Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms
Cardozo Gizzi, Andrés M., Cattoni, Diego I., Fiche, Jean-Bernard, Espinola, Sergio M., Gurgo, Julian, Messina, Olivier, Houbron, Christophe, Ogiyama, Yuki +4 more·2019·Molecular Cell
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- Additional file 1 of Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structuresHao, Xian, Jyotsana J. Parmar, Benoît Lelandais, Andrey I. Aristov, Wei Ouyang, Christian Weber, Christophe Zimmer · 2021 · Figshare
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- Additional file 6 of Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structuresHao, Xian, Jyotsana J. Parmar, Benoît Lelandais, Andrey I. Aristov, Wei Ouyang, Christian Weber, Christophe Zimmer · 2021 · Figshare
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- Additional file 1 of Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiencyLi, Yongzheng, Boxin Xue, Zhang, Mengling, Zhang, Liwei, Hou, Yingping, Yizhi Qin, Long, Haizhen, Su, Qian Peter, Wang, Yao, Xiaodong Guan et al. · 2021 · Figshare
- Additional file 4 of Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternal C. elegans chromosomesSilvia Gutnik, Jia Emil You, Ahilya N. Sawh, Aude Andriollo, Susan E. Mango · 2024 · Figshare
- Additional file 5 of Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiencyLi, Yongzheng, Boxin Xue, Zhang, Mengling, Zhang, Liwei, Hou, Yingping, Yizhi Qin, Long, Haizhen, Qian Peter Su, Wang, Yao, Xiaodong Guan et al. · 2021 · Figshare
- Additional file 5 of Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcriptionYing Feng, Wang, Yao, Wang, Xiangnan, Xiaohui He, Yang, Chen, Ardalan Naseri, Thoru Pederson, Jing Zheng, Zhang, Shaojie, Xiao, Xiao et al. · 2020 · Figshare
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- Additional file 7 of Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcriptionYing Feng, Wang, Yao, Wang, Xiangnan, Xiaohui He, Yang, Chen, Ardalan Naseri, Thoru Pederson, Jing Zheng, Zhang, Shaojie, Xiao, Xiao et al. · 2020 · Figshare
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