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The Current Protocols collection includes over 25,000 step-by-step techniques, procedures, and practical overviews that provide researchers with reliable, efficient methods to ensure reproducible results and pave the way for critical scientific discovery. With its emphasis on carefully curated, highly edited methods rich in detail, practical advice, and troubleshooting, Current Protocols enables researchers to advance their research with an efficiency of time and resources.

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Scope Expansion: Call for Proposals Current Protocols in Mouse Biology

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Synthesis of Oligodeoxynucleotide Containing Pseudo‐Deoxycytidine and Its Triphosphate Derivative

Ryo Miyahara, Yosuke Taniguchi, 
https://doi.org/10.1002/cpz1.70101
PROTOCOL
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Expression and Purification of SARS‐related Spike Glycoproteins for Cryo‐EM Analysis

Francesca R. Hills, Fátima Jorge, Laura N. Burga, Mihnea Bostina, 
https://doi.org/10.1002/cpz1.70115
PROTOCOL
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A Physiologically Relevant In Vitro Model of Nonreplicating Persistent Mycobacterium tuberculosis in Caseum

Min Xie, Paulina Osiecki, Suyapa Rodriguez, Véronique Dartois, Jansy Sarathy, 
https://doi.org/10.1002/cpz1.70118
PROTOCOL

Optimized, Efficient Measurement of the Expression of Undifferentiated Stem Cell Markers in Human Induced Pluripotent Stem Cells (iPSCs) by Flow Cytometry

Vaishanavi Saware, Wendy Runyon, Sam Hu, Benjamin van Soldt, Ritu Kumar, Jane Srivastava, 
https://doi.org/10.1002/cpz1.70105
PROTOCOL

Imaging the Intestinal Transcriptome With Multiplexed Error‐Robust Fluorescence In Situ Hybridization (MERFISH)

Paolo Cadinu, Evan Yang, Rosalind J. Xu, Brianna R. Watson, Josh Luce, Jeffrey R. Moffitt, 
https://doi.org/10.1002/cpz1.70111
PROTOCOL

Development, Characterization, and Therapeutic Utility of Paclitaxel‐Resistant Breast and Gastric Cancer In Vitro and In Vivo Models

Feng Tang, Hong Xu, Wen Cui, Xuelin Wang, Fangyi Ding, Yihan Zhang, Xiangnan Qiang, Qingyang Gu, Dong Wang, Zhixiang Zhang, 
https://doi.org/10.1002/cpz1.70113
PROTOCOL

Visualization of Efavirenz‐Induced Lipid Alterations in the Mouse Brain Using MALDI Mass Spectrometry Imaging

Nav Raj Phulara, Herana Kamal Seneviratne, 
https://doi.org/10.1002/cpz1.70108
ISSUE INFORMATION
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https://doi.org/10.1002/cpz1.70119

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Issue Information Issue 2, 2025

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Engineering Base Changes and Epitope‐Tagged Alleles in Mice Using Cas9 RNA‐Guided Nuclease

Marina Gertsenstein, Lauri G. Lintott, Lauryl M. J. Nutter, 
https://doi.org/10.1002/cpz1.70109
PROTOCOL

Development of Syngeneic Murine Glioma Models with Somatic Mismatch Repair Deficiency to Study Therapeutic Responses to Alkylating Agents and Immunotherapy

Deepti Bhatt, Ranjini K. Sundaram, Karla S. Lugo López, Teresa Lee, Susan E. Gueble, Juan C. Vasquez, 
https://doi.org/10.1002/cpz1.70097
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Streptozotocin‐Induced Diabetic Models in Mice and Rats

Brian L. Furman, 
https://doi.org/10.1002/cpz1.78
Open access

Working with Worms: Caenorhabditis elegans as a Model Organism

Philip M. Meneely, Caroline L. Dahlberg, Jacqueline K. Rose, 
https://doi.org/10.1002/cpet.35
Open access

BUSCO: Assessing Genomic Data Quality and Beyond

Mosè Manni, Matthew R. Berkeley, Mathieu Seppey, Evgeny M. Zdobnov, 
https://doi.org/10.1002/cpz1.323
Open access

Synthetic DNA Assembly Using Golden Gate Cloning and the Hierarchical Modular Cloning Pipeline

Sylvestre Marillonnet, Ramona Grützner, 
https://doi.org/10.1002/cpmb.115
Open access

Two Detailed Plaque Assay Protocols for the Quantification of Infectious SARS‐CoV‐2

Emelissa J. Mendoza, Kathy Manguiat, Heidi Wood, Michael Drebot, 
https://doi.org/10.1002/cpmc.105
Open access

Overview of Genotyping Technologies and Methods

Ingrid Kockum, Jesse Huang, Pernilla Stridh, 
https://doi.org/10.1002/cpz1.727
free access

Fluorescence Polarization (FP) Assays for Monitoring Peptide‐Protein or Nucleic Acid‐Protein Binding

Nathan J. Moerke, 
https://doi.org/10.1002/9780470559277.ch090102
Open access

Mouse and Rat Anesthesia and Analgesia

Sang Su Oh, Heather L. Narver, 
https://doi.org/10.1002/cpz1.995
Open access

Generating Single Cell–Derived Knockout Clones in Mammalian Cells with CRISPR/Cas9

Christopher J. Giuliano, Ann Lin, Vishruth Girish, Jason M. Sheltzer, 
https://doi.org/10.1002/cpmb.100
Open access

Optimizing PCR for Mouse Genotyping: Recommendations for Reliable, Rapid, Cost Effective, Robust and Adaptable to High‐Throughput Genotyping Protocol for Any Type of Mutation

Sylvie Jacquot, Nathalie Chartoire, Françoise Piguet, Yann Hérault, Guillaume Pavlovic, 
https://doi.org/10.1002/cpmo.65

The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses

Gil Stelzer, Naomi Rosen, Inbar Plaschkes, Shahar Zimmerman, Michal Twik, Simon Fishilevich, Tsippi Iny Stein, Ron Nudel, Iris Lieder, Yaron Mazor, Sergey Kaplan, Dvir Dahary, David Warshawsky, Yaron Guan-Golan, Asher Kohn, Noa Rappaport, Marilyn Safran, Doron Lancet, 
https://doi.org/10.1002/cpbi.5

Gene Set Knowledge Discovery with Enrichr

Zhuorui Xie, Allison Bailey, Maxim V. Kuleshov, Daniel J. B. Clarke, John E. Evangelista, Sherry L. Jenkins, Alexander Lachmann, Megan L. Wojciechowicz, Eryk Kropiwnicki, Kathleen M. Jagodnik, Minji Jeon, Avi Ma'ayan, 
https://doi.org/10.1002/cpz1.90

Using SPAdes De Novo Assembler

Andrey Prjibelski, Dmitry Antipov, Dmitry Meleshko, Alla Lapidus, Anton Korobeynikov, 
https://doi.org/10.1002/cpbi.102

From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline

Geraldine A. Van der Auwera, Mauricio O. Carneiro, Christopher Hartl, Ryan Poplin, Guillermo del Angel, Ami Levy-Moonshine, Tadeusz Jordan, Khalid Shakir, David Roazen, Joel Thibault, Eric Banks, Kiran V. Garimella, David Altshuler, Stacey Gabriel, Mark A. DePristo, 
https://doi.org/10.1002/0471250953.bi1110s43

Comparative Protein Structure Modeling Using MODELLER

Benjamin Webb, Andrej Sali, 
https://doi.org/10.1002/cpbi.3

Isolation and Characterization of Exosomes from Cell Culture Supernatants and Biological Fluids

Clotilde Théry, Sebastian Amigorena, Graça Raposo, Aled Clayton, 
https://doi.org/10.1002/0471143030.cb0322s30

ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide

Jason D. Buenrostro, Beijing Wu, Howard Y. Chang, William J. Greenleaf, 
https://doi.org/10.1002/0471142727.mb2129s109

Chlorophylls and Carotenoids: Measurement and Characterization by UV-VIS Spectroscopy

Hartmut K. Lichtenthaler, Claus Buschmann, 
https://doi.org/10.1002/0471142913.faf0403s01
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Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences

Maja Tarailo-Graovac, Nansheng Chen, 
https://doi.org/10.1002/0471250953.bi0410s25

Using ggtree to Visualize Data on Tree‐Like Structures

Guangchuang Yu, 
https://doi.org/10.1002/cpbi.96

Best of Current Protocols

Using OrthoMCL to Assign Proteins to OrthoMCL‐DB Groups or to Cluster Proteomes Into New Ortholog Groups


Isolation and Characterization of Exosomes from Cell Culture Supernatants and Biological Fluids


Fluorescence Polarization (FP) Assays for Monitoring Peptide‐Protein or Nucleic Acid‐Protein Binding


Flow Cytometry Method Validation Protocols


Preparation, Culture, and Analysis of Amniotic Fluid Samples


Trypan Blue Exclusion Test of Cell Viability


ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide
Gram Staining


Cre‐loxP‐Mediated Recombination: General Principles and Experimental Considerations 


RNA‐Seq for Bacterial Gene Expression


Miniscope GRIN Lens System for Calcium Imaging of Neuronal Activity from Deep Brain Structures in Behaving Animals


Fixation and Laser Capture Microdissection of Plant Tissue for RNA Extraction and RNASeq Library Preparation


Streptozotocin‐Induced Diabetic Models in Mice and Rats


BioID: A Screen for Protein‐Protein Interactions


FACS‐Mediated Isolation of Neuronal Cell Populations From Virus‐Infected Human Embryonic Stem Cell-Derived Cerebral Organoid Cultures


Behavioral Phenotyping for Autism Spectrum Disorders in Mice


Zebrafish: Development of a Vertebrate Model Organism