Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

Rodriques, Samuel G., Stickels, Robert R., Goeva, Aleksandrina, Martin, Carly A., Murray, Evan, Vanderburg, Charles R., Welch, Joshua, Chen, Linlin M., Chen, Fei, Macosko, Evan Z.·2019·Science

DOI 10.1126/science.aaw1219

Cited by (1,006)

Items 101–200 of 1,006

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Sorokin, Vitaly, Vickneson, Keeran, Kofidis, Theo, Woo, Chin Cheng, Lin, Xiao Yun, Foo, Roger, Shanahan, Catherine M. · 2020 · Frontiers in Immunology
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Amir Giladi, Merav Cohen, Chiara Medaglia, Yael Baran, Baoguo Li, Mor Zada, Pierre Bost, Ronnie Blecher‐Gonen, Tomer‐Meir Salame, Johannes U. Mayer et al. · 2020 · Nature Biotechnology
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Kashima, Yukie, Sakamoto, Yoshitaka, Kaneko, Keiya, Seki, Masahide, Suzuki, Yutaka, Suzuki, Ayako · 2020 · Experimental & Molecular Medicine
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Runmin Wei, Siyuan He, Shanshan Bai, Emi Sei, Min Shan Hu, Alastair Mark Thompson, Ken Chen, Savitri Krishnamurthy, Nicholas E. Navin · 2022 · Nature Biotechnology
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DeTomaso, David, Yosef, Nir · 2021 · Cell Systems
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Sanjay R Srivatsan, Mary C. Regier, Eliza R. Barkan, Jennifer M. Franks, Jonathan S. Packer, Parker Grosjean, Madeleine Duran, Sarah H. Saxton, Jon J. Ladd, Malte Spielmann et al. · 2021 · Science
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Lewis Au, Emine Hatipoglu, Marc Robert de Massy, Kevin Litchfield, Gordon Beattie, Andrew Rowan, Désirée Schnidrig, R. Houston Thompson, Fiona Byrne, Stuart D. Horswell et al. · 2021 · Cancer Cell
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SPARK-X: non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies
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Single-cell technologies in hepatology: new insights into liver biology and disease pathogenesis
Ramachandran, Prakash, Matchett, Kylie P., Dobie, Ross, Wilson-Kanamori, John R., Henderson, Neil C. · 2020 · Nature Reviews Gastroenterology & Hepatology
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Zhen Miao, Benjamin D. Humphreys, Andrew P. McMahon, Junhyong Kim · 2021 · Nature Reviews Nephrology
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Kevin Wei, Hung N. Nguyen, Michael B. Brenner · 2021 · Journal of Clinical Investigation
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Changde Cheng, Wenan Chen, Hongjian Jin, Xiang 'Anthony' Chen · 2023 · Cells
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Haoyang Li, Juexiao Zhou, Zhongxiao Li, Siyuan Chen, Xingyu Liao, Bin Zhang, Ruochi Zhang, Yu Wang, Shiwei Sun, Xin Gao · 2023 · Nature Communications
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Navarro Negredo, Paloma, Yeo, Robin W., Brunet, Anne · 2020 · Cell Stem Cell
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Longqi Liu, Ao Chen, Yuxiang Li, Jan Mulder, Holger Heyn, Xun Xu · 2024 · Cell
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Jonah Langlieb, Nina Sachdev, Karol S. Balderrama, Naeem M. Nadaf, Mukund Raj, Evan M. Murray, James T. Webber, Charles R. Vanderburg, Vahid Gazestani, Daniel Jacob Tward et al. · 2023 · Nature
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Armand, Ethan J., Li, Junhao, Xie, Fangming, Luo, Chongyuan, Mukamel, Eran A. · 2021 · Neuron
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Zhe Sage Chen, Prathamesh Kulkarni, Isaac R. Galatzer‐Levy, Benedetta Bigio, Carla Nasca, Yu Zhang · 2022 · Patterns
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Denis Schapiro, Artem Sokolov, Clarence Yapp, Yu‐An Chen, Jeremy L. Muhlich, Joshua M. Hess, Allison Creason, Ajit J. Nirmal, Gregory J. Baker, Maulik K. Nariya et al. · 2021 · Nature Methods
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Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex
Chen, Ao, Sun, Yidi, Lei, Ying, Li, Chao, Liao, Sha, Meng, Juan, Bai, Yiqin, Liu, Zhen, Liang, Zhifeng, Zhu, Zhiyong et al. · 2023 · Cell
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Russell, Andrew J. C., Weir, Jackson A., Nadaf, Naeem M., Shabet, Matthew, Kumar, Vipin, Kambhampati, Sandeep, Raichur, Ruth, Marrero, Giovanni J., Liu, Sophia, Balderrama, Karol S. et al. · 2024 · Nature
Spatial multi-omics analyses of the tumor immune microenvironment
Wan-Chen Hsieh, Bugi Ratno Budiarto, Yi‐Fu Wang, Chih‐Yu Lin, Mao-Chun Gwo, Dorothy Kazuno So, Yi-Shiuan Tzeng, Shih-Yu Chen · 2022 · Journal of Biomedical Science
Systematic comparison of sequencing-based spatial transcriptomic methods
You, Yue, Fu, Yuting, Li, Lanxiang, Zhang, Zhongmin, Jia, Shikai, Lu, Shihong, Ren, Wenle, Liu, Yifang, Xu, Yang, Liu, Xiaojing et al. · 2024 · Nature Methods
Spatial biology of cancer evolution
Zaira Seferbekova, Artem Lomakin, Lucy R. Yates, Moritz Gerstung · 2022 · Nature Reviews Genetics
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Dominik Klein, Giovanni Palla, Marius Lange, Michal Klein, Zoe Piran, Manuel Gander, Laetitia Meng-Papaxanthos, Michael Sterr, Lama Saber, Changying Jing et al. · 2025 · Nature
Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data
Brendan F. Miller, Feiyang Huang, Lyla Atta, Arpan Sahoo, Jean Fan · 2022 · Nature Communications
Clinical and translational values of spatial transcriptomics
Linlin Zhang, Dongsheng Chen, Dongli Song, Xiaoxia Liu, Yanan Zhang, Xun Xu, Xiangdong Wang · 2022 · Signal Transduction and Targeted Therapy
Glial and myeloid heterogeneity in the brain tumour microenvironment
Brian M. Andersen, Camilo Faust Akl, Michael A. Wheeler, Ennio Antonio Chiocca, David A. Reardon, Francisco Javier Quintana · 2021 · Nature reviews. Cancer
Spatial genomics maps the structure, nature and evolution of cancer clones
Artem Lomakin, Jessica Svedlund, Carina Strell, Milana Gatarić, Artem Shmatko, Gleb D. Rukhovich, Jun Sung Park, Young Seok Ju, Stefan C. Dentro, Vitalii Kleshchevnikov et al. · 2022 · Nature
Spatial transcriptomics prediction from histology jointly through Transformer and graph neural networks
Zeng, Yuansong, Wei, Zhuoyi, Yu, Weijiang, Yin, Rui, Yuan, Yuchen, Li, Bingling, Tang, Zhonghui, Lu, Yutong, Yang, Yuedong · 2022 · Briefings in Bioinformatics
Integrated single-cell analysis-based classification of vascular mononuclear phagocytes in mouse and human atherosclerosis
Alma Zernecke, Florian Erhard, Tobias Weinberger, Christian Schulz, Klaus F. Ley, Antoine‐Emmanuel Saliba, Clément Cochain · 2022 · Cardiovascular Research
The tumor microenvironment’s role in the response to immune checkpoint blockade
Konstantinos Aliazis, Anthos Christofides, Rushil Shah, Yao Yu Yeo, Sizun Jiang, Alain Charest, Vassiliki A. Boussiotis · 2025 · Nature Cancer
SpaGE: Spatial Gene Enhancement using scRNA-seq
Abdelaal, Tamim, Mourragui, Soufiane, Mahfouz, Ahmed, Reinders, Marcel J T · 2020 · Nucleic Acids Research
Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk
Xin Shao, Chengyu Li, Haihong Yang, Xiaoyan Lu, Jie Liao, Jingyang Qian, Kai Wang, Junyun Cheng, Penghui Yang, Huajun Chen et al. · 2022 · Nature Communications
The interaction of CD4+ helper T cells with dendritic cells shapes the tumor microenvironment and immune checkpoint blockade response
Merav Cohen, Amir Giladi, Oren Barboy, Pauline Hamon, Baoguo Li, Mor Zada, Anna Gurevich‐Shapiro, Cristian G. Beccaría, Eyal David, Barbara B. Maier et al. · 2022 · Nature Cancer
The diversity of GABAergic neurons and neural communication elements
Huang, Z. Josh, Paul, Anirban · 2019 · Nature Reviews Neuroscience
Gene regulatory programmes of tissue regeneration
Goldman, Joseph A., Poss, Kenneth D. · 2020 · Nature Reviews Genetics
Advances in spatial transcriptomics and related data analysis strategies
Jun Du, Yuchen Yang, Zhi-Jie An, Minghui Zhang, Xue-Hang Fu, Zoufang Huang, Ye Yuan, Jian Hou · 2023 · Journal of Translational Medicine
The landscape of cell–cell communication through single-cell transcriptomics
Almet, Axel A., Cang, Zixuan, Jin, Suoqin, Nie, Qing · 2021 · Current Opinion in Systems Biology
SM-Omics is an automated platform for high-throughput spatial multi-omics
Sanja Vicković, Britta Lötstedt, Johanna Klughammer, Simon Mages, Åsa Segerstolpe, Orit Rozenblatt–Rosen, Aviv Regev · 2022 · Nature Communications
Single-cell sequencing to multi-omics: technologies and applications
Wu, Xiangyu, Yang, Xin, Dai, Yunhan, Zhao, Zihan, Zhu, Junmeng, Guo, Hongqian, Yang, Rong · 2024 · Biomarker Research
Temporal modelling using single-cell transcriptomics
Ding, Jun, Sharon, Nadav, Bar-Joseph, Ziv · 2022 · Nature Reviews Genetics
Clinical application of advanced multi-omics tumor profiling: Shaping precision oncology of the future
Dilara Akhoundova, Mark A. Rubin · 2022 · Cancer Cell
Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges
Mengnan Cheng, Yujia Jiang, Jiangshan Xu, Alexios‐Fotios A. Mentis, Shuai Wang, Huiwen Zheng, Sunil Kumar Sahu, Longqi Liu, Xun Xu · 2023 · Journal of genetics and genomics/Journal of Genetics and Genomics
Decoding the tumor microenvironment with spatial technologies
Logan A. Walsh, Daniela F. Quail · 2023 · Nature Immunology
Diversity and dynamism in the cerebellum
Chris I. De Zeeuw, Stephen G. Lisberger, Jennifer L Raymond · 2020 · Nature Neuroscience
Spatially resolved isotope tracing reveals tissue metabolic activity
Lin Wang, Xi Xing, Xianfeng Zeng, Stona R. Jackson, Tara A. TeSlaa, Osama Al‐Dalahmah, Laith Z. Samarah, Katharine Goodwin, Lifeng Yang, Melanie R. McReynolds et al. · 2022 · Nature Methods
Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows
Sergio Marco Salas, Louis Benedikt Kuemmerle, Christoffer Mattsson Langseth, Sebastian Tiesmeyer, Christophe Avenel, Taobo Hu, Habib Rehman, Marco Grillo, Paulo Czarnewski, Saga Helgadóttir et al. · 2025 · Nature Methods
Super-resolved spatial transcriptomics by deep data fusion
Bergenstråhle, Ludvig, He, Bryan, Bergenstråhle, Joseph, Abalo, Xesús, Mirzazadeh, Reza, Thrane, Kim, Ji, Andrew L., Andersson, Alma, Larsson, Ludvig, Stakenborg, Nathalie et al. · 2022 · Nature Biotechnology
Growth Plate Chondrocytes: Skeletal Development, Growth and Beyond
Shawn A. Hallett, Wanida Ono, Noriaki Ono · 2019 · International Journal of Molecular Sciences
Integration of spatial and single-cell transcriptomics localizes epithelial cell–immune cross-talk in kidney injury
Ricardo Melo Ferreira, Angela R. Sabo, Seth Winfree, Kimberly S. Collins, Danielle Janosevic, Connor J. Gulbronson, Ying‐Hua Cheng, Lauren Casbon, Daria Barwinska, Michael J. Ferkowicz et al. · 2021 · JCI Insight
High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE
Milad Rafiee Vahid, Erin L. Brown, Chloé Beate Steen, Wubing Zhang, Hyun Soo Jeon, Minji Kang, Andrew J. Gentles, Aaron M. Newman · 2023 · Nature Biotechnology
Statistical and machine learning methods for spatially resolved transcriptomics data analysis
Zeng, Zexian, Li, Yawei, Li, Yiming, Luo, Yuan · 2022 · Genome Biology
A transcriptomic axis predicts state modulation of cortical interneurons
Stéphane Bugeon, Joshua A. M. Duffield, Mario Dipoppa, Anne Ritoux, Isabelle Prankerd, Dimitris Nicoloutsopoulos, David Orme, Maxwell Shinn, Han Peng, Hamish Forrest et al. · 2022 · Nature
Digital microfluidic isolation of single cells for -Omics
Julian Lamanna, E. Scott, Harrison S. Edwards, Michael Dean Chamberlain, Michael D. M. Dryden, Jiaxi Peng, Barbara Mair, Adam Lee, Calvin C. H. Chan, Alexandros A. Sklavounos et al. · 2020 · Nature Communications
Liver Zonation – Revisiting Old Questions With New Technologies
Rory P. Cunningham, Natalie Porat‐Shliom · 2021 · Frontiers in Physiology
Advances in spatial transcriptomics and its applications in cancer research
Yang Jin, Yuanli Zuo, Gang Li, Wenrong Liu, Yitong Pan, Ting Fan, Xin Fu, Xiaojun Yao, Yong Peng · 2024 · Molecular Cancer
Single-cell and spatial multi-omics in the plant sciences: Technical advances, applications, and perspectives
Xiaole Yu, Zhixin Liu, Xuwu Sun · 2022 · Plant Communications
BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies
Zheng Li, Xiang Zhou · 2022 · Genome biology
The changing mouse embryo transcriptome at whole tissue and single-cell resolution
Peng He, Brian A. Williams, Diane E. Trout, Georgi K. Marinov, Henry Amrhein, Libera Berghella, Say-Tar Goh, Ingrid Plajzer-Frick, Veena Afzal, Len A. Pennacchio et al. · 2020 · Nature
Shaping the brain vasculature in development and disease in the single-cell era
Thomas Wälchli, Jeroen Bisschop, Peter Carmeliet, Gelareh Mohammed Zadeh, Philippe Patrick Monnier, Katrien De Bock, Ivan Radovanovic · 2023 · Nature reviews. Neuroscience
Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis
Chang Xin Liu, Rui Li, Young Li, Xiumei Lin, Kaichen Zhao, Qun Liu, Shuowen Wang, Xueqian Yang, Xuyang Shi, Yuting Ma et al. · 2022 · Developmental Cell
The Human Cell Atlas from a cell census to a unified foundation model
Jennifer Rood, Samantha Wynne, Lucia Robson, Anna Hupalowska, John Randell, Sarah Amalia Teichmann, Aviv Regev · 2024 · Nature
Spatial metatranscriptomics resolves host–bacteria–fungi interactomes
Sami Saarenpää, Or Shalev, Haim Ashkenazy, Vanessa Carlos, Derek S. Lundberg, Detlef Weigel, Stefania Giacomello · 2023 · Nature Biotechnology
Tissue damage induces a conserved stress response that initiates quiescent muscle stem cell activation
Machado, Léo, Geara, Perla, Camps, Jordi, Dos Santos, Matthieu, Teixeira-Clerc, Fatima, Van Herck, Jens, Varet, Hugo, Legendre, Rachel, Pawlotsky, Jean-Michel, Sampaolesi, Maurilio et al. · 2021 · Cell Stem Cell
A single-cell tumor immune atlas for precision oncology
Paula Nieto, Marc Elosua-Bayés, Juan L. Trincado, Doménica Marchese, Ramon Massoni-Badosa, Maria Salvany, Ana Raquel Henriques, Juan Camilo Nieto, Sergio Aguilar-Fernández, Elisabetta Mereu et al. · 2021 · Genome Research
Recording development with single cell dynamic lineage tracing
Aaron McKenna, James A. Gagnon · 2019 · Development
Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities
Brendan F. Miller, Dhananjay Bambah-Mukku, Catherine G. Dulac, Xiaowei Zhuang, Jean Fan · 2021 · Genome Research
Stem cell quiescence: the challenging path to activation
Noelia Urbán, Tom H. Cheung · 2021 · Development
Deep learning applications in single-cell genomics and transcriptomics data analysis
Nafiseh Erfanian, A. Ali Heydari, Adib Miraki Feriz, Pablo Iáñez Picazo, Afshin Derakhshani, Mohammad GhasemiGol, Mohsen Farahpour, Seyyed Mohammad Razavi, Saeed Nasseri, Hossein Safarpour et al. · 2023 · Biomedicine & Pharmacotherapy
Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)
Sanjay R. Jain, Liming Pei, Jeffrey M. Spraggins, Michael Angelo, James P. Carson, Nils Gehlenborg, Fiona Ginty, Joana P. Gonçalves, James S. Hagood, John W. Hickey et al. · 2023 · Nature Cell Biology