Protocol for constructing in vivo and in vitro models integrating clinical and proteomic subtypes of chordoma by Jianxuan Gao, Jinbo Hu, Tong Meng

“…Summary: Here, we present a protocol for constructing both in vivo and in vitro models of chordoma, integrating clinical and proteomic subtyping to enable a comprehensive analysis. …”
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Protocol for measuring force in skinned diaphragm muscle fibers of myopathic SEPN1 knockout mice following chronic tauroursodeoxycholic acid treatment by Leonardo Nogara, Serena Germani, Cosimo De Napoli, Bert Blaauw, Ester Zito

“…Summary: Selenoprotein N1 (SEPN1) is a type II endoplasmic reticulum (ER) glycoprotein. …”
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Protocol for inducing beige adipocytes in white adipose tissue of mouse using cold exposure and CL316,243 injection by Yalan Wu, Chenguang Wang, Xiao Yu Tian

“…Summary: White adipose tissue (WAT) beiging holds significant therapeutic potential for combating obesity. …”
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Protocol for capturing genome-wide chromatin interactions in Arabidopsis by Jiayue Shu, Suxin Xiao, Dingyue Wang, Minqi Yang, Yue Zhou

“…Summary: High-order chromatin structure is essential for the regulation of plant growth and development. …”
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Gamma synchronization between the medial temporal lobe and medial frontal cortex for goal-directed visual attention in humans by Jie Zhang, Jing Xia, Huihui Zhou, Shuo Wang

“…Summary: Goal-directed visual attention is a fundamental cognitive function that engages multiple brain regions, yet the neural circuit mechanisms in humans remain unclear. …”
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Protocol for high-quality RNA sequencing, cell surface protein analysis, and genotyping in single cells using TARGET-seq+ by N. Asger Jakobsen, Sven Turkalj, Paresh Vyas

“…Summary: Studying the consequences of somatic mutations in pre-malignant and cancerous tissues is challenging due to noise in single-cell transcriptome data and difficulty in identifying the clonal identity of single cells. …”
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Protocol for AI-based segmentation and quantification of interstitial cells of Cajal in murine gastric muscle by Egan L. Choi, Negar Taheri, Yujiro Hayashi

“…Summary: Interstitial cells of Cajal (ICCs), pacemaker and neuromodulator cells in the gastrointestinal (GI) tract, play an important role in GI motility. …”
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Protocol to quantitatively assess glycolysis and related carbon metabolic fluxes using stable isotope tracing in Crabtree-positive yeasts by Shreyas Niphadkar, Sreesa Sreedharan, Vineeth Vengayil, Sunil Laxman

“…Summary: Crabtree-positive yeasts rapidly consume glucose via glycolysis, making it difficult to experimentally estimate their actual glycolytic rate or flux. …”
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Protocol to generate PDMS topographical patterns for hiPSC-derived or rat primary neuronal cultures by Anna-Christina Haeb, Mireia Olives-Verger, Jordi Soriano

“…Summary: Soft lithography is a promising technique to fabricate tailored substrates on polydimethylsiloxane (PDMS) casts. …”
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Protocol for differentiation of human embryonic stem cells into surface epithelium and functional keratinocytes by Jiafeng Liu, Huaxing Huang, Hong Ouyang

“…Summary: The normal development and function of the epidermis and other ectodermal appendages depend on the proper formation of the surface epithelium (SE). …”
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Protocol to identify small-molecule inhibitors against cancer drug resistance by Juan Wei, She-Yu Zhang, Xue-Yuan Zhou, Yong Wei, Hao-Ran Jia, Qin Wu, Weihong Tan

“…Summary: Drug resistance has emerged as a critical challenge in clinical cancer treatment. …”
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Protocol to denoise spatially resolved transcriptomics data utilizing optimal transport-based gene filtering algorithm by Lin Du, Jingmin Kang, Jie Li, Hua Qin, Yong Hou, Hai-Xi Sun

“…Summary: Spatially resolved transcriptomics (SRT) data contain intricate noise due to the diffusion of transcripts caused by tissue fixation, permeabilization, and cell lysis during the experiment. …”
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Protocol for engineering poly(ethylene terephthalate) hydrolases via directed evolution using a high-throughput screening assay by Thomas M. Groseclose, Zoe K. Taylor, Lexy A. Lujan, Taraka Dale, Hau B. Nguyen

“…Summary: Poly(ethylene terephthalate) (PET) hydrolases, which depolymerize PET to its monomers, have gained attention for their potential to facilitate bio-industrial recycling of this waste plastic. …”
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Protocol for characterizing cell motility and extracellular signal-regulated kinase dynamics in epithelial monolayers using FRET imaging data by Julio Cesar Sanchez-Rendon, Lara Hundsdorfer, Effie E. Bastounis

“…Summary: Extracellular signal-regulated kinase (ERK) activity waves regulate critical processes like wound healing and bacterial pathogen dissemination by altering host cell motility and biomechanics. …”
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Protocol to measure endogenous GlcNAc-1-phosphotransferase activity in SK-MEL-30 cells by Balraj Doray, Danielle Henn, Xi Yang, Ming Li, Patricia Dickson

“…Summary: GlcNAc-1-phosphotransferase (GNPT) is the key enzyme for tagging lysosomal hydrolases with the mannose 6-phosphate moiety for delivery to the lysosome. …”
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Protocol for identifying genomic binding sites of mitotic bookmarkers in Drosophila neural stem cells and cultured mammalian cells by Yuying Shen, Jie Liu, Yan Song

“…Summary: Mitotic bookmarkers label key gene loci on highly condensed chromosomes to preserve cell fate memory across mitosis. …”
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Protocol for adaptive laboratory evolution of S. cerevisiae by PEG/LiAc transformation and sequencing by Bei Jiang, Chuyao Xiao, Li Liu

“…Summary: Gene deletions perturb cellular homeostasis, affecting gene expression and phenotypes. …”
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Cell-based ELISpot protocol to detect and quantify antigen-specific antibody-secreting cells in murine whole-organ single-cell suspensions by Christina Brunner, Shannon R. Menzel, Franziska Rost, Joana Côrte-Real, Katharina Pracht

“…Summary: Antibody-secreting cells (ASCs) are the hallmark of the adaptive immune response to vaccines or infections. …”
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Protocol to isolate glycoproteins from cultured mammalian cells and tissue samples using wheat germ agglutinin precipitation by Simran Chopra, Otsuware Linda-Josephine Kadiri, Kai Kappert, André Kleinridders

“…Summary: Wheat germ agglutinin (WGA) precipitation enables selective enrichment of glycoproteins such as density-enhanced phosphatase (DEP-1) from protein lysates. …”
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Opto-Avoidance-Elevated Plus Maze protocol to study positive or negative valence upon optogenetic stimulation in the mouse brain by Gian Pietro Serra, François Georges, Åsa Wallén-Mackenzie

“…Summary: The elevated plus maze (EPM) apparatus consists of two open arms that provide aversive spaces and two closed arms that provide protective and welcoming spaces. …”
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