Webinar: Mapping the Elusive

Analysis Of Cellular Expression Using the Esper as a Method for Detailed Tissue Mapping and Structural Patterns Recognition

Rebus BioSystem’s Esper™ enables analysis of biomarkers on the subcellular, single-molecule level, all within the context of the tissue environment. Brett Cook, PhD, Senior Product Manager at Rebus provides an overview of the Esper system. Marcos Otero-Garcia, PhD, Senior Scientist at Rebus, compares mouse disease models of neurodegeneration with the Esper. (11:52) Simone Codeluppi, PhD, Principal Scientist of Bioinformatics, discusses spatial organization of cell types in the mouse cortex revealed by multiplexed single-molecule fluorescent in situ hybridization. (25:01) A Q&A session follows the last presentation. Webinar recorded November 10, 2021.

An Overview of the Esper Spatial Omics Platform

Dr. Brett Cook, Senior Product Manager


Abstract:  Traditional cell biology and microscopy recently merged with genomics to create spatial omics, a powerful new approach for studying biology. The Esper is an integrated platform that combines resolution-enhancing Synthetic Aperture Optics (SAO) with automated fluidics to enable multiple types of assays for detecting and quantifying biomarkers at single-molecule, subcellular resolution. The Esper’s High Fidelity Assay for spatial transcriptomics is the first to be available and automates single-molecule FISH to quantify 30 custom genes across ~1 cm2 of tissue in ~2.5 days.

About the speakerBrett joined Rebus Biosystems in 2018 and is focused on defining new products for life science. Prior to joining Rebus, Brett was a scientist at Biosearch Technologies where he developed new DNA products for therapeutic and diagnostic applications. At Biosearch, he optimized DNA synthesis approaches for hot-start PCR, electrochemical DNA biosensors, and aptamer-based biotherapeutics. Brett has authored over 18 publications and abstracts and is an inventor on one patent.

Brett obtained his PhD in Biomolecular Science and Engineering from the University of California, Santa Barbara, and a BS in Molecular Biology from the University of Washington, Seattle. At UCSB, he earned a certificate from the Technology Management Program and was an enthusiastic member of the local startup community.

Comparing Mouse Disease Models of Neurodegeneration with the Esper

Dr. Marcos Otero-Garcia, Senior Scientist


AbstractWe took advantage of the large imaging area of the Esper spatial omics platform to process brain sections from three mouse genotypes in parallel – one wild type and two disease models – to reduce costs and minimize batch effect. The combination of low technical variation and balanced experimental design allowed us to integrate more than 500,000 cells from multiple datasets for analysis without the need for batch correction. We were able to identify more than 12 neuronal and glial cell type clusters using 20 cell type-specific genes, and further dissect these cell types by anatomical structures utilizing the spatial information. We then looked at the gene expression of 10 disease-related genes and cell-type composition across disease models.

About the speaker Marcos Otero-Garcia is a passionate neuroscientist focused on utilizing microscopy, single-cell omics and NGS data analysis to unveil the complex organization of the brain. Marcos joined Rebus Biosystems as a Senior Scientist in 2020 where he has since developed new single cell spatial omics methods and pipelines to better understand neurological diseases. Marcos received his PhD in Neuroscience from the University of Valencia and did Postdoctoral training at both UCLA and Stanford where he authored work using single cell RNA sequencing on human Alzheimer’s brain.

Spatial organization of cell types in the mouse cortex revealed by multiplexed single-molecule fluorescent in situ hybridization

Dr. Simone Codeluppi, Principal Scientist of Bioinformatics


The recent developments in single cell transcriptomics enable the unbiased classification of cell types, revealing the heterogeneity and complexity of many brain regions. However, since single cell RNA sequencing requires tissue dissociation, the spatial information is absent from the generated datasets. Therefore, while the molecular identity of the tissue constituents is known, it remains poorly understood how all these cell types are spatially organized in the tissue. The aim of this work is to generate a quantitative high resolution cell-type map of the mouse somatosensory cortex, hippocampal CA1 and ventricle. We applied a cyclic three-target single molecule Fluorescent in situ Hybridization (smFISH) method, named ouroboros-FISH (oFISH), to quantify the expression level of 33 marker genes in 6,000 cells. Along with the cell’s position in the tissue, the molecular identity of each cell was classified based on cell types identified by single cell RNA-seq. These quantitative spatial data provide important insights into the abundance, patterning and region specific distribution of cell types. Furthermore, it gives a comprehensive view on complex functional units that involve many different cell types, such as the ones that regulate blood vessels function in the brain. This study demonstrates the potential of osmFISH as an extremely versatile technique that can reconnect single cell data with the tissue of origin. Moreover, it can be used to make a quantitative high resolution whole brain cell type maps, which will be a valuable resource for neuroscience.

About the SpeakerSimone Codeluppi joined Rebus Biosystems as Principal Scientist, Bioinformatics in 2021. Prior to that he was an Assistant Professor at the Karolinska Institutet in Stockholm, Sweden. During his time at the Karolinska Institutet he led a team focused on the development and automation of single molecule fluorescence hybridization (smFISH) technologies. Simone earned his PhD in Molecular Pathology from the University of California, San Diego and the Sanford Burnham Prebys Medical Discovery Institute and his BS in Molecular Biology from University of Parma.

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About Us

Rebus Biosystems is a venture-backed Silicon Valley-based life science technology company creating revolutionary tools to enable spatial omics research without compromise. The company’s first instrument, the Esper, is a fully integrated, automated spatial omics platform that delivers quantitative single molecule, single-cell data with subcellular resolution. Advanced imaging with resolution-enhancing Synthetic Aperture Optics (SAO), on-system chemistry, and intuitive software have been combined to provide an end-to-end solution requiring minimal hands-on time. Rebus Biosystems provides all-inclusive assay kits to empower researchers with the resolution, scale and speed of the Esper for multiple applications.