Protocol for single-cell ATAC sequencing using combinatorial indexing in mouse lung adenocarcinoma by Del Priore, Isabella, Ma, Sai, Strecker, Jonathan, Jacks, Tyler, LaFave, Lindsay M, Buenrostro, Jason D

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Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin by Ma, Sai, Zhang, Bing, LaFave, Lindsay M, Earl, Andrew S, Chiang, Zachary, Hu, Yan, Ding, Jiarui, Brack, Alison, Kartha, Vinay K, Tay, Tristan, Law, Travis, Lareau, Caleb, Hsu, Ya-Chieh, Regev, Aviv, Buenrostro, Jason D

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In situ genome sequencing resolves DNA sequence and structure in intact biological samples by Payne, Andrew C, Chiang, Zachary D, Reginato, Paul L, Mangiameli, Sarah M, Murray, Evan M, Yao, Chun-Chen, Markoulaki, Styliani, Earl, Andrew S, Labade, Ajay S, Jaenisch, Rudolf, Church, George M, Boyden, Edward S, Buenrostro, Jason D, Chen, Fei

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In situ genome sequencing resolves DNA sequence and structure in intact biological samples by Payne, Andrew C, Chiang, Zachary D, Reginato, Paul L, Mangiameli, Sarah M, Murray, Evan M, Yao, Chun-Chen, Markoulaki, Styliani, Earl, Andrew S, Labade, Ajay S, Jaenisch, Rudolf, Church, George M, Boyden, Edward S, Buenrostro, Jason D, Chen, Fei

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PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes by Weintraub, Abraham S., Buenrostro, Jason D., Cheng, Christine S., Regev, Aviv, Young, Richard A., Soto Feliciano, Yadira M., Bartlebaugh, Jordan M. E., Sanchez-Rivera, Francisco Javier, Bhutkar, Arjun, Jacks, Tyler E., Hemann, Michael, Liu, Yunpeng,S.M.Massachusetts Institute of Technology.

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Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields by Agbleke, Andrews Akwasi, Amitai, Assaf, Buenrostro, Jason D, Chakrabarti, Aditi, Chu, Lingluo, Hansen, Anders S, Koenig, Kristen M, Labade, Ajay S, Liu, Sirui, Nozaki, Tadasu, Ovchinnikov, Sergey, Seeber, Andrew, Shaban, Haitham A, Spille, Jan-Hendrik, Stephens, Andrew D, Su, Jun-Han, Wadduwage, Dushan

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Spatial genomics enables multi-modal study of clonal heterogeneity in tissues by Zhao, Tongtong, Chiang, Zachary D, Morriss, Julia W, LaFave, Lindsay M, Murray, Evan M, Del Priore, Isabella, Meli, Kevin, Lareau, Caleb A, Nadaf, Naeem M, Li, Jilong, Earl, Andrew S, Macosko, Evan Z, Jacks, Tyler, Buenrostro, Jason D, Chen, Fei

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Hyperactivation of sympathetic nerves drives depletion of melanocyte stem cells by Zhang, Bing, Ma, Sai, Rachmin, Inbal, He, Megan, Baral, Pankaj, Choi, Sekyu, Gonçalves, William A., Shwartz, Yulia, Fast, Eva M., Su, Yiqun, Zon, Leonard I., Regev, Aviv, Buenrostro, Jason D., Cunha, Thiago M., Chiu, Isaac M., Fisher, David E., Hsu, Ya-Chieh

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Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma by LaFave, Lindsay M, Kartha, Vinay K, Ma, Sai, Meli, Kevin, Del Priore, Isabella, Lareau, Caleb, Naranjo, Santiago, Westcott, Peter MK, Duarte, Fabiana M, Sankar, Venkat, Chiang, Zachary, Brack, Alison, Law, Travis, Hauck, Haley, Okimoto, Annalisa, Regev, Aviv, Buenrostro, Jason D, Jacks, Tyler

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Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma by LaFave, Lindsay M., Kartha, Vinay K., Ma, Sai, Meli, Kevin, Del Priore, Isabella, Lareau, Caleb, Naranjo, Santiago, Westcott, Peter M.K., Duarte, Fabiana M., Sankar, Venkat, Chiang, Zachary, Brack, Alison, Law, Travis, Hauck, Haley, Okimoto, Annalisa, Regev, Aviv, Buenrostro, Jason D., Jacks, Tyler

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A transcription factor atlas of directed differentiation by Joung, Julia, Ma, Sai, Tay, Tristan, Geiger-Schuller, Kathryn R, Kirchgatterer, Paul C, Verdine, Vanessa K, Guo, Baolin, Arias-Garcia, Mario A, Allen, William E, Singh, Ankita, Kuksenko, Olena, Abudayyeh, Omar O, Gootenberg, Jonathan S, Fu, Zhanyan, Macrae, Rhiannon K, Buenrostro, Jason D, Regev, Aviv, Zhang, Feng

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Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling by Lareau, Caleb A, Ludwig, Leif S, Muus, Christoph, Gohil, Satyen H, Zhao, Tongtong, Chiang, Zachary, Pelka, Karin, Verboon, Jeffrey M, Luo, Wendy, Christian, Elena, Rosebrock, Daniel, Getz, Gad, Boland, Genevieve M, Chen, Fei, Buenrostro, Jason D, Hacohen, Nir, Wu, Catherine J, Aryee, Martin J, Regev, Aviv, Sankaran, Vijay G

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Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms by Guo, Michael H., Nandakumar, Satish K., Ulirsch, Jacob C., Buenrostro, Jason D., Natarajan, Pradeep, Salem, Rany M., Chiarle, Roberto, Mitt, Mario, Kals, Mart, Pärn, Kalle, Fischer, Krista, Milani, Lili, Mägi, Reedik, Palta, Priit, Metspalu, Andres, Esko, Tõnu, Zekavat, Seyedeh M., Gabriel, Stacey, Lander, Eric Steven, Kathiresan, Sekar, Sankaran, Vijay G., Hirschhorn, Joel N.

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SMARCA4 inactivation promotes lineage-specific transformation and early metastatic features in the lung by Concepcion, Carla P, Ma, Sai, LaFave, Lindsay M, Bhutkar, Arjun, Liu, Manyuan, DeAngelo, Lydia P, Kim, Jonathan Y, Del Priore, Isabella, Schoenfeld, Adam J, Miller, Manon, Kartha, Vinay K, Westcott, Peter MK, Sánchez-Rivera, Francisco J, Meli, Kevin, Gupta, Manav, Bronson, Roderick T, Riely, Gregory J, Rekhtman, Natasha, Rudin, Charles M, Kim, Carla F, Regev, Aviv, Buenrostro, Jason D, Jacks, Tyler

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