Optimized single-nucleus transcriptional profiling by combinatorial indexing
Nature Protocols, Published online: 19 October 2022; doi:10.1038/s41596-022-00752-0This protocol presents an optimized version of the single-cell combinatorial indexing RNA sequencing protocol that is faster, less expensive and suitable for profiling tissues rich in RNases, as well as a ‘Tiny-Sci’ protocol for limited input samples. (Source: Nature Protocols)
Source: Nature Protocols - October 19, 2022 Category: Biomedical Science Authors: Beth K. Martin Chengxiang Qiu Eva Nichols Melissa Phung Rula Green-Gladden Sanjay Srivatsan Ronnie Blecher-Gonen Brian J. Beliveau Cole Trapnell Junyue Cao Jay Shendure Source Type: research
Direct delivery and fast-treated Agrobacterium co-culture (Fast-TrACC) plant transformation methods for Nicotiana benthamiana
Nature Protocols, Published online: 17 October 2022; doi:10.1038/s41596-022-00749-9This protocol comprises two Agrobacterium-based methods (direct delivery and fast-treated Agrobacterium co-culture) that use developmental regulators to induce de novo meristems to create genetic modifications on either sterilely grown or soil-grown Nicotiana benthamiana plants. (Source: Nature Protocols)
Source: Nature Protocols - October 17, 2022 Category: Biomedical Science Authors: Jon P. Cody Michael F. Maher Ryan A. Nasti Colby G. Starker James C. Chamness Daniel F. Voytas Source Type: research
Induction of human trophoblast stem cells
Nature Protocols, Published online: 14 October 2022; doi:10.1038/s41596-022-00744-0The authors describe a technique for reprogramming human somatic cells into induced trophoblast stem cells and the conversion of human naive and extended pluripotent stem cells into converted trophoblast stem cells, with functional assays for their differentiation potential. (Source: Nature Protocols)
Source: Nature Protocols - October 14, 2022 Category: Biomedical Science Authors: Ga ël Castel Laurent David Source Type: research
Establishment of human induced trophoblast stem cells via reprogramming of fibroblasts
Nature Protocols, Published online: 14 October 2022; doi:10.1038/s41596-022-00742-2Stem cell models for the trophoblast lineage have been lacking. This protocol describes the reprogramming of human fibroblasts into induced trophoblast stem cells, alongside steps for their molecular and functional characterization. (Source: Nature Protocols)
Source: Nature Protocols - October 14, 2022 Category: Biomedical Science Authors: Jia Ping Tan Xiaodong Liu Jose M. Polo Source Type: research
Off-the-shelf proximity biotinylation using ProtA-TurboID
Nature Protocols, Published online: 12 October 2022; doi:10.1038/s41596-022-00748-wThis protocol describes proximity biotinylation in cells without transfection or transduction using an off-the-shelf recombinant ProtA-TurboID enzyme consisting of a biotin ligase fused to an antibody-recognizing moiety, which, combined with a bait-protein-specific antibody, can be used to identify bait-proximal proteins. (Source: Nature Protocols)
Source: Nature Protocols - October 12, 2022 Category: Biomedical Science Authors: Irene Santos-Barriopedro Guido van Mierlo Michiel Vermeulen Source Type: research
Isolation of ready-made rat microvessels and its applications in effective in vivo vascularization and in angiogenic studies in vitro
Nature Protocols, Published online: 12 October 2022; doi:10.1038/s41596-022-00743-1Protocol for isolating ready-made rat microvessels from adipose tissue and their incorporation into 3D collagen hydrogels. These microvessel gels can be used for in vitro angiogenic assays or transplanted into mice for in vivo vascularization studies. (Source: Nature Protocols)
Source: Nature Protocols - October 12, 2022 Category: Biomedical Science Authors: Xuetao Sun Yasaman Aghazadeh Sara S. Nunes Source Type: research
Enzyme-free targeted DNA demethylation using CRISPR–dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression
Nature Protocols, Published online: 07 October 2022; doi:10.1038/s41596-022-00741-3This protocol provides an enzyme-free method to achieve targeted DNA demethylation based on steric hindrance by dCas9 bound at or close to CpG sites of interest to identify DNA methylation marks causal to altered gene expression. (Source: Nature Protocols)
Source: Nature Protocols - October 7, 2022 Category: Biomedical Science Authors: Daniel M. Sapozhnikov Moshe Szyf Source Type: research
Multispectral confocal 3D imaging of intact healthy and tumor tissue using mLSR-3D
Nature Protocols, Published online: 30 September 2022; doi:10.1038/s41596-022-00739-xMultispectral large-scale single-cell resolution 3D imaging allows up to eight fluorophores to be captured in a single acquisition. This protocol enables the visualization and exploration of large intact tissue volumes. (Source: Nature Protocols)
Source: Nature Protocols - September 30, 2022 Category: Biomedical Science Authors: Ravian L. van Ineveld Rapha ël Collot Mario Barrera Rom án Anna Pagliaro Nils Bessler Hendrikus C. R. Ariese Michiel Kleinnijenhuis Marcel Kool Maria Alieva Susana M. Chuva de Sousa Lopes Ellen J. Wehrens Anne C. Rios Source Type: research
Measuring key human carbohydrate digestive enzyme activities using high-performance anion-exchange chromatography with pulsed amperometric detection
Nature Protocols, Published online: 30 September 2022; doi:10.1038/s41596-022-00736-0Inhibitors for carbohydrate digestive enzymes are used to manage conditions like diabetes. In this assay for digestive enzyme activity, sugars are quantified by using high-performance anion-exchange chromatography with pulsed amperometric detection. (Source: Nature Protocols)
Source: Nature Protocols - September 30, 2022 Category: Biomedical Science Authors: Elizabeth Barber Michael J. Houghton Rizliya Visvanathan Gary Williamson Source Type: research
Metagenome analysis using the Kraken software suite
Nature Protocols, Published online: 28 September 2022; doi:10.1038/s41596-022-00738-yThe authors provide a guide to using the Kraken suite for metagenomics analysis, including classification, quantification and visualization, illustrated by quantification of species in the microbiome and identification of pathogens in a clinical sample. (Source: Nature Protocols)
Source: Nature Protocols - September 28, 2022 Category: Biomedical Science Authors: Jennifer Lu Natalia Rincon Derrick E. Wood Florian P. Breitwieser Christopher Pockrandt Ben Langmead Steven L. Salzberg Martin Steinegger Source Type: research
Cultivation of previously uncultured microorganisms with a continuous-flow down-flow hanging sponge (DHS) bioreactor, using a syntrophic archaeon culture obtained from deep marine sediment as a case study
Nature Protocols, Published online: 14 September 2022; doi:10.1038/s41596-022-00735-1This two-stage bioreactor-mediated approach for culturing previously uncultured microorganisms involves enrichment of indigenous organisms by using a continuous-flow down-flow hanging sponge bioreactor and subsequent selective batch cultivation. (Source: Nature Protocols)
Source: Nature Protocols - September 14, 2022 Category: Biomedical Science Authors: Hiroyuki Imachi Masaru K. Nobu Masayuki Miyazaki Eiji Tasumi Yumi Saito Sanae Sakai Miyuki Ogawara Akiyoshi Ohashi Ken Takai Source Type: research
Neuroscience robotics for controlled induction and real-time assessment of hallucinations
Nature Protocols, Published online: 12 September 2022; doi:10.1038/s41596-022-00737-zLittle is known about the brain mechanisms of hallucinations. This protocol describes the use of a robotic device and sensorimotor method to reproducibly induce and measure presence hallucinations by behavioral assay and fMRI. (Source: Nature Protocols)
Source: Nature Protocols - September 12, 2022 Category: Biomedical Science Authors: Fosco Bernasconi Eva Blondiaux Giulio Rognini Herberto Dhanis Laurent Jenni Jevita Potheegadoo Masayuki Hara Olaf Blanke Source Type: research
Monitoring cell membrane recycling dynamics of proteins using whole-cell fluorescence recovery after photobleaching of pH-sensitive genetic tags
Nature Protocols, Published online: 05 September 2022; doi:10.1038/s41596-022-00732-4The cell membrane turnover kinetics of the main glial glutamate transporter GLT1 are quantified by fusing it to a pH-sensitive fluorescent protein and performing measurements using whole-cell fluorescence recovery after photobleaching. (Source: Nature Protocols)
Source: Nature Protocols - September 5, 2022 Category: Biomedical Science Authors: Piotr Michaluk Dmitri A. Rusakov Source Type: research
MOF-derived nanoporous carbons with diverse tunable nanoarchitectures
Nature Protocols, Published online: 05 September 2022; doi:10.1038/s41596-022-00718-2Direct carbonization of zeolitic imidazolate framework-type metal-organic frameworks, as described in this protocol, results in nanoporous carbons that can be used for diverse electrochemical applications. (Source: Nature Protocols)
Source: Nature Protocols - September 5, 2022 Category: Biomedical Science Authors: Minjun Kim Ruijing Xin Jacob Earnshaw Jing Tang Jonathan P. Hill Aditya Ashok Ashok Kumar Nanjundan Jeonghun Kim Christine Young Yoshiyuki Sugahara Jongbeom Na Yusuke Yamauchi Source Type: research
Synthesis of cyclodextrin derivatives for enantiodifferentiating photocyclodimerization of 2-anthracenecarboxylate
Nature Protocols, Published online: 31 August 2022; doi:10.1038/s41596-022-00722-6Photochemical methods are increasingly being used in chemical synthesis. This protocol describes how to optimize the reaction conditions for a standard chiral example using cyclodextrin derivatives as supramolecular hosts. (Source: Nature Protocols)
Source: Nature Protocols - August 31, 2022 Category: Biomedical Science Authors: Xueqin Wei Jiecheng Ji Yongxin Nie Liangjian Tang Ming Rao Xiaoqian Wang Wanhua Wu Dan Su Zhihui Zhong Cheng Yang Source Type: research
