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.

Application & Technical Notes

Gel-free Sample Preparation Protocol

This technical note describes a MERSCOPE sample preparation protocol for cultured cells without the gel embedding steps, which simplifies the standard workflow and shortens the protocol by one day without compromising data quality. Additional sample…

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Product Literature

eBook: Advancing Your Research with Spatial Genomics

In the past half-century, multiomic analysis—genomics, proteomics, transcriptomics, and beyond—has revolutionized our understanding of biology. However, there is still a vast wealth of information left to uncover through the integration of spatial context and transcriptomic…

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Publications

Spatially resolved transcriptomics and the kidney: Many opportunities

Eryn E. Dixon, Haojia Wu, Elizabeth Sulvarán-Guel, Juanru Guo, Benjamin D. Humphreys
Kidney International (2022)

Abstract: Defining changes in gene expression during health and disease is critical for the understanding of human physiology. In recent years, single cell/nuclei RNA sequencing (sc/snRNAseq) has revolutionized the definition and discovery of cell types…

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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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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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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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