145 Result(s)
within
Protocol
Da** Chen
Human Genetics
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Protocol
Quantification of Muscle Satellite Stem Cell Divisions by High-Content Analysis
High-content is commonly performed on 2D cultured cells, which is but has low biological relevance. In contrast, single assay preserves the satellite between the basal lamina and sarcolemma and conse...
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Controlling Batch Effect in Epigenome-Wide Association Study
Methylation data, similar to other omics data, is susceptible to various technical issues that are potentially associated with unexplained or unrelated factors. Any difference in the measurement of DNA methyla...
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Phosphate-Methylated Oligonucleotides as a Novel Primer for PCR and RT-PCR
This chapter introduces neutralized DNA (nDNA) as a novel design for the primers of PCR and RT-PCR by methylating phosphate groups of some oligonucleotides in their structures. It starts with an introduction ...
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Designing Overlap Extension PCR Primers for Protein Mutagenesis: A Programmatic Approach
Overlap extension PCR is one of the routinely used methods to generate mutagenic genes for the functional and structural study of proteins. However, it is time-consuming to design the overlap** mutagenic pri...
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Site-Directed Mutagenesis Method Mediated by Cas9
This study presents an in vitro CRISPR/Cas9-mediated mutagenic (ICM) system that allows rapid construction of designed mutants or site-saturation mutagenesis libraries in a PCR-independent manner. The plasmid ...
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DNA Methylation and Atopic Diseases
The prevalence of allergic diseases such as asthma is globally increasing, posing threat to the life quality of the affected population. Genome-wide association studies (GWAS) suggest that genetic variations o...
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Increase the Power of Epigenome-Wide Association Testing Using ICC-Based Hypothesis Weighting
For large-scale hypothesis testing such as epigenome-wide association testing, adaptively focusing power on the more promising hypotheses can lead to a much more powerful multiple testing procedure. In this ch...
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Analyzing High-Order Epistasis from Genotype-Phenotype Maps Using ‘Epistasis’ Package
Epistasis is the phenomenon about the interactions between genes, leading to complex phenotypic effects. The interactions between three or more mutations called “high-order epistasis” aroused significant inter...
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Epistasis Detection Based on Epi-GTBN
Epistasis detection is a hot topic in bioinformatics due to its relevance to the detection of specific phenotypic traits and gene–gene interactions. Here, we present a step-by-step protocol to apply Epi-GTBN, ...
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mito-Ψ-Seq: A High-Throughput Method for Systematic Map** of Pseudouridine Within Mitochondrial RNA
RNA modifications are present in most cellular RNAs and are formed posttranscriptionally by enzymatic machineries that involve hundreds of enzymes and cofactors. RNA modifications impact the life cycle of the ...
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FREMSA: A Method That Provides Direct Evidence of the Interaction between microRNA and mRNA
microRNAs (miRNAs) modulate the expression of enzymes responsible for activation or detoxification of xenobiotics and toxicants. miRNAs are dysregulated in response to environmental exposure and have been impl...
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Delivering Molecular Beacons via an Electroporation-Based Approach Enables Live-Cell Imaging of Single RNA Transcripts and Genomic Loci
Molecular beacons (MBs) are synthetic oligonucleotide probes that are designed to fluoresce upon hybridization to complementary nucleic acid targets. In contrast to genetically encoded probes that can be readi...
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Methods for Establishing and Using a Stable Cell Line Expressing Both Gaussia Luciferase and Firefly Luciferase to Screen for Endoplasmic Reticulum Stress
Endoplasmic reticulum (ER) stress is one of the major mechanisms underlying the etiology of multiple diseases and drug-induced toxicity. Gaussia luciferase (Gluc) is a naturally secreted protein that has been use...
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Using a Lentivirus-Based Inducible RNAi Vector to Silence a Gene
RNA interference (RNAi) is a powerful approach for inhibiting gene expression and its wide applications have expanded our understanding of gene functions. Short hairpin RNAs (shRNAs) are artificially synthesiz...
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Detection of Loss of Heterozygosity in Tk-Deficient Mutants from L5178Y Tk+/−-3.7.2C Mouse Lymphoma Cells
The mouse lymphoma assay (MLA), a forward mutation assay using the Tk+/−-3.7.2C clone of the L5178Y mouse lymphoma cell line and the Thymidine kinase (Tk) gene, has been widely used as an in vitro genetic toxicit...
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Single-Molecule Analysis of RNA Dynamics in Living Cells Using Molecular Beacons
Over the past decade, emerging evidence has indicated that long intergenic noncoding RNAs (lincRNAs), a class of RNA transcripts greater than 200 nt in length, function as key regulators of gene expression in ...
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LncVar: Deciphering Genetic Variations Associated with Long Noncoding Genes
Long noncoding RNAs (lncRNAs) are pervasively transcribed in various species and play important roles in many biological processes. The biological functions of most lncRNAs remain to be explored. Previous stud...
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High-Throughput Screening of G-Quadruplex Ligands by FRET Assay
Fluorescence resonance energy transfer (FRET) is a distance-dependent process by which energy is transferred from an excited donor fluorophore to an acceptor molecule when the donor and acceptor are in close p...
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Engineering a Bioartificial Human Colon Model Through Decellularization and Recellularization
The tissue engineering method of decellularization and recellularization has been successfully used in a variety of regenerative medicine applications. The protocols used to de/recellularize various organs and...
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Genome-Wide Annotation of circRNAs and Their Alternative Back-Splicing/Splicing with CIRCexplorer Pipeline
Circular RNAs (circRNAs) derived from back-spliced exons were sporadically identified about 25 years ago, and have been recently re-discovered genome-wide across different species. Interestingly, one gene locu...
