Resources Hub

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

Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH

Rongxin Fang, Chenglong Xia, Jennie L. Close, Meng Zhang, Jiang He, Zhengkai Huang, Aaron R. Halpern, Brian Long, Jeremy A. Miller, Ed S. Lein, Xiaowei Zhuang
Science (2022)

Abstract: The human cerebral cortex has tremendous cellular diversity. How different cell types are organized in the human cortex and how cellular organization varies across species remain unclear. In this study, we performed spatially resolved…

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Publications

Orexin neurons inhibit sleep to promote arousal

Roberto De Luca, Stefano Nardone, Kevin P. Grace, Anne Venner, Michela Cristofolini, Sathyajit S. Bandaru, Lauren T. Sohn, Dong Kong, Takatoshi Mochizuki, Bianca Viberti, Lin Zhu, Antonino Zito, Thomas E. Scammell, Clifford B. Saper, Bradford B. Lowell, Patrick M. Fuller, Elda Arrigoni
Nature Communications (2022)

Abstract: Humans and animals lacking orexin neurons exhibit daytime sleepiness, sleep attacks, and state instability. While the circuit basis by which orexin neurons contribute to consolidated wakefulness remains unclear, existing models posit that orexin neurons…

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User Guides

Vizgen MERSCOPE Vizualizer Clustering Template

This notebook demonstrates how to use Scanpy to perform data pre-processing, dimensionality reduction, and single-cell Leiden clustering. This notebook is designed to take the Anndata output from the MERSCOPE Vizualizer and return a new Anndata…

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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…

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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….

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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…

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Publications

Concordance 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 (2022)

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

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Product Literature

Vizgen MERSCOPE™ FFPE Solution

MERSCOPE FFPE Data Advantages • High reproducibility between matched fresh frozen and formalin fixed paraffin embedded tissue samples ensures biologically impactful data • Unmatched accuracy with bulk RNA-sequencing data across the entire expression profile provides…

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Application & Technical Notes

Molecular Atlassing with MERSCOPE

A New Spatial Transcriptomics Technique Accurately Reveals the Organization of The Mouse Brain Transcriptome This application note describes how the MERFISH Mouse Brain Receptor map was generated by MERSCOPE and demonstrates how the platform can…

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