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An operant social self-administration and choice model in rats Nat. Protoc. (IF 11.334) Pub Date : 2020-03-20 Marco Venniro; Yavin Shaham
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Toward a unified framework for interpreting machine-learning models in neuroimaging Nat. Protoc. (IF 11.334) Pub Date : 2020-03-18 Lada Kohoutová; Juyeon Heo; Sungmin Cha; Sungwoo Lee; Taesup Moon; Tor D. Wager; Choong-Wan Woo
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Reductive amination using cobalt-based nanoparticles for synthesis of amines Nat. Protoc. (IF 11.334) Pub Date : 2020-03-18 Kathiravan Murugesan; Vishwas G. Chandrashekhar; Thirusangumurugan Senthamarai; Rajenahally V. Jagadeesh; Matthias Beller
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Author Correction: Decellularization and antibody staining of mouse tissues to map native extracellular matrix structures in 3D Nat. Protoc. (IF 11.334) Pub Date : 2020-03-16 Alejandro E. Mayorca-Guiliani; Oliver Willacy; Chris D. Madsen; Maria Rafaeva; Stefanie Elisabeth Heumüller; Felix Bock; Gerhard Sengle; Manuel Koch; Thomas Imhof; Frank Zaucke; Raimund Wagener; Takako Sasaki; Janine T. Erler; Raphael Reuten
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Clonal tracking using embedded viral barcoding and high-throughput sequencing Nat. Protoc. (IF 11.334) Pub Date : 2020-03-04 Charles Bramlett; Du Jiang; Anna Nogalska; Jiya Eerdeng; Jorge Contreras; Rong Lu
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Manual and automated Cu-mediated radiosynthesis of the PARP inhibitor [18F]olaparib. Nat. Protoc. (IF 11.334) Pub Date : 2020-02-28 Florian Guibbal,Patrick G Isenegger,Thomas C Wilson,Anna Pacelli,Damien Mahaut,Jeroen B I Sap,Nicholas J Taylor,Stefan Verhoog,Sean Preshlock,Rebekka Hueting,Bart Cornelissen,Véronique Gouverneur
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CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes. Nat. Protoc. (IF 11.334) Pub Date : 2020-02-26 Mirjana Efremova,Miquel Vento-Tormo,Sarah A Teichmann,Roser Vento-Tormo
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Engineering primary T cells with chimeric antigen receptors for rewired responses to soluble ligands. Nat. Protoc. (IF 11.334) Pub Date : 2020-02-26 ZeNan L Chang,Andrew J Hou,Yvonne Y Chen
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Identification, quantification and bioinformatic analysis of RNA-dependent proteins by RNase treatment and density gradient ultracentrifugation using R-DeeP Nat. Protoc. (IF 11.334) Pub Date : 2020-02-24 Maiwen Caudron-Herger; Elsa Wassmer; Isha Nasa; Astrid-Solveig Schultz; Jeanette Seiler; Arminja N. Kettenbach; Sven Diederichs
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A whole-tissue RNA-seq toolkit for organism-wide studies of gene expression with PME-seq. Nat. Protoc. (IF 11.334) Pub Date : 2020-02-19 Surya Pandey,Michihiro Takahama,Adam Gruenbaum,Makda Zewde,Katerina Cheronis,Nicolas Chevrier
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Quantification of mRNA translation in live cells using single-molecule imaging. Nat. Protoc. (IF 11.334) Pub Date : 2020-02-19 Deepak Khuperkar,Tim A Hoek,Stijn Sonneveld,Bram M P Verhagen,Sanne Boersma,Marvin E Tanenbaum
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Author Correction: GRID-seq for comprehensive analysis of global RNA-chromatin interactions. Nat. Protoc. (IF 11.334) Pub Date : 2020-02-14 Bing Zhou,Xiao Li,Daji Luo,Do-Hwan Lim,Yu Zhou,Xiang-Dong Fu
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Rapid identification of human mast cell degranulation regulators using functional genomics coupled to high-resolution confocal microscopy. Nat. Protoc. (IF 11.334) Pub Date : 2020-02-14 Jelle Folkerts,Nicolas Gaudenzio,Marcus Maurer,Rudi W Hendriks,Ralph Stadhouders,See-Ying Tam,Stephen J Galli
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A preclinical large-animal model for the assessment of critical-size load-bearing bone defect reconstruction. Nat. Protoc. (IF 11.334) Pub Date : 2020-02-14 David S Sparks,Siamak Saifzadeh,Flavia Medeiros Savi,Constantin E Dlaska,Arne Berner,Jan Henkel,Johannes C Reichert,Martin Wullschleger,Jiongyu Ren,Amaia Cipitria,Jacqui A McGovern,Roland Steck,Michael Wagels,Maria Ann Woodruff,Michael A Schuetz,Dietmar W Hutmacher
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Metal-free photocatalysts for the oxidation of non-activated alcohols and the oxygenation of tertiary amines performed in air or oxygen. Nat. Protoc. (IF 11.334) Pub Date : 2020-02-12 Yu Zhang,Waldemar Schilling,Daniel Riemer,Shoubhik Das
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CellTagging: combinatorial indexing to simultaneously map lineage and identity at single-cell resolution. Nat. Protoc. (IF 11.334) Pub Date : 2020-02-12 Wenjun Kong,Brent A Biddy,Kenji Kamimoto,Junedh M Amrute,Emily G Butka,Samantha A Morris
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Superresolution imaging of chromatin fibers to visualize epigenetic information on replicative DNA. Nat. Protoc. (IF 11.334) Pub Date : 2020-02-12 Matthew Wooten,Yingying Li,Jonathan Snedeker,Zehra F Nizami,Joseph G Gall,Xin Chen
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DNA copy-number measurement of genome replication dynamics by high-throughput sequencing: the sort-seq, sync-seq and MFA-seq family. Nat. Protoc. (IF 11.334) Pub Date : 2020-02-12 Dzmitry G Batrakou,Carolin A Müller,Rosemary H C Wilson,Conrad A Nieduszynski
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Formation and growth of sub-3-nm aerosol particles in experimental chambers. Nat. Protoc. (IF 11.334) Pub Date : 2020-02-12 Lubna Dada,Katrianne Lehtipalo,Jenni Kontkanen,Tuomo Nieminen,Rima Baalbaki,Lauri Ahonen,Jonathan Duplissy,Chao Yan,Biwu Chu,Tuukka Petäjä,Kari Lehtinen,Veli-Matti Kerminen,Markku Kulmala,Juha Kangasluoma
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Measurement of differential chromatin interactions with absolute quantification of architecture (AQuA-HiChIP). Nat. Protoc. (IF 11.334) Pub Date : 2020-02-12 Berkley E Gryder,Javed Khan,Benjamin Z Stanton
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Long-term in vivo imaging of Drosophila larvae. Nat. Protoc. (IF 11.334) Pub Date : 2020-02-10 Parisa Kakanj,Sabine A Eming,Linda Partridge,Maria Leptin
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Formaldehyde-assisted isolation of regulatory DNA elements from Arabidopsis leaves. Nat. Protoc. (IF 11.334) Pub Date : 2020-02-10 Stephani Baum,Eva-Maria Reimer-Michalski,Michal R Jaskiewicz,Uwe Conrath
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Skilled reaching tasks for head-fixed mice using a robotic manipulandum. Nat. Protoc. (IF 11.334) Pub Date : 2020-02-07 Mark J Wagner,Joan Savall,Tony Hyun Kim,Mark J Schnitzer,Liqun Luo
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Author Correction: SHERLOCK: nucleic acid detection with CRISPR nucleases. Nat. Protoc. (IF 11.334) Pub Date : 2020-03-01 Max J Kellner,Jeremy G Koob,Jonathan S Gootenberg,Omar O Abudayyeh,Feng Zhang
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Selective isolation of large segments from individual microbial genomes and environmental DNA samples using transformation-associated recombination cloning in yeast. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-31 Natalay Kouprina,Vladimir N Noskov,Vladimir Larionov
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Isolation of tissue-resident vascular endothelial stem cells from mouse liver. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-31 Hisamichi Naito,Taku Wakabayashi,Masako Ishida,Chang-Hyun Gil,Tomohiro Iba,Fitriana Nur Rahmawati,Shota Shimizu,Mervin C Yoder,Nobuyuki Takakura
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Rapid online buffer exchange for screening of proteins, protein complexes and cell lysates by native mass spectrometry. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-31 Zachary L VanAernum,Florian Busch,Benjamin J Jones,Mengxuan Jia,Zibo Chen,Scott E Boyken,Aniruddha Sahasrabuddhe,David Baker,Vicki H Wysocki
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Multicolor two-photon imaging of in vivo cellular pathophysiology upon influenza virus infection using the two-photon IMPRESS. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-29 Hiroshi Ueki,I-Hsuan Wang,Dongming Zhao,Matthias Gunzer,Yoshihiro Kawaoka
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Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-29 Claudio Lo Giudice,Marco Antonio Tangaro,Graziano Pesole,Ernesto Picardi
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Facilitating chemical and biochemical experiments with electronic microcontrollers and single-board computers. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-29 Gurpur Rakesh D Prabhu,Tzu-Hsien Yang,Chun-Yao Hsu,Chun-Pei Shih,Chun-Ming Chang,Pei-Han Liao,Hsiang-Ting Ni,Pawel L Urban
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Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-24 Arya Kaul,Sourya Bhattacharyya,Ferhat Ay
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Direct and simultaneous observation of transcription and chromosome architecture in single cells with Hi-M. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-22 Andrés M Cardozo Gizzi,Sergio M Espinola,Julian Gurgo,Christophe Houbron,Jean-Bernard Fiche,Diego I Cattoni,Marcelo Nollmann
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Isolation of satellite cells and transplantation into mice for lineage tracing in muscle. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-22 Peter Feige,Michael A Rudnicki
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Addendum: A guide to small-molecule structure assignment through computation of (¹H and ¹³C) NMR chemical shifts. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-16 Patrick H Willoughby,Matthew J Jansma,Thomas R Hoye
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Chemically defined and xenogeneic-free culture method for human epidermal keratinocytes on laminin-based matrices. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-15 Monica Suryana Tjin,Alvin Wen Choong Chua,Karl Tryggvason
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Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-15 Jasmine Chong,Peng Liu,Guangyan Zhou,Jianguo Xia
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Direct characterization of overproduced proteins by native mass spectrometry. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-15 Shay Vimer,Gili Ben-Nissan,Michal Sharon
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Multiparameter screening method for developing optimized red-fluorescent proteins. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-15 Daphne S Bindels,Marten Postma,Lindsay Haarbosch,Laura van Weeren,Theodorus W J Gadella
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Machine learning workflows to estimate class probabilities for precision cancer diagnostics on DNA methylation microarray data. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-13 Máté E Maros,David Capper,David T W Jones,Volker Hovestadt,Andreas von Deimling,Stefan M Pfister,Axel Benner,Manuela Zucknick,Martin Sill
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Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-13 Carlo Vermeulen,Amin Allahyar,Britta A M Bouwman,Peter H L Krijger,Marjon J A M Verstegen,Geert Geeven,Christian Valdes-Quezada,Ivo Renkens,Roy Straver,Wigard P Kloosterman,Jeroen de Ridder,Wouter de Laat
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On-chip 3D neuromuscular model for drug screening and precision medicine in neuromuscular disease. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-13 Tatsuya Osaki,Sebastien G M Uzel,Roger D Kamm
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FLOW-MAP: a graph-based, force-directed layout algorithm for trajectory mapping in single-cell time course datasets. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-13 Melissa E Ko,Corey M Williams,Kristen I Fread,Sarah M Goggin,Rohit S Rustagi,Gabriela K Fragiadakis,Garry P Nolan,Eli R Zunder
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Activation and expansion of human T cells using artificial antigen-presenting cell scaffolds. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-13 David K Y Zhang,Alexander S Cheung,David J Mooney
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Real-time physiological measurements of oxygen using a non-invasive self-referencing optical fiber microsensor. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-10 Fernando Ferreira,Guillaume Luxardi,Brian Reid,Li Ma,VijayKrishna Raghunathan,Min Zhao
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Biomimetic smoking robot for in vitro inhalation exposure compatible with microfluidic organ chips. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-10 Kambez H Benam,Richard Novak,Thomas C Ferrante,Youngjae Choe,Donald E Ingber
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Understanding chemical reactivity using the activation strain model. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-10 Pascal Vermeeren,Stephanie C C van der Lubbe,Célia Fonseca Guerra,F Matthias Bickelhaupt,Trevor A Hamlin
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Recording transcriptional histories using Record-seq. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-10 Tanmay Tanna,Florian Schmidt,Mariia Y Cherepkova,Michal Okoniewski,Randall J Platt
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Long-term ex vivo expansion of mouse hematopoietic stem cells. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-08 Adam C Wilkinson,Reiko Ishida,Hiromitsu Nakauchi,Satoshi Yamazaki
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Manipulating the hydrophobicity of DNA as a universal strategy for visual biosensing. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-08 Zhong Feng Gao,Rui Liu,Jinhua Wang,Jun Dai,Wei-Hua Huang,Mingjie Liu,Shutao Wang,Fan Xia,Shusheng Zhang,Lei Jiang
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Manipulating gene translation in plants by CRISPR-Cas9-mediated genome editing of upstream open reading frames. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-08 Xiaomin Si,Huawei Zhang,Yanpeng Wang,Kunling Chen,Caixia Gao
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A comprehensive guide to dynamic analysis of microbial gene expression using the 3D-printed PFIbox and a fluorescent reporter library. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-08 Shawn French,Amelia Bing Ya Guo,Eric D Brown
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Using TTchem-seq for profiling nascent transcription and measuring transcript elongation. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-08 Lea H Gregersen,Richard Mitter,Jesper Q Svejstrup
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Unraveling human adult hippocampal neurogenesis. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-08 Miguel Flor-García,Julia Terreros-Roncal,Elena P Moreno-Jiménez,Jesús Ávila,Alberto Rábano,María Llorens-Martín
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A toolbox for the longitudinal assessment of healthspan in aging mice. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-08 I Bellantuono,R de Cabo,D Ehninger,C Di Germanio,A Lawrie,J Miller,S J Mitchell,I Navas-Enamorado,P K Potter,T Tchkonia,J L Trejo,D W Lamming
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Analysis pipelines for cancer genome sequencing in mice. Nat. Protoc. (IF 11.334) Pub Date : 2020-01-06 Sebastian Lange,Thomas Engleitner,Sebastian Mueller,Roman Maresch,Maximilian Zwiebel,Laura González-Silva,Günter Schneider,Ruby Banerjee,Fengtang Yang,George S Vassiliou,Mathias J Friedrich,Dieter Saur,Ignacio Varela,Roland Rad
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A workflow for generating multi-strain genome-scale metabolic models of prokaryotes. Nat. Protoc. (IF 11.334) Pub Date : 2019-12-20 Charles J Norsigian,Xin Fang,Yara Seif,Jonathan M Monk,Bernhard O Palsson
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Sequential phosphoproteomics and N-glycoproteomics of plasma-derived extracellular vesicles. Nat. Protoc. (IF 11.334) Pub Date : 2019-12-20 Hillary Andaluz Aguilar,Anton B Iliuk,I-Hsuan Chen,W Andy Tao
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Tumor organoid-T-cell coculture systems. Nat. Protoc. (IF 11.334) Pub Date : 2019-12-18 Chiara M Cattaneo,Krijn K Dijkstra,Lorenzo F Fanchi,Sander Kelderman,Sovann Kaing,Nienke van Rooij,Stieneke van den Brink,Ton N Schumacher,Emile E Voest
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Real-time imaging of multivesicular body-plasma membrane fusion to quantify exosome release from single cells. Nat. Protoc. (IF 11.334) Pub Date : 2019-12-13 Maarten P Bebelman,Philippe Bun,Stephan Huveneers,Guillaume van Niel,D Michiel Pegtel,Frederik J Verweij
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Solid-state nanopore fabrication by automated controlled breakdown. Nat. Protoc. (IF 11.334) Pub Date : 2019-12-13 Matthew Waugh,Kyle Briggs,Dylan Gunn,Mathieu Gibeault,Simon King,Quinn Ingram,Aura Melissa Jimenez,Samuel Berryman,Dmytro Lomovtsev,Lukasz Andrzejewski,Vincent Tabard-Cossa
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