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Reprogramming fibroblast into human iBlastoids Nat. Protoc. (IF 14.8) Pub Date : 2024-04-17 Jia Ping Tan, Xiaodong Liu, Jose M. Polo
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Noninvasive in vivo microscopy of single neutrophils in the mouse brain via NIR-II fluorescent nanomaterials Nat. Protoc. (IF 14.8) Pub Date : 2024-04-11 Ying Chen, Yiwei Yang, Fan Zhang
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Control of DNA replication in vitro using a reversible replication barrier Nat. Protoc. (IF 14.8) Pub Date : 2024-04-09 Emma J. Vontalge, Tamar Kavlashvili, Steven N. Dahmen, Matthew T. Cranford, James M. Dewar
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Anaerobic cryoEM protocols for air-sensitive nitrogenase proteins Nat. Protoc. (IF 14.8) Pub Date : 2024-04-04 Rebeccah A. Warmack, Belinda B. Wenke, Thomas Spatzal, Douglas C. Rees
Single-particle cryo-electron microscopy (cryoEM) provides an attractive avenue for advancing our atomic resolution understanding of materials, molecules and living systems. However, the vast majority of published cryoEM methodologies focus on the characterization of aerobically purified samples. Air-sensitive enzymes and microorganisms represent important yet understudied systems in structural biology
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Packaging and containerization of computational methods Nat. Protoc. (IF 14.8) Pub Date : 2024-04-02 Mohammed Alser, Brendan Lawlor, Richard J. Abdill, Sharon Waymost, Ram Ayyala, Neha Rajkumar, Nathan LaPierre, Jaqueline Brito, André M. Ribeiro-dos-Santos, Nour Almadhoun, Varuni Sarwal, Can Firtina, Tomasz Osinski, Eleazar Eskin, Qiyang Hu, Derek Strong, Byoung-Do (B.D) Kim, Malak S. Abedalthagafi, Onur Mutlu, Serghei Mangul
Methods for analyzing the full complement of a biomolecule type, e.g., proteomics or metabolomics, generate large amounts of complex data. The software tools used to analyze omics data have reshaped the landscape of modern biology and become an essential component of biomedical research. These tools are themselves quite complex and often require the installation of other supporting software, libraries
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A practical guide for the preparation of C1-labeled α-amino acids using aldehyde catalysis with isotopically labeled CO2 Nat. Protoc. (IF 14.8) Pub Date : 2024-03-28 Michael G. J. Doyle, Braeden A. Mair, Anna Sib, Odey Bsharat, Maxime Munch, Volker Derdau, Benjamin H. Rotstein, Rylan J. Lundgren
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Standardized production of hPSC-derived cardiomyocyte aggregates in stirred spinner flasks Nat. Protoc. (IF 14.8) Pub Date : 2024-03-28 Nils Kriedemann, Wiebke Triebert, Jana Teske, Mira Mertens, Annika Franke, Kevin Ullmann, Felix Manstein, Lika Drakhlis, Alexandra Haase, Caroline Halloin, Ulrich Martin, Robert Zweigerdt
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Generating human bone marrow organoids for disease modeling and drug discovery Nat. Protoc. (IF 14.8) Pub Date : 2024-03-26 Aude-Anais Olijnik, Antonio Rodriguez-Romera, Zoë C. Wong, Yuqi Shen, Jasmeet S. Reyat, Natalie J. Jooss, Julie Rayes, Bethan Psaila, Abdullah O. Khan
The bone marrow supports and regulates hematopoiesis, responding to physiological requirements for blood cell production over ontogeny and during pathological challenges. Interactions between hematopoietic cells and niche components are challenging to study mechanistically in the human context, but are important to delineate in order to explore the pathobiology of blood and bone marrow disorders. Organoids
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Light-mediated intracellular polymerization Nat. Protoc. (IF 14.8) Pub Date : 2024-03-21 Mohamed Abdelrahim, Quan Gao, Yichuan Zhang, Weishuo Li, Qi Xing, Mark Bradley, Jin Geng
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Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach Nat. Protoc. (IF 14.8) Pub Date : 2024-03-21 Hongwei Yu, Yuli Li, Wentao Han, Lisui Bao, Fuyun Liu, Yuanting Ma, Zhongqi Pu, Qifan Zeng, Lingling Zhang, Zhenmin Bao, Shi Wang
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BridGE: a pathway-based analysis tool for detecting genetic interactions from GWAS Nat. Protoc. (IF 14.8) Pub Date : 2024-03-21 Mehrad Hajiaghabozorgi, Mathew Fischbach, Michael Albrecht, Wen Wang, Chad L. Myers
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Comprehensive synthesis of Ti3C2Tx from MAX phase to MXene Nat. Protoc. (IF 14.8) Pub Date : 2024-03-19 Marley Downes, Christopher E. Shuck, Bernard McBride, Jeffrey Busa, Yury Gogotsi
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An optimized culture system for efficient derivation of porcine expanded potential stem cells from preimplantation embryos and by reprogramming somatic cells Nat. Protoc. (IF 14.8) Pub Date : 2024-03-20 Degong Ruan, Yiyi Xuan, Timothy Theodore Ka Ki Tam, ZhuoXuan Li, Xiao Wang, Shao Xu, Doris Herrmann, Heiner Niemann, Liangxue Lai, Xuefei Gao, Monika Nowak-Imialek, Pentao Liu
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Stress-free single-cell transcriptomic profiling and functional genomics of murine eosinophils Nat. Protoc. (IF 14.8) Pub Date : 2024-03-19 Costanza Borrelli, Alessandra Gurtner, Isabelle C. Arnold, Andreas E. Moor
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BEHAV3D: a 3D live imaging platform for comprehensive analysis of engineered T cell behavior and tumor response Nat. Protoc. (IF 14.8) Pub Date : 2024-03-19 Maria Alieva, Mario Barrera Román, Sam de Blank, Diana Petcu, Amber L. Zeeman, Noël M. M. Dautzenberg, Annelisa M. Cornel, Cesca van de Ven, Rob Pieters, Monique L. den Boer, Stefan Nierkens, Friso G. J. Calkoen, Hans Clevers, Jürgen Kuball, Zsolt Sebestyén, Ellen J. Wehrens, Johanna F. Dekkers, Anne C. Rios
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Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX Nat. Protoc. (IF 14.8) Pub Date : 2024-03-15 Yupeng Wang, Haibao Tang, Xiyin Wang, Ying Sun, Paule V. Joseph, Andrew H. Paterson
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Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host–microbiota and other multi-omic interactions Nat. Protoc. (IF 14.8) Pub Date : 2024-03-12 Nolan K. Newman, Matthew S. Macovsky, Richard R. Rodrigues, Amanda M. Bruce, Jacob W. Pederson, Jyothi Padiadpu, Jigui Shan, Joshua Williams, Sankalp S. Patil, Amiran K. Dzutsev, Natalia Shulzhenko, Giorgio Trinchieri, Kevin Brown, Andrey Morgun
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Single-molecule magnetic tweezers to probe the equilibrium dynamics of individual proteins at physiologically relevant forces and timescales Nat. Protoc. (IF 14.8) Pub Date : 2024-03-11 Rafael Tapia-Rojo, Marc Mora, Sergi Garcia-Manyes
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Design and fabrication of wearable electronic textiles using twisted fiber-based threads Nat. Protoc. (IF 14.8) Pub Date : 2024-03-01 Kailin Zhang, Xiang Shi, Haibo Jiang, Kaiwen Zeng, Zihao Zhou, Peng Zhai, Lihua Zhang, Huisheng Peng
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Profiling native pulmonary basement membrane stiffness using atomic force microscopy Nat. Protoc. (IF 14.8) Pub Date : 2024-03-01 Bastian Hartmann, Lutz Fleischhauer, Monica Nicolau, Thomas Hartvig Lindkær Jensen, Florin-Andrei Taran, Hauke Clausen-Schaumann, Raphael Reuten
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Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets Nat. Protoc. (IF 14.8) Pub Date : 2024-02-29 Andreas Müller, Deborah Schmidt, Jan Philipp Albrecht, Lucas Rieckert, Maximilian Otto, Leticia Elizabeth Galicia Garcia, Gunar Fabig, Michele Solimena, Martin Weigert
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Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy Nat. Protoc. (IF 14.8) Pub Date : 2024-02-26 G. Heinrich, M. Kondratiuk, L. J. Gooßen, M. P. Wiesenfeldt
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High-throughput fabrication of antimicrobial phage microgels and example applications in food decontamination Nat. Protoc. (IF 14.8) Pub Date : 2024-02-27 Lei Tian, Kyle Jackson, Leon He, Shadman Khan, Mathura Thirugnanasampanthar, Mellissa Gomez, Fereshteh Bayat, Tohid F. Didar, Zeinab Hosseinidoust
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Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples Nat. Protoc. (IF 14.8) Pub Date : 2024-02-23 Tim H. H. Coorens, Michael Spencer Chapman, Nicholas Williams, Inigo Martincorena, Michael R. Stratton, Jyoti Nangalia, Peter J. Campbell
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rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data Nat. Protoc. (IF 14.8) Pub Date : 2024-02-23 Yuanyuan Wang, Zhijie Xie, Eric Kutschera, Jenea I. Adams, Kathryn E. Kadash-Edmondson, Yi Xing
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GlYcoLISA: antigen-specific and subclass-specific IgG Fc glycosylation analysis based on an immunosorbent assay with an LC–MS readout Nat. Protoc. (IF 14.8) Pub Date : 2024-02-21 David Falck, Manfred Wuhrer
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Web-based multi-omics integration using the Analyst software suite Nat. Protoc. (IF 14.8) Pub Date : 2024-02-14 Jessica D. Ewald, Guangyan Zhou, Yao Lu, Jelena Kolic, Cara Ellis, James D. Johnson, Patrick E. Macdonald, Jianguo Xia
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Isoform-specific RNA structure determination using Nano-DMS-MaP Nat. Protoc. (IF 14.8) Pub Date : 2024-02-12 Anne-Sophie Gribling-Burrer, Patrick Bohn, Redmond P. Smyth
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Using high-resolution microscopy data to generate realistic structures for electromagnetic FDTD simulations from complex biological models Nat. Protoc. (IF 14.8) Pub Date : 2024-02-08 John M. Ball, Wei Li
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Engineering megabase-sized genomic deletions with MACHETE (Molecular Alteration of Chromosomes with Engineered Tandem Elements) Nat. Protoc. (IF 14.8) Pub Date : 2024-02-07 Francisco M. Barriga, Scott W. Lowe
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Functionalized tetrahedral DNA frameworks for the capture of circulating tumor cells Nat. Protoc. (IF 14.8) Pub Date : 2024-02-05 Yirong Chen, Meihua Lin, Dekai Ye, Shaopeng Wang, Xiaolei Zuo, Min Li
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Comprehensive multiscale analysis of lactate metabolic dynamics in vitro and in vivo using highly responsive biosensors Nat. Protoc. (IF 14.8) Pub Date : 2024-02-02 Aoxue Wang, Yejun Zou, Shuning Liu, Xiuze Zhang, Ting Li, Lijuan Zhang, Ruwen Wang, Yale Xia, Xie Li, Zhuo Zhang, Tiemin Liu, Zhenyu Ju, Ru Wang, Joseph Loscalzo, Yi Yang, Yuzheng Zhao
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Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids Nat. Protoc. (IF 14.8) Pub Date : 2024-02-01 João Pedro Alves-Lopes, Frederick C. K. Wong, M. Azim Surani
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Quantitative profiling of posttranslational modifications of pathological tau via sarkosyl fractionation and mass spectrometry Nat. Protoc. (IF 14.8) Pub Date : 2024-01-30 Kathrin Wenger, Arthur Viode, Mukesh Kumar, Hanno Steen, Judith A. Steen
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Mapping protein–RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2) Nat. Protoc. (IF 14.8) Pub Date : 2024-01-26 Martin Lewinski, Mirko Brüggemann, Tino Köster, Marlene Reichel, Thorsten Bergelt, Katja Meyer, Julian König, Kathi Zarnack, Dorothee Staiger
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Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments Nat. Protoc. (IF 14.8) Pub Date : 2024-01-24 Coral Barcenilla, José F. Cobo-Díaz, Francesca De Filippis, Vincenzo Valentino, Raul Cabrera Rubio, Dominic O’Neil, Lisa Mahler de Sanchez, Federica Armanini, Niccolò Carlino, Aitor Blanco-Míguez, Federica Pinto, Inés Calvete-Torre, Carlos Sabater, Susana Delgado, Patricia Ruas-Madiedo, Narciso M. Quijada, Monika Dzieciol, Sigurlaug Skírnisdóttir, Stephen Knobloch, Alba Puente, Mercedes López, Miguel
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An end-to-end workflow for nondestructive 3D pathology Nat. Protoc. (IF 14.8) Pub Date : 2024-01-23 Kevin W. Bishop, Lindsey A. Erion Barner, Qinghua Han, Elena Baraznenok, Lydia Lan, Chetan Poudel, Gan Gao, Robert B. Serafin, Sarah S. L. Chow, Adam K. Glaser, Andrew Janowczyk, David Brenes, Hongyi Huang, Dominie Miyasato, Lawrence D. True, Soyoung Kang, Joshua C. Vaughan, Jonathan T. C. Liu
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OptADMET: a web-based tool for substructure modifications to improve ADMET properties of lead compounds Nat. Protoc. (IF 14.8) Pub Date : 2024-01-23 Jiacai Yi, Shaohua Shi, Li Fu, Ziyi Yang, Pengfei Nie, Aiping Lu, Chengkun Wu, Yafeng Deng, Changyu Hsieh, Xiangxiang Zeng, Tingjun Hou, Dongsheng Cao
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GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution Nat. Protoc. (IF 14.8) Pub Date : 2024-01-22 Weiguo Shen, Hanxiao Sun, Cong Liu, Yunpeng Yi, Yongkang Hou, Ye Xiao, Yufei Hu, Bo Lu, Jinying Peng, Jing Wang, Chengqi Yi
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Irreversible light-activated SpyLigation mediates split-protein assembly in 4D Nat. Protoc. (IF 14.8) Pub Date : 2024-01-22 Brizzia G. Munoz-Robles, Cole A. DeForest
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Production and use of antigen tetramers to study antigen-specific B cells Nat. Protoc. (IF 14.8) Pub Date : 2024-01-19 Allyssa Phelps, Diego Pazos-Castro, Francesca Urselli, Emily Grydziuszko, Olivia Mann-Delany, Allison Fang, Tina D. Walker, Rangana Talpe Guruge, Jaime Tome-Amat, Araceli Diaz-Perales, Susan Waserman, Jim Boonyaratanakornkit, Manel Jordana, Justin J. Taylor, Joshua F. E. Koenig
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Hyperspectral confocal imaging for high-throughput readout and analysis of bio-integrated microlasers Nat. Protoc. (IF 14.8) Pub Date : 2024-01-18 Vera M. Titze, Soraya Caixeiro, Vinh San Dinh, Matthias König, Matthias Rübsam, Nachiket Pathak, Anna-Lena Schumacher, Maximilian Germer, Christian Kukat, Carien M. Niessen, Marcel Schubert, Malte C. Gather
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Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0 Nat. Protoc. (IF 14.8) Pub Date : 2024-01-18 Yu Chen, Johan Gustafsson, Albert Tafur Rangel, Mihail Anton, Iván Domenzain, Cheewin Kittikunapong, Feiran Li, Le Yuan, Jens Nielsen, Eduard J. Kerkhoven
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Bacterial genome engineering using CRISPR-associated transposases Nat. Protoc. (IF 14.8) Pub Date : 2024-01-12 Diego Rivera Gelsinger, Phuc Leo H. Vo, Sanne E. Klompe, Carlotta Ronda, Harris H. Wang, Samuel H. Sternberg
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Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy Nat. Protoc. (IF 14.8) Pub Date : 2024-01-11 Duo Zhang, Abigail H. Cleveland, Elisavet Krimitza, Katherine Han, Chenlong Yi, Andrea L. Stout, Wei Zou, Jay F. Dorsey, Yanqing Gong, Yi Fan
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Streamlining spatial omics data analysis with Pysodb Nat. Protoc. (IF 14.8) Pub Date : 2023-12-22 Senlin Lin, Fangyuan Zhao, Zihan Wu, Jianhua Yao, Yi Zhao, Zhiyuan Yuan
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Nano-CUT&Tag for multimodal chromatin profiling at single-cell resolution Nat. Protoc. (IF 14.8) Pub Date : 2023-12-21 José Ramón Bárcenas-Walls, Federico Ansaloni, Bastien Hervé, Emilia Strandback, Tomas Nyman, Gonçalo Castelo-Branco, Marek Bartošovič
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Collections from Nature Protocols Nat. Protoc. (IF 14.8) Pub Date : 2023-12-19
In 2023, Nature Protocols launched four new collections (on organoids, neural probes, cognitive neuroscience frameworks and neurostimulation) to help readers navigate our content and highlight areas of particular current interest.
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Profiling human brain vascular cells using single-cell transcriptomics and organoids Nat. Protoc. (IF 14.8) Pub Date : 2023-12-15 Elizabeth E. Crouch, Loukas N. Diafos, Edward J. Valenzuela, Kaylee Wedderburn-Pugh, Janeth Ochoa Birrueta, Jaela Caston, Tara Joseph, Madeline G. Andrews, Aparna Bhaduri, Eric J. Huang
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Design and build of small-scale magnetic soft-bodied robots with multimodal locomotion Nat. Protoc. (IF 14.8) Pub Date : 2023-12-14 Ziyu Ren, Metin Sitti
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High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities Nat. Protoc. (IF 14.8) Pub Date : 2023-12-13 Patrick Müller, Jacobo de la Cuesta-Zuluaga, Michael Kuhn, Maral Baghai Arassi, Tim Treis, Sonja Blasche, Michael Zimmermann, Peer Bork, Kiran Raosaheb Patil, Athanasios Typas, Sarela Garcia-Santamarina, Lisa Maier
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Optimized whole-genome sequencing workflow for tumor diagnostics in routine pathology practice Nat. Protoc. (IF 14.8) Pub Date : 2023-12-13 Kris G. Samsom, Linda J. W. Bosch, Luuk J. Schipper, Daoin Schout, Paul Roepman, Mirjam C. Boelens, Ferry Lalezari, Elisabeth G. Klompenhouwer, Adrianus J. de Langen, Tineke E. Buffart, Berit M. H. van Linder, Kelly van Deventer, Kay van den Burg, Unga Unmehopa, Efraim H. Rosenberg, Roelof Koster, Frans B. L. Hogervorst, José G. van den Berg, Immy Riethorst, Lieke Schoenmaker, Daphne van Beek, Ewart
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Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz Nat. Protoc. (IF 14.8) Pub Date : 2023-12-12 Marco Schiavina, Lorenzo Bracaglia, Maria Anna Rodella, Rainer Kümmerle, Robert Konrat, Isabella C. Felli, Roberta Pierattelli
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Automated human induced pluripotent stem cell culture and sample preparation for 3D live-cell microscopy Nat. Protoc. (IF 14.8) Pub Date : 2023-12-12 Benjamin W. Gregor, Mackenzie E. Coston, Ellen M. Adams, Joy Arakaki, Antoine Borensztejn, Thao P. Do, Margaret A. Fuqua, Amanda Haupt, Melissa C. Hendershott, Winnie Leung, Irina A. Mueller, Aditya Nath, Angelique M. Nelson, Susanne M. Rafelski, Emmanuel E. Sanchez, Madison J. Swain-Bowden, W. Joyce Tang, Derek J. Thirstrup, Winfried Wiegraebe, Brian P. Whitney, Calysta Yan, Ruwanthi N. Gunawardane
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In vivo identification of astrocyte and neuron subproteomes by proximity-dependent biotinylation Nat. Protoc. (IF 14.8) Pub Date : 2023-12-07 Joselyn S. Soto, Yasaman Jami-Alahmadi, James A. Wohlschlegel, Baljit S. Khakh
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Head-mounted central venous access during optical recordings and manipulations of neural activity in mice Nat. Protoc. (IF 14.8) Pub Date : 2023-12-06 Christine Liu, Daniel J. Freeman, Stephan Lammel
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Small RNA structural biochemistry in a post-sequencing era Nat. Protoc. (IF 14.8) Pub Date : 2023-12-06 Juan Pablo Tosar, Mauricio Castellano, Bruno Costa, Alfonso Cayota
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Synthesis and functionalization of scalable and versatile 2D protein films via amyloid-like aggregation Nat. Protoc. (IF 14.8) Pub Date : 2023-12-04 Yongchun Liu, Shuting Miao, Hao Ren, Lihua Tian, Jian Zhao, Peng Yang
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Biomimetic tail-to-head terpene cyclizations using the resorcin[4]arene capsule catalyst Nat. Protoc. (IF 14.8) Pub Date : 2023-12-01 Ivan Cornu, Leonidas-Dimitrios Syntrivanis, Konrad Tiefenbacher
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Reproducible strategy for excisional skin-wound-healing studies in mice Nat. Protoc. (IF 14.8) Pub Date : 2023-11-29 Matan Yampolsky, Ido Bachelet, Yaron Fuchs