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STAR Protocols
Scopus
ISSN 2666-1667 · Elsevier · 3.962 artikel di indeks
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Artikel Jurnal
Protocol to study mRNA levels during endoreplication in Arabidopsis thaliana through nuclei extraction and a sorting strategy
Summary: In plants, differentiation and expansion of some cell types is accompanied by exit from cell division and onset of endoreplication. Here, we describe a protocol to study changes in mRNA levels during endoreplication in Arabidopsis thaliana cotyledons. We provide detailed steps for the…
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Protocol for the simultaneous detection of nuclear long non-coding RNAs and proteins in human iPSC-derived cardiomyocytes
Summary: Nuclear-enriched long non-coding RNAs (lncRNAs) can regulate gene expression by interacting with specific RNA-binding proteins (RBPs). Here, we present a protocol to directly image these lncRNAs at the single-molecule level together with their protein interactors in human cardiomyocytes…
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Protocol for the quantitative imaging and segmentation of spatial patterns in Hibiscus trionum petals
Summary: Most developmental processes underpinning the diversity of floral forms remain unexplored due to limitations in current imaging approaches. Here, we present a protocol to spatially analyze tissue-wide cell growth dynamics through confocal imaging and segmentation of the adaxial petal…
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Protocol for non-invasive delivery of CRISPR RNPs via virus-like particles for mouse model generation
Summary: CRISPR-virus-like particle (VLP)-induced targeted mutagenesis (CRISPR-VIM) enables genome editing in mouse embryos through non-invasive delivery of CRISPR ribonucleoproteins (RNPs) via VLPs, eliminating the need for physical manipulation and specialized expertise. We detail protocols for…
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Protocol for biomass and carbon storage estimation in tropical rainforests via remote sensing imagery
Summary: Here, we present a protocol for estimating biomass and carbon sequestration in tropical rainforests. We describe steps for combining remotely sensed data from Sentinel-2 imagery with data collected from standard field surveys. This protocol provides a cost-effective and time-efficient…
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Artikel Jurnal
Protocol for the isolation and immunoprecipitation of cell surface proteins from Drosophila melanogaster pupae
Summary: Transmembrane proteins are notoriously difficult to isolate from tissue samples due to their hydrophobic nature and often low abundance. Here, we describe a protocol for the isolation, enrichment, and detection of the high-molecular-weight adhesion-type G protein-coupled receptor (aGPCR)…
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Artikel Jurnal
Protocol to build open-source Discrimin8 maze to study discrimination of reward-context associations in mice during open-field foraging
Summary: The hippocampus is known to process context-specific memories. We provide a protocol for studying context discrimination in mice utilizing the open-source Discrimin8 maze. We describe the steps for building the maze and using custom-written codes implementing the task. Finally…
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Protocol for generating a 3D hydrogel-based tumor resection model in vitro using pancreatic cancer cells
Summary: We present a protocol for the generation of two distinct in vitro tumor resection models to evaluate cellular responses at tumor margins in 3D. We describe steps for patterning pancreatic cancer cells (Panc-01) embedded in hydrogels using a custom 96-pin metal lid to create standardized…
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Protocol for identifying surface membrane proteins and their associated proteome from mouse cortical neuron cultures by in situ biotinylation
Summary: Modifications to the plasma membrane proteome reflect neuronal physiological states. Here, we present a protocol to profile surface proteins from mouse cortical neuron cultures using in situ biotinylation. The workflow includes neuron culture, surface labeling, enrichment of biotinylated…
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Protocol for the formulation and characterization of extracellular vesicle-crosslinked supramolecular hydrogels
Summary: Extracellular vesicles (EVs) can serve as supramolecular crosslinkers to form injectable, intrinsically bioactive hydrogels. This protocol details the formulation, rheological characterization, and analysis of EV-crosslinked hydrogels with tunable mechanics. We describe steps for preparing…
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Protocol for geographical mapping of pesticide contamination
Summary: Pesticide residues in the environment threaten agricultural and human health. Here, we present a framework for mapping and comparing the contamination levels of pesticides across specific environmental compartments in various regions. We describe steps for applying the pesticide residual…
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Protocol for preparing and characterizing samples for combined microsecond freeze-hyperquenching and electron paramagnetic resonance spectroscopy
Summary: Microsecond freeze-hyperquenching (MHQ) coupled with pulsed electron-electron double resonance spectroscopy (PELDOR) can resolve conformational changes in biomolecules over space and time. Here, we present a protocol for preparing MHQ samples of a cyclic nucleotide-binding domain by rapid…
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Computational protocol for hierarchical Bayesian modeling of perception and generalization in fear conditioning
Summary: Understanding human generalization behavior requires disentangling underlying cognitive and perceptual mechanisms. Here, we present a computational protocol to analyze individual differences in fear generalization by integrating a Bayesian state-space perceptual model with a hierarchical…
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Protocol for generating megakaryocytes from patient induced pluripotent stem cells for disease modeling and compound screening
Summary: Here, we present a protocol for generating megakaryocytes from patient induced pluripotent stem cells (iPSCs). We describe steps for expanding and dissociating iPSCs into single cells and aggregating them into spin embryoid bodies (EBs). We detail procedures for lineage commitment and…
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Protocol for the preparation of flexible material from the mycelium of wood-decay fungal strains and mechanical property investigation
Summary: Extraction of chitin-glucan-based materials from fungi has several advantages over animal-based chitin. Here, we present a protocol for extracting chitin-glucan material from the mycelium of wood-decay fungal strains and investigating its mechanical properties. We describe steps for…
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Protocol for formulation and evaluation of phytosterol-based lipid nanoparticles as cholesterol alternatives for mRNA delivery
Summary: We present a protocol for formulating and evaluating lipid nanoparticles (LNPs) that incorporate the plant-derived sterols ginsenoside Rg2 and protopanaxadiol (PPD) as substitutes for cholesterol. The protocol describes mRNA preparation, manual mRNA-LNP encapsulation, and physicochemical…
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Protocol for rapid tRNA enrichment and chemiluminescent northern blot detection of tRNA and tRNA-derived fragments
Summary: Transfer RNA (tRNA), its post-transcriptional modifications, and tRNA-derived fragments (tRFs) play essential roles in cellular processes and gene regulation. Here, we present a fast and efficient tRNA enrichment protocol using silica spin columns. To analyze tRNA and tRFs, we describe…
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Protocol for non-invasive tumor monitoring and diagnosis based on interpretable deep learning
Summary: Tumor-specific DNA methylation profiling in plasma cell-free DNA (cfDNA) offers a promising approach for non-invasive tumor detection. Here, we present a protocol that uses Oncoder, an interpretable deep-learning-based framework, to monitor treatment response by tracking dynamic changes in…
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Artikel Jurnal
Protocol to perform cell-type-specific transcriptome-wide association study using scPrediXcan framework
Summary: The scPrediXcan framework enables cell-type-specific transcriptome-wide association studies (TWASs) by integrating deep learning-based prediction of gene expression from DNA sequence and epigenetic features. We present a protocol for scPrediXcan: training cell-type-specific models for…
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