Protocol for adeno-associated virus-mediated gene delivery to accelerate pancreatic carcinogenesis in mice by Hongzhen Li, Zhao Shi, Shanshan Shen, Bo Kong

“…Summary: Introducing additional genetic modifications or environmental stimuli accelerates early pancreatic carcinogenesis in the p48Cre/+; LSL-KrasG12D/+ (KC) mouse model. …”
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Protocol for unlocking alternative polyadenylation insights from bulk RNA-seq data with PolyAMiner-Bulk by Venkata Jonnakuti, Sriya Jonnakuti, Hari Krishna Yalamanchili

“…The major steps involve input data preparation, executing PolyAMiner-Bulk, and interpreting the results. …”
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Protocol for cell image-based spatiotemporal proteomics in budding yeast by Athanasios Litsios, Myra Paz David Masinas, Helena Friesen, Charles Boone, Brenda J. Andrews

“…Summary: The eukaryotic cell division cycle is a highly conserved process, featuring fluctuations in protein localization and abundance required for key cell cycle transitions. …”
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Protocol for the removal of polyvinyl chloride microplastics from water using activated jute stick charcoal by Nur Alom, Tapati Roy, Tanny Sarkar, Md Rasel, Md Sanwar Hossain, Mamun Jamal

“…Summary: We present a protocol to remove polyvinyl chloride-based microplastics (MPs) from aquatic environments using jute stick activated charcoal (JSAC) as an adsorbent. …”
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Protocol for producing brain-derived neurotrophic factor and neurotrophin-4 in their pro and active form in Escherichia coli by Christoph Holzner, Katharina Böttinger, Christian G. Huber, Elfriede Dall, Hans Brandstetter

“…Summary: Brain-derived neurotrophic factor (BDNF) and neurotrophin-4 (NT4) are neurotrophic growth factors, signaling primarily via the tropomyosin receptor kinase B (TrkB). …”
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Protocol for effective surface passivation for single-molecule studies of chromatin and topoisomerase II by Tung T. Le, Xiang Gao, Seong Ha Park, Jaeyoon Lee, James T. Inman, Michelle D. Wang

“…Summary: For single-molecule studies requiring surface anchoring of biomolecules, poorly passivated surfaces can result in alterations of biomolecule structure and function that lead to artifacts. …”
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Protocol for assisting frequency band definition and decoding neural dynamics using hierarchical clustering and multivariate pattern analysis by Chengpeng Li, Isao Hasegawa, Hisashi Tanigawa

“…Summary: Traditional fixed frequency band divisions often limit neural data analysis accuracy. …”
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Protocol for in vitro modeling of specification and morphogenesis of early pancreas development using human pluripotent stem cell-based organoid differentiation by Chenglei Tian, Ulf Tiemann, Florian Hermann, Henrik Semb

“…Summary: Here, we present a protocol to generate key pancreatic cell types in vitro using human pluripotent stem cell (hPSC)-based Matrigel-overlay organoid differentiation. …”
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Learning-augmented sketching offers improved performance for privacy preserving and secure GWAS by Junyan Xu, Kaiyuan Zhu, Jieling Cai, Can Kockan, Natnatee Dokmai, Hyunghoon Cho, David P. Woodruff, S. Cenk Sahinalp

“…Summary: Trusted execution environments (TEEs), such as Intel SGX, enable secure, privacy-preserving computations but may have computational resource constraints. …”
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Protocol for identifying protein synthesis activity in specific cell types of the testicular lumen by Dingfeng Zou, Kai Li, Yan Lu, Wei Yan, Wei Song

“…Summary: Protein synthesis could control spermatogenic cell fate transitions. …”
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Protocol for isolating and characterizing human vitreous immune cell infiltrates by flow cytometry and single-cell transcriptomic studies by Sandhya Rani Bhanja, Sayantan Ghosh, Pankaj Kumar, Tulasi Nagabandi, Arun Raina, Kaiser Alam, John V. Forrester, Soumyava Basu

“…Summary: Vitreous infiltrating immune cells represent an accessible tissue sample that can provide valuable information on the intraocular immune response without compromising the structural and functional integrity of the eye. …”
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Protocol for phenotyping mouse myeloid and lymphoid cells by mass cytometry by Laura Morin, Brice Autier, Patrice Hemon, Simon Le Gallou, Mikael Roussel, Sarah Dion, Valérie Lecureur

“…Summary: Cytometry by time of flight (CyTOF) is a flow cytometry-based technique using metal-tagged antibodies, allowing immunophenotyping. …”
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Protocol for differentiating hematopoietic progenitor cells from human pluripotent stem cells in chemically defined monolayer culture by Shaokang Mo, Kengyuan Qu, Jun Shen, Kuangyu Yen

“…Summary: Human pluripotent stem cells (hPSCs) provide a powerful platform for generating hematopoietic progenitor cells (HPCs) and investigating hematopoietic development. …”
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Protocol to decipher complex spatial transcriptomics data using STMiner by Peisen Sun, Mingxuan Li, Kai Ye

“…Summary: Complex spatial transcriptomics (ST) data analysis can be challenging due to uneven sampling, sparsity, and ambiguous tissue boundaries. …”
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Protocol to distinguish pre-mRNA from mRNA in RNA-protein interaction studies by Christina Zeiler, Annika Bestehorn, Pavel Kovarik

“…Summary: Transcriptome-wide studies on interactions between RNA-binding proteins (RBPs) and protein-coding RNAs in general preclude interpretations regarding RBP preference for binding to the more abundant mRNA over the less abundant pre-mRNA. …”
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Protocol for using MYOD1-transduced human urine-derived cells as a predictive platform for exon skipping therapy in Duchenne muscular dystrophy by Katsuhiko Kunitake, Takami Ishizuka, Eri Takeshita, Hirofumi Komaki, Yoshitsugu Aoki

“…Summary: Antisense oligonucleotide (ASO)-based exon skipping is a splice-modulating therapy effective for Duchenne muscular dystrophy (DMD) caused by dystrophin deficiency. …”
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Protocol to measure spontaneous locomotion, graded exercise oxygen consumption, and cross-sectional area of skeletal muscle cells in zebrafish by Mauricio Castro-Sepulveda, Cassandra Tabasso, Dogan Grepper, Adrien Martinotti, Axel K.F. Aguettaz, Sylviane Lagarrigue, Francesca Amati

“…Summary: Skeletal muscle function and quality are strong indicators of metabolic health. …”
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Protocol for predicting the single-cell network-based gene activity landscape during human B cell development by Xin Huang, Xuetong Hou, Yizhen Li, Jun J. Yang, Jiyang Yu

“…Summary: Owing to inconsistencies in human B cell classification and the difficulty in distinguishing heterogeneous subpopulations, we present a protocol to construct gene regulatory networks and gene activity landscapes for human B cell developmental stages. …”
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Protocol for isolation of endothelial cells from adult mouse brain by Audrey G. Miglietta, Jennifer David-Bercholz, Roeben N. Munji, Robert S. Pulido, Allison L. Soung, Niccolò Terrando, Richard Daneman, Ting Yang

“…Summary: Brain endothelial cells (ECs) line blood vessel walls and form the blood-brain barrier (BBB), facilitating interactions between the brain and the periphery. …”
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Protocol for microindentation analysis of human cartilage and methacrylated gelatin hydrogels with varying stiffness in ATDC5 cell cultures by Han Wang, Tianyou Kan, Lin Sun, Hanjun Li, Liao Wang, Mengning Yan, Zhifeng Yu

“…Summary: Here, we present a protocol for evaluating mechanical properties of human cartilage specimens and methacrylated gelatin (GelMA) hydrogels with varying Young’s moduli for cultures of ATDC5 chondrocytes using microindentation. …”
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