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Optimized identification and characterization of small RNAs with PANDORA-seq - Nature Protocols This Protocol describes optimized procedures for purification and sequencing of small noncoding RNAs from a variety of samples to characterize these diverse RNA species and map them to the parental RNAs from which they originate.

#NewNProt for #genomewide characterization of a diverse set of #smallnoncodingRNAs in cells and tissues

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Quantitative molecular imaging using deep magnetic resonance fingerprinting - Nature Protocols A comprehensive protocol for designing and performing magnetic resonance fingerprinting from chemical exchange saturation transfer and semi-solid magnetization transfer imaging using artificial intell...

#NewNProt: #MolecularMRI using deep MR fingerprinting provides quantitative #biomarkers for proteins, metabolites & pH bit.ly/4ljmLwT

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Cyborg organoids integrated with stretchable nanoelectronics can be functionally mapped during development - Nature Protocols The integration of stretchable mesh nanoelectronics with stem cells enables the creation of cyborg organoid tissue, which can be longitudinally characterized during development to improve organoid mod...

#NewNProt: A stretchable #nanoelectronic mesh which expands in a growing #organoid enables long-term #electricaldata acquisition bit.ly/3FNdCfD

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A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector - Nature Protocols This protocol describes a versatile computational tool for reference-free or reference-guided assessment and correction of errors in de novo genome assembly based on long-read sequencing data, showcas...

#NewNProt for evaluation and error correction of #genomeassemblies based on #longreadsequencing data bit.ly/4chEHnp

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CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data - Nature Protocols CellPhoneDB combines a curated database of receptor–ligand interactions with methods to infer cell–cell communication from single-cell expression data. This protocol update describes an expanded datab...

#NewNProt: Protocol Update of #CellPhoneDB, describing an expanded database of molecular interactors and new approaches to infer, prioritise and visualise the results bit.ly/4lbG2Af and see associated News & Views article

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Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq - Nature Protocols In this Protocol Extension, the authors describe procedures for spatial barcoding in tissue sections using a microfluidic chip followed by sequencing-based joint genome-wide profiling of transcriptome...

#NewNProt: Protocol Extension describing joint spatially resolved epigenomic and transcriptomic profiling on a tissue section using #microfluidic chips bit.ly/4hLs7xT #spatialtranscriptomics #spatialepigenomics see also associated News & Views

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DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity - Nature Protocols The DARLIN mouse enables the study of the cell lineages of millions of cells and at a high efficiency in vivo, through the incorporation of three barcoding arrays and a Cas9–TdT to improve editing div...

#NewNProt: DARLIN mouse for in vivo #lineagetracing at high efficiency and clonal diversity bit.ly/4hFeoZm

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Live-cell synthesis of biocompatible quantum dots - Nature Protocols Quantum dots can be synthesized in live yeast, bacterial and mammalian cells by controlling the temporal and spatial pattern of specific metabolic reactions via the timed supply of chemicals.

#NewNProt: live-cell synthesis of #quantumdots overcomes the limited biocompatibility of their conventionally synthesized counterparts bit.ly/3RhxUAi

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Standardized measurements for monitoring and comparing multiphoton microscope systems - Nature Protocols A set of procedures is described here for standardizing the evaluation of multiphoton microscope performance, covering laser power, pulse width optimizations, field of view, resolution and photomultip...

#NewNProt for standardising the evaluation of #multiphotonmicroscope performance; the art of multiphoton microscope maintenance bit.ly/3FEDeLF

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Live STED imaging of functional neuroanatomy - Nature Protocols Super-resolution microscopy using a confocal STED microscope enables analyzing the relationship between morphological and functional neuronal structures at nanoscale resolution in living brain slices.

#NewNProt for how to combine #STEDmicroscopy of #nanostructures with #functionalimaging in live settings. Find all you need to know for performing #superresolution #STED including troubleshooting solutions! Check it out bit.ly/4bXv7Wt

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Preparation, maintenance and propagation of synchronous cultures of photoactive Chlamydomonas cells - Nature Protocols Catalan et al. present a protocol covering the selection and characterization of experimental Chlamydomonas strains driven by specific applications, where culture synchronicity, population growth rate...

#NewNProt: Controlled culturing and selection of #Chlamydomonas strains with differing characteristics, tailored for a variety of applications bit.ly/41wdEjj

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mRNA lipid nanoparticle formulation, characterization and evaluation - Nature Protocols Lipid nanoparticles have emerged as leading candidates for encapsulating mRNA drugs and have shown success in in vivo applications. Here, the authors provide a step-by-step guide for mRNA lipid nanopa...

#NewNProt for mRNA #lipidnanoparticle formulation, characterization, and evaluation bit.ly/4kSBj6d #mRNALNP

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Unraveling cell–cell communication with NicheNet by inferring active ligands from transcriptomics data - Nature Protocols NicheNet is a computational tool to infer the ligand–receptor interactions that potentially regulate gene expression changes in receiver cell populations, by producing a list of prioritized ligands an...

#NewNProt for unraveling #cellcellcommunication with #NicheNet by inferring active ligands from #transcriptomics data bit.ly/41FP0xK

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Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) in primary human immune cells and hematopoietic stem cells - Nature Protocols Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) uses an amphiphilic peptide reagent to mediate intracellular delivery of CRISPR enzymes for high-efficiency editing of stimulated immune cells and cultured hematopoietic stem and progenitor cells (HSPCs).

#NewNProt for Peptide-enabled #ribonucleoprotein delivery for #CRISPR engineering (PERC) for ex vivo #genomeediting of primary human cells bit.ly/3DdsrY0

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Retina-specific laminin-based generation of photoreceptor progenitors from human pluripotent stem cells under xeno-free and chemically defined conditions - Nature Protocols This protocol describes the generation of photoreceptor progenitors from human pluripotent stem cells under xeno-free and chemically defined conditions, as well as steps to produce the retina-specific...

#NewNProt for generation of #photoreceptor progenitors from #humanpluripotentstemcells under xeno-free and chemically defined conditions bit.ly/3F6Nqwd

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Circular Vectors as an efficient, fully synthetic, cell-free approach for preparing small circular DNA as a plasmid substitute for guide RNA expression in CRISPR–Cas9 genome editing - Nature Protocols Oliynyk and Church present a protocol for designing, synthesizing and purifying transfection-ready, small, circular, double-stranded DNA templates for expression of gRNAs for different genome-editing ...

#NewNProt for designing, synthesizing and purifying transfection-ready small circular double-stranded #DNA templates for expression of #gRNAs bit.ly/3DiBPtf

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Linking single-cell transcriptomes with secretion using SEC-seq - Nature Protocols SEC-seq is a single-cell method linking the secretion of a target protein to the cell’s transcriptome. Nanovials isolate cells and capture their secretions, and oligonucleotide-labeled antibodies tag ...

#NewNProt: SEC-seq to link #singlecell #transcriptomes with target #proteinsecretion bit.ly/41eqaDZ

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Measuring plasma membrane fluidity using confocal microscopy - Nature Protocols Membrane fluidity is a crucial feature in understanding cellular physiology. This protocol describes a robust pipeline for measuring plasma membrane fluidity using confocal imaging and new environment...

#NewNProt: Measuring #plasmamembrane fluidity using #confocalmicroscopy bit.ly/4bie557 #membranefluidity

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Synthesis of bicyclo[3.1.1]heptanes, meta-substituted arene isosteres, from [3.1.1]propellane - Nature Protocols Replacing benzene rings with small-ring bridged hydrocarbons can improve a drug’s physicochemical and pharmacokinetic profile. This protocol describes the synthesis of the potential meta-arene isoster...

#NewNProt: #Synthesis of bicyclo[3.1.1]heptanes, meta-substituted arene isosteres, from [3.1.1]propellane bit.ly/4ibZ0Ez

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Construction of RNA reference materials for improving the quantification of transcriptomic data - Nature Protocols The Quartet reference materials enable the integration and standardization of multiomics datasets acquired over a variety of instruments, samples and methods and the quantitative comparison of RNA seq...

#NewNProt: Construction of #RNAseq reference materials for standardising the quantification of #omics data across different instruments and methods bit.ly/41G83Z7

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Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues - Nature Protocols Mass spectrometry-based proteomic studies involve tissue lysis. Herein, we updated our 2018 protocol1 by implementing a sonication step into urea-based tissue lysis to improve the detection of membran...

#NewNProt: Sonication-assisted #proteinextraction improves proteomic detection of membrane-bound and #DNAbindingproteins from tumor tissues bit.ly/438vGub

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Structural connectome construction using constrained spherical deconvolution in multi-shell diffusion-weighted magnetic resonance imaging - Nature Protocols This is a comprehensive protocol for the analysis of white matter diffusion-weighted magnetic resonance imaging data, which enables the representation of neuroanatomical atlases by using network-based...

#NewNProt: Structural connectome atlases using #MRtrix3 software to process #dMRI data bit.ly/4hdlMuZ

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Fabrication of thin-film electrodes and organic electrochemical transistors for neural implants - Nature Protocols The fabrication of thin-film poly(ethylene dioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) electrodes and electrochemical transistors via photolithography enables the reliable construction of mech...

#NewNProt details the fabrication of thin-film #neuralimplants, small, flexible electronic devices less than ten micrometers in thickness bit.ly/3CUSFhX #bioelectronics #neuroscience @GeorgeMalliaras @AlexanderJBoys

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