Resources

Vizgen is developing the next generation of genomics tools to expand on the capabilities of spatially resolved transcriptomics. Our technology will aide the acceleration of biological research and discovery to advance human health. Access supporting resources by selecting the category below.

Publications

Intratumoral mregDC and CXCL13 T helper niches enable local differentiation of CD8 T cells following PD-1 blockade

Assaf Magen, Pauline Hamon, Nathalie Fiaschi, Leanna Troncoso, Etienne Humblin, Darwin D'souza, Travis Dawson, Matthew D. Park, Joel Kim, Steven Hamel, Mark Buckup, Christie Chang, Alexandra Tabachnikova, Hara Schwartz, Nausicaa Malissen, Yonit Lavin, Alessandra Soares-Schanoski, Bruno Giotti, Samarth Hegde, Raphael Mattiuz, Clotilde Hennequin, Jessica Le Berichel, Zhen Zhao, Stephen Ward, Isabel Fiel, Colles Price, Nicolas Fernandez, Jiang He, Baijun Kou, Michael Dobosz, Lianjie Li, Christina Adler, Min Ni, Yi Wei, Wei Wang, Namita T. Gupta, Kunal Kundu, Kamil Cygan, Raquel P. Deering, Alex Tsankov, Seunghee Kim-Schulze, Sacha Gnjatic, Ephraim Kenigsberg, Myron Schwartz, Thomas U. Marron, Gavin Thurston, Alice O. Kamphorst, Miriam Merad
bioRxiv doi:10.1101/2022.06.22.497216 (2022)

Abstract: Here, we leveraged a large neoadjuvant PD-1 blockade trial in patients with hepatocellular carcinoma (HCC) to search for correlates of response to immune checkpoint blockade (ICB) within T cell-rich tumors. We show that ICB…

Read More
Publications

Spatial Transcriptomics-correlated Electron Microscopy

Peter Androvic, Martina Schifferer, Katrin Perez Anderson, Ludovico Cantuti-Castelvetri, Hao Ji, Lu Liu, Simon Besson-Girard, Johanna Knoferle, Mikael Simons, Ozgun Gokce
bioRxiv doi:10.1101/2022.05.18.492475

Current spatial transcriptomics methods identify cell states in a spatial context but lack morphological information. Scanning electron microscopy, in contrast, provides structural details at nanometer resolution but lacks molecular decoding of the diverse cellular states….

Read More
Publications

AGBT 2022 Poster: In Situ Single-cell Transcriptomic Imaging in Formalin-fixed Paraffin-embedded Tissues with MERSCOPETM

Jiang He, Lizhi He, Timothy Wiggin, Alex S Genshaft, Rob Foreman, Natalia Petrenko, Nicholas Fernandez, Renchao Chen, Colles Price, George Emanuel

Formalin-fixed paraffin-embedded (FFPE) tissues are widely used clinical sample types for histology and molecular diagnosis. However, due to RNA degradation and protein cross-linking, FFPE samples are often challenging for single-cell transcriptomic analysis. Vizgen’s in situ…

Read More
Publications

Spatial transcriptomic reconstruction of the mouse olfactory glomerular map suggests principles of odor processing

I-Hao Wang, Evan Murray, Greg Andrews, Hao-Ching Jiang, Sung Jin Park, Elisa Donnard, Violeta Durán-Laforet, Daniel M. Bear, Travis E. Faust, Manuel Garber, Christina E. Baer, Dorothy P. Schafer, Zhiping Weng, Fei Chen, Evan Z. Macosko & Paul L. Greer
Nature Neuroscience (2022)

The olfactory system’s ability to detect and discriminate between the vast array of chemicals present in the environment is critical for an animal’s survival. In mammals, the first step of this odor processing is executed…

Read More
Publications

Comparative analysis of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing

Jonathan Liu, Vanessa Tran, Venkata Naga Pranathi Vemuri, Ashley Byrne, Michael Borja, Snigdha Agarwal, Ruofan Wang, Kyle Awayan, Abhishek Murti, Aris Taychameekiatchai, Bruce Wang, George Emanuel, Jiang He, John Haliburton, Angela Oliveira Pisco, Norma Neff
bioRxiv doi:10.1101/2022.03.04.483068

Spatial transcriptomics extends single cell RNA sequencing (scRNA-seq) technologies by providing spatial context for cell type identification and analysis. In particular, imaging-based spatial technologies such as Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH) can achieve…

Read More
Publications

SFN 2021 Poster: Molecular Atlassing with MERSCOPE

Biological systems are comprised of numerous cell types, intricately organized to form functional tissues and organs. Building molecular atlases to fully understand the structure and function of each cell within the brain is now a…

Read More
Publications

Advances in spatial transcriptomic data analysis

Ruben Dries, Jiaji Chen, Natalie del Rossi, Mohammed Muzamil Khan, Adriana Sistig, and Guo-Cheng Yuan
Genome Research

Spatial transcriptomics is a rapidly growing field that promises to comprehensively characterize tissue organization and architecture at the single-cell or subcellular resolution. Such information provides a solid foundation for mechanistic understanding of many biological processes…

Read More
Publications

Cell segmentation in imaging-based spatial transcriptomics

Viktor Petukhov, Rosalind J. Xu, Ruslan A. Soldatov, Paolo Cadinu, Konstantin Khodosevich, Jeffrey R. Moffitt & Peter V. Kharchenko
Nature Biotechnology (2021)

Single-molecule spatial transcriptomics protocols based on in situ sequencing or multiplexed RNA fluorescent hybridization can reveal detailed tissue organization. However, distinguishing the boundaries of individual cells in such data is challenging and can hamper downstream…

Read More
Top