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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

Spatial Transcriptomics Arena (STAr): an Integrated Platform for Spatial Transcriptomics Methodology Research

Xi Jiang, Danni Luo, Esteban Fernández, Jie Yang, Huimin Li, Kevin W. Jin, Yuanchun Zhan, Bo Yao, Suhana Bedi, Guanghua Xiao, Xiaowei Zhan, Qiwei Li, Yang Xie
bioRxiv (2023)

Abstract The emerging field of spatially resolved transcriptomics (SRT) has revolutionized biomedical research. SRT quantifies expression levels at different spatial locations, providing a new and powerful tool to interrogate novel biological insights. An essential question…

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Publications

Distinct Th17 effector cytokines differentially promote microglial and blood-brain barrier inflammatory responses during post-infectious encephalitis

Charlotte R Wayne, Luca I Bremner, Travis E Faust, Violeta Durán-Laforet, Nicole Ampatey, Sarah J Ho, Philip A Feinberg, Panos Arvanitis, Bogoljub Ciric, Shannon L Delaney, Wendy Vargas-Deming, Susan Swedo, Vilas Menon, Dorothy P Schafer, Tyler Cutforth, Dritan Agalliu
bioRxiv (2023)

Abstract Group A Streptococcus (GAS) infections can cause neuropsychiatric sequelae in children due to post-infectious encephalitis. Multiple GAS infections induce migration of Th17 lymphocytes from the nose into the brain, which are critical for microglial activation, blood-brain…

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Publications

A molecularly defined and spatially resolved cell atlas of the whole mouse brain

Meng Zhang, Xingjie Pan, Won Jung, Aaron Halpern, Stephen W Eichhorn, Zhiyun Lei, Limor Cohen, Kimberly A Smith, Bosiljka Tasic, Zizhen Yao, Hongkui Zeng, View ORCID ProfileXiaowei Zhuang
bioRxiv (2023)

Abstract In mammalian brains, tens of millions to billions of cells form complex interaction networks to enable a wide range of functions. The enormous diversity and intricate organization of cells in the brain have so…

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Publications

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

Zizhen Yao, Cindy T. J. van Velthoven, Michael Kunst, Meng Zhang, Delissa McMillen, Changkyu Lee, Won Jung, Jeff Goldy, Aliya Abdelhak, Pamela Baker, Eliza Barkan, Darren Bertagnolli, Jazmin Campos, Daniel Carey, Tamara Casper, Anish Bhaswanth Chakka, Rushil Chakrabarty, Sakshi Chavan, Min Chen, Michael Clark, Jennie Close, Kirsten Crichton, Scott Daniel, Tim Dolbeare, Lauren Ellingwood, James Gee, Alexandra Glandon, Jessica Gloe, Joshua Gould, James Gray, Nathan Guilford, Junitta Guzman, Daniel Hirschstein, Windy Ho, Kelly Jin, Matthew Kroll, Kanan Lathia, Arielle Leon, Brian Long, Zoe Maltzer, Naomi Martin, Rachel McCue, Emma Meyerdierks, Thuc Nghi Nguyen, Trangthanh Pham, Christine Rimorin, Augustin Ruiz, Nadiya Shapovalova, Cliff Slaughterbeck, Josef Sulc, Michael Tieu, Amy Torkelson, Herman Tung, Nasmil Valera Cuevas, Katherine Wadhwani, Katelyn Ward, Boaz Levi, Colin Farrell, Carol L. Thompson, Shoaib Mufti, Chelsea Pagan, Lauren Kruse, Nick Dee, Susan M. Sunkin, Luke Esposito, Michael J. Hawrylycz, Jack Waters, Lydia Ng, Kimberly A. Smith, Bosiljka Tasic, Xiaowei Zhuang, Hongkui Zeng
bioRxiv (2023)

Abstract The mammalian brain is composed of millions to billions of cells that are organized into numerous cell types with specific spatial distribution patterns and structural and functional properties. An essential step towards understanding brain…

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Publications

High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE

Milad R. Vahid, Erin L. Brown, Chloé B. Steen, Wubing Zhang, Hyun Soo Jeon, Minji Kang, Andrew J. Gentles & Aaron M. Newman
Nature Biotechnology (2023)

Abstract: Recent studies have emphasized the importance of single-cell spatial biology, yet available assays for spatial transcriptomics have limited gene recovery or low spatial resolution. Here we introduce CytoSPACE, an optimization method for mapping individual…

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Publications

Spatial organization of the mouse retina at single cell resolution

Jongsu Choi, Jin Li, Salma Ferdous, Qingnan Liang, Jeffrey R. Moffitt, Rui Chen
bioRxiv (2022)

Summary The visual signal processing in the retina requires the precise organization of diverse neuronal types working in concert. We performed spatial transcriptomic profiling of over 100,000 cells from the mouse retina, uncovering the spatial…

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