Most read Protocols
Efficient Agrobacterium-mediated Transformation of the Elite–Indica Rice Variety Komboka
Genetic transformation is crucial for both investigating gene functions and for engineering of crops to introduce new traits. Rice (Oryza sativa L.) is an important model in plant research, since it is the staple food for more than half of the world’s population. As a result, numerous transformation methods have been developed for both ...
Confocal and Super-resolution Imaging of RNA in Live Bacteria Using a Fluorogenic Silicon Rhodamine-binding Aptamer
Authors:  Regina Wirth, Peng Gao, G. Ulrich Nienhaus, Murat Sunbul and Andres Jäschke, date: 05/05/2020, view: 2289, Q&A: 0
Genetically encoded light-up RNA aptamers have been shown to be promising tools for the visualization of RNAs in living cells, helping us to advance our understanding of the broad and complex life of RNA. Although a handful of light-up aptamers spanning the visible wavelength region have been developed, none of them have yet been reported to be ...
Single Cell Migration Assay Using Human Breast Cancer MDA-MB-231 Cell Line
Authors:  David M. Gau and Partha Roy, date: 04/20/2020, view: 2173, Q&A: 0
Cell migration is a fundamental cellular process that plays a crucial role in many physioglogical and pathological processes such as wound healing or cancer metastasis. Many assays have been developed to examine cell migration, such as the wound healing or scratch assay, Boyden Chamber or transwell assay, and the method we will describe here, ...
Unbiased and Tailored CRISPR/Cas gRNA Libraries by Synthesizing Covalently-closed-circular (3Cs) DNA
Authors:  Martin Wegner, Koraljka Husnjak and Manuel Kaulich, date: 01/05/2020, view: 2832, Q&A: 0
Simplicity, efficiency and versatility of the CRISPR/Cas system greatly contributed to its rapid use in a broad range of fields. Applications of unbiased CRISPR/Cas screenings are increasing and thus there is a growing need for unbiased and tailored CRISPR/Cas gRNA libraries. Conventional methods for gRNA library generation apply PCR and cloning ...
Tryptophan Fluorescence Quenching Assays for Measuring Protein-ligand Binding Affinities: Principles and a Practical Guide
Authors:  Anthony Yammine, Jinlong Gao and Ann H. Kwan, date: 06/05/2019, view: 8702, Q&A: 0
Tryptophan fluorescence quenching is a type of fluorescence spectroscopy used for binding assays. The assay relies on the ability to quench the intrinsic fluorescence of tryptophan residues within a protein that results from changes in the local environment polarity experienced by the tryptophan(s) upon the addition of a binding partner or ligand. ...
Straight Channel Microfluidic Chips for the Study of Platelet Adhesion under Flow
Authors:  Alexander Dupuy, Lining Arnold Ju and Freda H Passam, date: 03/20/2019, view: 7016, Q&A: 0
Microfluidic devices have become an integral method of cardiovascular research as they enable the study of shear force in biological processes, such as platelet function and thrombus formation. Furthermore, microfluidic chips offer the benefits of ex vivo testing of platelet adhesion using small amounts of blood or purified platelets. ...
Detection of mRNA by Whole Mount in situ Hybridization and DNA Extraction for Genotyping of Zebrafish Embryos
Authors:  Rachna Narayanan and Andrew C. Oates, date: 03/20/2019, view: 7605, Q&A: 0
In situ hybridization is used to visualize the spatial distribution of gene transcripts in tissues and in embryos, providing important information about disease and development. Current methods involve the use of complementary riboprobes incorporating non-radioactive labels that can be detected by immunohistochemistry and coupled to ...
Induced Germinal Center B Cell Culture System
Authors:  Kei Haniuda and Daisuke Kitamura, date: 02/20/2019, view: 6741, Q&A: 0
The germinal center (GC) is the site where B cells undergo clonal expansion, affinity-based selection, and differentiation into memory B cells or plasma cells. It has been difficult to elucidate regulatory mechanisms for the dynamic GC B cell maturation and differentiation, partly because experimental manipulation of GC B cells in vivo ...
Induction and Analysis of Anti-CD40-induced Colitis in Mice
Authors:  Barbara Joyce-Shaikh, Daniel J. Cua and David Bauché, date: 02/05/2019, view: 4933, Q&A: 0
Colon inflammation or colitis affects more than 1 million people worldwide. Several pre-clinical models, including chemical-induced (i.e., DSS, TNBS) or pathogen-induced (i.e., Citrobacter rodentium) have been used to study mechanisms involved in the development and regulation of colitis. Anti-CD40 induced colitis model ...
Evaluation of Anticancer activity of Silver Nanoparticles on the A549 Human Lung Carcinoma Cell Lines through Alamar Blue Assay
Authors:  Nikita Sharma, Geeta Arya, R. Mankamna Kumari, Nidhi Gupta and Surendra Nimesh, date: 01/05/2019, view: 7249, Q&A: 0
Silver nanoparticles have been widely studied to possess antimicrobial as well as anticancer activity, and have found its applications in various fields including pharmaceutical industry, diagnostics, drug delivery, food industry, and others. For this purpose, several cell proliferation assays are widely used for the evaluation of anticancer ...
Analysis of the Mitochondrial Membrane Potential Using the Cationic JC-1 Dye as a Sensitive Fluorescent Probe
Authors:  Farzane Sivandzade, Aditya Bhalerao and Luca Cucullo, date: 01/05/2019, view: 10857, Q&A: 0
In recent years, fluorescent dyes have been frequently used for monitoring mitochondrial membrane potential to evaluate mitochondrial viability and function. However, the reproducibility of the results across laboratories strongly depends upon following well validated and reliable protocols along with the appropriate controls. Herein, we provide a ...
Single-molecule Fluorescence in situ Hybridization (smFISH) for RNA Detection in Adherent Animal Cells
Authors:  Gal Haimovich and Jeffrey E. Gerst, date: 11/05/2018, view: 18453, Q&A: 1
Transcription and RNA decay play critical roles in the process of gene expression and the ability to accurately measure cellular mRNA levels is essential for understanding this regulation. Here, we describe a single-molecule fluorescent in situ hybridization (smFISH) method (as performed in Haimovich et al., 2017) that detects ...
mRNA Stability Assay Using Transcription Inhibition by Actinomycin D in Mouse Pluripotent Stem Cells
Authors:  Madara Ratnadiwakara and Minna-Liisa Änkö, date: 11/05/2018, view: 15756, Q&A: 2
Gene expression is regulated through multiple steps at both transcriptional and post-transcriptional levels. The net abundance of mature mRNA species in cells is determined by the balance between transcription and degradation. Thus, the regulation of mRNA stability is a key post-transcriptional event that can greatly affect the net level of mRNAs ...
Cell Synchronization by Double Thymidine Block
Authors:  Guo Chen and Xingming Deng, date: 09/05/2018, view: 21236, Q&A: 1
Cell synchronization is widely used in studying mechanisms involves in regulation of cell cycle progression. Through synchronization, cells at distinct cell cycle stage could be obtained. Thymidine is a DNA synthesis inhibitor that can arrest cell at G1/S boundary, prior to DNA replication. Here, we present the protocol to synchronize cells at ...
Isothermal Titration Calorimetry: A Biophysical Method to Characterize the Interaction between Label-free Biomolecules in Solution
Author:  Andrea Saponaro, date: 08/05/2018, view: 15477, Q&A: 0
This protocol can be applied to analyze the direct interaction between a soluble protein and a target ligand molecule using Isothermal Titration Calorimetry (ITC, Malvern). ITC allows the biophysical characterization of binding between label-free, non-immobilized and in-solution biomolecules by providing the stoichiometry of the interaction, the ...
Measurement of Oxygen Consumption Rate (OCR) and Extracellular Acidification Rate (ECAR) in Culture Cells for Assessment of the Energy Metabolism
Authors:  Birte Plitzko and Sandra Loesgen, date: 05/20/2018, view: 47729, Q&A: 0
Mammalian cells generate ATP by mitochondrial (oxidative phosphorylation) and non-mitochondrial (glycolysis) metabolism. Cancer cells are known to reprogram their metabolism using different strategies to meet energetic and anabolic needs (Koppenol et al., 2011; Zheng, 2012). Additionally, each cancer tissue has its own individual ...
Transmission Electron Microscopy for Analysis of Mitochondria in Mouse Skeletal Muscle
Authors:  Joseph D. McMillan and Michael A. Eisenback, date: 05/20/2018, view: 10754, Q&A: 0
Skeletal muscle is the most abundant tissue in the human body and regulates a variety of functions including locomotion and whole-body metabolism. Skeletal muscle has a plethora of mitochondria, the organelles that are essential for aerobic generation of ATP which provides the chemical energy to fuel vital functions such as contraction. The number ...
Generation of Luciferase-expressing Tumor Cell Lines
Authors:  Todd V. Brennan, Liwen Lin, Xiaopei Huang and Yiping Yang, date: 04/20/2018, view: 11609, Q&A: 1
Murine tumor models have been critical to advances in our knowledge of tumor physiology and for the development of effective tumor therapies. Essential to these studies is the ability to both track tumor development and quantify tumor burden in vivo. For this purpose, the introduction of genes that confer tumors with bioluminescent ...
Detection and Analysis of Circular RNAs by RT-PCR
Authors:  Amaresh C Panda and Myriam Gorospe, date: 03/20/2018, view: 11948, Q&A: 4
Gene expression in eukaryotic cells is tightly regulated at the transcriptional and posttranscriptional levels. Posttranscriptional processes, including pre-mRNA splicing, mRNA export, mRNA turnover, and mRNA translation, are controlled by RNA-binding proteins (RBPs) and noncoding (nc)RNAs. The vast family of ncRNAs comprises diverse regulatory ...
Single-step Precision Genome Editing in Yeast Using CRISPR-Cas9
Genome modification in budding yeast has been extremely successful largely due to its highly efficient homology-directed DNA repair machinery. Several methods for modifying the yeast genome have previously been described, many of them involving at least two-steps: insertion of a selectable marker and substitution of that marker for the intended ...
Quantification of Plant Cell Death by Electrolyte Leakage Assay
Authors:  Noriyuki Hatsugai and Fumiaki Katagiri, date: 03/05/2018, view: 13948, Q&A: 1
We describe a protocol to measure the electrolyte leakage from plant tissues, resulting from loss of cell membrane integrity, which is a common definition of cell death. This simple protocol is designed to measure the electrolyte leakage from a tissue sample over a time course, so that the extent of cell death in the tissue can be monitored ...
Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq
Most nematodes are small worms that lack enough RNA for regular RNA-seq protocols without pooling hundred to thousand of individuals. We have adapted the Smart-seq2 protocol in order to sequence the transcriptome of an individual worm. While developed for individual Steinernema carpocapsae and Caenorhabditis elegans larvae as ...
Isolation and Establishment of Mesenchymal Stem Cells from Wharton’s Jelly of Human Umbilical Cord
Authors:  Umesh Goyal, Chitra Jaiswal and Malancha Ta, date: 02/20/2018, view: 11659, Q&A: 4
Mesenchymal stem cells (MSCs) are currently considered as ‘medicinal signaling cells’ and a promising resource in regard to cell-based regenerative therapy. Umbilical cord is a human term perinatal tissue which is easily attainable, and a promising source of stem cells with no associated ethical concerns. MSCs have been isolated from different ...
Obtaining Acute Brain Slices
Authors:  Thomas Papouin and Philip G. Haydon, date: 01/20/2018, view: 13740, Q&A: 1
Obtaining acute brain slices for electrophysiology or amperometric recordings has become a routine procedure in most labs in the field of neuroscience. Yet, protocols describing the step by step process are scarce, in particular for routine acute preparations such as from the mouse hippocampus. Here we provide a detailed protocol for the ...
Multiple Stepwise Gene Knockout Using CRISPR/Cas9 in Escherichia coli
Authors:  Enrico König, Francesca Zerbini, Ilaria Zanella, Davide Fraccascia and Guido Grandi, date: 01/20/2018, view: 18570, Q&A: 1
With the recent implementation of the CRISPR/Cas9 technology as a standard tool for genome editing, laboratories all over the world are undergoing one of the biggest advancements in molecular biology since PCR. The key advantage of this method is its simplicity and universal applicability for species of any phylum. Of particular interest is the ...
Targeted Nucleotide Substitution in Mammalian Cell by Target-AID
Authors:  Takayuki Arazoe, Keiji Nishida and Akihiko Kondo, date: 06/05/2017, view: 10219, Q&A: 0
Programmable RNA-guided nucleases based on CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated protein) systems have been applied to various type of cells as powerful genome editing tools. By using activation-induced cytidine deaminase (AID) in place of the nuclease activity of the CRISPR/Cas9 system, we have ...
Chromatin Immunoprecipitation Experiments from Whole Drosophila Embryos or Larval Imaginal Discs
Chromatin Immunoprecipitation coupled either to qPCR (qChIP) or high-throughput sequencing (ChIP-Seq) has been extensively used in the last decades to identify the DNA binding sites of transcription factors or the localization of various histone marks along the genome. The ChIP experiment generally includes 7 steps: collection of biological ...
Muscle Histology Characterization Using H&E Staining and Muscle Fiber Type Classification Using Immunofluorescence Staining
Authors:  Chao Wang, Feng Yue and Shihuan Kuang, date: 05/20/2017, view: 16749, Q&A: 1
Muscle function is determined by its structure and fiber type composition. Here we describe a protocol to examine muscle histology and myofiber types using hematoxylin and eosin (H&E) and immunofluorescence staining, respectively. H&E stain nucleus in blue and cytoplasm in red, therefore allowing for morphological analyses, such as myofiber ...
Murine Bronchoalveolar Lavage
Authors:  Fan Sun, Gutian Xiao and Zhaoxia Qu, date: 05/20/2017, view: 17823, Q&A: 1
A basic Bronchoalveolar lavage (BAL) procedure in mouse is described here. Cells and fluids obtained from BAL can be analyzed by Hema3-staining, immunostaining, Fluorescence-activated cell sorting (FACS), PCR, bicinchoninic acid protein assay, enzyme-linked immunosorbent assay (ELISA), luminex assays, etc., to examine the immune cells, ...
Robust Generation of Knock-in Cell Lines Using CRISPR-Cas9 and rAAV-assisted Repair Template Delivery
Authors:  Giel Vandemoortele, Delphine De Sutter and Sven Eyckerman, date: 04/05/2017, view: 16211, Q&A: 0
The programmable Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated nuclease 9 (Cas9) technology revolutionized genome editing by providing an efficient way to cut the genome at a desired location (Ledford, 2015). In mammalian cells, DNA lesions trigger the error-prone non-homologous end joining (NHEJ) DNA repair ...
Polysome Fractionation to Analyze mRNA Distribution Profiles
Authors:  Amaresh C. Panda, Jennifer L. Martindale and Myriam Gorospe, date: 02/05/2017, view: 19437, Q&A: 5
Eukaryotic cells adapt to changes in external or internal signals by precisely modulating the expression of specific gene products. The expression of protein-coding genes is controlled at the transcriptional and post-transcriptional levels. Among the latter steps, the regulation of translation is particularly important in cellular processes that ...
Dot Blot Analysis of N6-methyladenosine RNA Modification Levels
Authors:  Lisha Shen, Zhe Liang and Hao Yu, date: 01/05/2017, view: 18075, Q&A: 2
N6-methyladenosine (m6A) is the most prevalent internal modification of eukaryotic messenger RNA (mRNA). The total amount of m6A can be detected by several methods, such as dot blot analysis using specific m6A antibodies and quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) (Fu et al ...
Sulforhodamine B (SRB) Assay in Cell Culture to Investigate Cell Proliferation
Authors:  Esteban A. Orellana and Andrea L. Kasinski, date: 11/05/2016, view: 37738, Q&A: 0
The SRB assay has been used since its development in 1990 (Skehan et al., 1990) to inexpensively conduct various screening assays to investigate cytotoxicity in cell based studies (Vichai and Kirtikara, 2006). This method relies on the property of SRB, which binds stoichiometrically to proteins under mild acidic conditions and then can be ...
BODIPY 493/503 Staining of Neutral Lipid Droplets for Microscopy and Quantification by Flow Cytometry
Authors:  Bo Qiu and M. Celeste Simon, date: 09/05/2016, view: 41598, Q&A: 0
Lipid droplets (LDs) are ubiquitous, dynamic organelles and function as a storage depot for neutral lipids, including triglycerides and cholesterol esters (Walther and Farese, 2012). The movement of lipid species into and out of LDs impacts a variety of cellular processes, such as energy homeostasis, lipid-based signaling, and membrane homeostasis ...
Hemagglutination Inhibition (HI) Assay of Influenza Viruses with Monoclonal Antibodies
Heamagglutination is inhibited when antibodies are present because antibodies to the influenza virus will prevent attachment of the virus to red blood cells. The highest dilution of antibody that prevents hemagglutination is called the HI titer. Human monoclonal antibodies generated from single human B cells were tested to characterize their ...
Differentiation of THP1 Cells into Macrophages for Transwell Co-culture Assay with Melanoma Cells
Authors:  Michael Peter Smith, Helen Young, Adam Hurlstone and Claudia Wellbrock, date: 11/05/2015, view: 34208, Q&A: 2
Understanding how immune cells such as macrophages interact with cancer cells is of increasing interest, as cancer treatments move towards combing both targeted- and immuno-therapies in new treatment regimes. This protocol is using THP-1 cells, a human leukemia monocytic cell line that can be differentiated into macrophages. This allows studying ...
Analysis of Protein Stability by the Cycloheximide Chase Assay
Comparison of protein stability in eukaryotic cells has been achieved by cycloheximide, which is an inhibitor of protein biosynthesis due to its prevention in translational elongation. It is broadly used in cell biology in terms of determining the half-life of a given protein and has gained much popularity in cancer research. Here we present a ...
Infectious Focus Assays and Multiplicity of Infection (MOI) Calculations for Alpha-herpesviruses
Authors:  Anna Sloutskin and Ronald S. Goldstein, date: 11/20/2014, view: 35473, Q&A: 0
Titration of viral stocks is a critical process before any experimental use of the virus. Here we describe an infectious focus assay for several alphaherpesviruses, a titration method for fluorescently labeled viruses, based on the original plaque assay. In addition, the calculation of multiplicity of infection (MOI) is presented.
Novel Object Recognition for Studying Memory in Mice
Authors:  Tzyy-Nan Huang and Yi-Ping Hsueh, date: 10/05/2014, view: 27025, Q&A: 0
Memory tests are important indexes of the brain functions for rodents behavior assay. Many memory tasks require external forces (e.g. electric shocks) or intrinsic forces (e.g. hunger and thirsty) to trigger the responses. Under those conditions, rodents are under stresses, such as pain, tired, malnutrition or dehydration, which ...
Targeted Gene Mutation in Rice Using a CRISPR-Cas9 System
Authors:  Kabin Xie, Bastian Minkenberg and Yinong Yang, date: 09/05/2014, view: 26810, Q&A: 0
RNA-guided genome editing (RGE) using bacterial type II cluster regularly interspaced short palindromic repeats (CRISPR)–associated nuclease (Cas) has emerged as a simple and versatile tool for genome editing in many organisms including plant and crop species. In RGE based on the Streptococcus pyogenes CRISPR-Cas9 system, the Cas9 ...
In vitro Protein Ubiquitination Assays
Authors:  Qingzhen Zhao and Qi Xie, date: 10/05/2013, view: 36988, Q&A: 0
Ubiquitin can be added to substrate protein as a protein tag by the concerted actions of ubiquitin activating enzyme (E1), ubiquitin conjugating enzyme (E2) and ubiquitin protein ligase (E3). At the present of E1 and ubiquitin, E2 activity can be determined by the thio-ester formation. The E3 activity of a putative protein as well as the E2/E3 or ...
Isolation of Mouse Tumor-Infiltrating Leukocytes by Percoll Gradient Centrifugation
Authors:  Ying Liu, Keqiang Chen, Chunyan Wang, Wanghua Gong, Teizo Yoshimura, Ji Ming Wang and Mingyong Liu, date: 09/05/2013, view: 34768, Q&A: 0
A hallmark of cancer-associated inflammation is the infiltration of leukocytes into tumors, which is believed to be recruited by chemokines. Some infiltrating leukocytes such as macrophages often promote tumor growth by producing growth-inducing and angiogenic factors. Here, we described a method of isolating tumor-infiltrating leukocytes with ...
ImmunoPrecipitation of Nuclear Protein with Antibody Affinity Columns
Authors:  Saïda Dadi, Dominique Payet-Bornet and Pierre Ferrier, date: 02/05/2013, view: 29847, Q&A: 1
Co-Immunoprecipitation (Co-IP) is the method used to pull down protein partners of a protein of interest using an antibody that specifically binds to this specific protein in order to test protein-protein interaction. “Pulled down” proteins can be analyzed by western blot for suspected protein partner, or by Mass spectrometry for high throughput ...
Scratch Wound Healing Assay
Author:  Yanling Chen, date: 03/05/2012, view: 110242, Q&A: 6
The scratch wound healing assay has been widely adapted and modified to study the effects of a variety of experimental conditions, for instance, gene knockdown or chemical exposure, on mammalian cell migration and proliferation. In a typical scratch wound healing assay, a “wound gap” in a cell monolayer is created by scratching, and the “healing” ...
Transwell Cell Migration Assay Using Human Breast Epithelial Cancer Cell
Author:  Yanling Chen, date: 02/20/2012, view: 64929, Q&A: 6
Transwell migration assays have been widely used for studying the motility of different types of cells including metastatic cancer cells. The assay is also useful in screens for compounds that act as chemoattractants or inhibitors of chemotaxis for cells. The assay employs a permeable layer of support, usually a tissue-culture-treated microporous ...



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