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

Cell segmentation-free inference of cell types from in situ transcriptomics data

Jeongbin Park, Wonyl Choi, Sebastian Tiesmeyer, Brian Long, Lars E. Borm, Emma Garren, Thuc Nghi Nguyen, Bosiljka Tasic, Simone Codeluppi, Tobias Graf, Matthias Schlesner, Oliver Stegle, Roland Eils & Naveed Ishaque
Nature Communications 12, 3545 (2021)

Multiplexed fluorescence in situ hybridization techniques have enabled cell-type identification, linking transcriptional heterogeneity with spatial heterogeneity of cells. However, inaccurate cell segmentation reduces the efficacy of cell-type identification and tissue characterization. Here, we present a…

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Publications

Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma

Toshiro Hara, Rony Chanoch-Myers, Nathan D. Mathewson, Chad Myskiw, Lyla Atta, Lillian Bussema, Stephen W. Eichhorn, Alissa C. Greenwald, Gabriela S. Kinker, Christopher Rodman, L. Nicolas Gonzalez Castro, Hiroaki Wakimoto, Orit Rozenblatt-Rosen, Xiaowei Zhuang, Jean Fan, Tony Hunter, Inder M. Verma, Kai W. Wucherpfennig, Aviv Regev, Mario L. Suva` & Itay Tirosh
Cancer Cell (2021)

The mesenchymal subtype of glioblastoma is thought to be determined by both cancer cell-intrinsic alterations and extrinsic cellular interactions, but remains poorly understood. Here, we dissect glioblastoma-to-microenvironment interactions by single-cell RNA sequencing analysis of human tumors and model systems, combined…

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Publications

Spatial organization of the transcriptome in individual neurons

Guiping Wang, Cheen-Euong Ang, Jean Fan, Andrew Wang, Jeffrey R. Moffitt, Xiaowei Zhuang
bioRxiv doi:10.1101/2020.12.07.414060 (2020)

Neurons are highly polarized cells with complex neurite morphology. Spatial organization and local translation of RNAs in dendrites and axons play an important role in many neuronal functions. Here we performed super-resolution spatial profiling of…

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Publications

Molecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomics

Meng Zhang, Stephen W. Eichhorn, Brian Zingg, Zizhen Yao, Hongkui Zeng, Hongwei Dong, Xiaowei Zhuang
bioRxiv doi:10.1101/2020.06.04.105700 (2020)

A mammalian brain is comprised of numerous cell types organized in an intricate manner to form functional neural circuits. Single-cell RNA sequencing provides a powerful approach to identify cell types based on their gene expression…

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Publications

Multiplexed imaging of nucleome architectures in single cells of mammalian tissue

Miao Liu, Yanfang Lu, Bing Yang, Yanbo Chen, Jonathan S. D. Radda, Mengwei Hu, Samuel G. Katz & Siyuan Wang
Nature Communications 11, 2907 (2020)

The three-dimensional architecture of the genome affects genomic functions. Multiple genome architectures at different length scales, including chromatin loops, domains, compartments, and lamina- and nucleolus-associated regions, have been discovered. However, how these structures are arranged…

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Publications

Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization

Chong Wanga,Tian Lua, George Emanuel, Hazen P. Babcock and Xiaowei Zhuang
PNAS 116 (22) 10842-10851 (2019)

Pooled-library CRISPR screening provides a powerful means to discover genetic factors involved in cellular processes in a high-throughput manner. However, the phenotypes accessible to pooled-library screening are limited. Complex phenotypes, such as cellular morphology and…

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Publications

Mammalian gene expression variability is explained by underlying cell state

Robert Foreman, Roy Wollman
Mol Syst Biol (2020)16:e9146

Gene expression variability in mammalian systems plays an important role in physiological and pathophysiological conditions. This variability can come from differential regulation related to cell state (extrinsic) and allele-specific transcriptional bursting (intrinsic). Yet, the relative…

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Publications

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

Chenglong Xia, Jean Fan, George Emanuel, Junjie Hao, and Xiaowei Zhuang
PNAS 116, 19490-19499 (2019)

The expression profiles and spatial distributions of RNAs regulate many cellular functions. Image-based transcriptomic approaches provide powerful means to measure both expression and spatial information of RNAs in individual cells within their native environment. Among…

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