  1. genome-scale omics data (gene transcripts, epigenetic markers, proteins, metabolites, etc.) with
  2. high-resolution spatial information

to better understand molecular, cellular, and tissue-level processes.

Spatial omics has enormous potential because it connects the rich but abstract world of high-dimensional omics measurements to the three-dimensional, tangible world of physical processes. Biological function is carried out by molecules but fundamentally situated in space, so measuring both these quantities together can give a more complete understanding of how things work. Nature Methods named spatial transcriptomics Method of Year in 2020 and the technology is at the forefront of a new generation of biological research.

Spatial transcriptomics data from human U2OS cells, imaged by the Han lab at the University of Illinois.
Spatially resolved, single-molecule resolution gene expression in human U2OS cells, imaged by the Han Lab at the University of Illinois. a) Each dot is an RNA molecule and each color represents a gene. b) Gene expression quantified from the spatial omics data are highly correlated with bulk RNA-seq on a biological replicate.

This new field is reaching a critical point. Its promise is evident, but its foundational concepts and techniques have not yet been fully codified. There are currently dozens of competing experimental approaches, hundreds of available analytic tools, and likely thousands of researchers formulating the right questions to ask. Spatial omics needs new, paradigm-shifting ideas.

These breakthroughs will likely arise from a convergence of disciplines, because spatial omics pertains to a wide range of areas:

  1. its questions can come from biology and medicine,
  2. its concepts might borrow from spatial ecology and geographic information systems,
  3. its measurement technology requires engineering and instrumentation, and
  4. its data analysis needs machine learning and artificial intelligence.

Because it crosses disciplines, research in spatial omics promises to catalyze new discoveries across multiple fields. Questions in biology can motivate new directions in engineering and analytics, which in turn can inspire new biological questions.

The strength and diversity of research at the University of Illinois make it uniquely positioned to make major, fundamental contributions to this fast-growing field. The purpose of this Spatial Omics Initiative is to build the cross-campus collaborations necessary to make this happen.