166 Result(s)
within
Protocol
Lu**g Li
English
Human Genetics
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Protocol
DNA Methylation Imputation Across Platforms
In this chapter, we will provide a review on imputation in the context of DNA methylation, specifically focusing on a penalized functional regression (PFR) method we have previously developed. We will start wi...
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qPrimerDB: A Powerful and User-Friendly Database for qPCR Primer Design
Real-time quantitative polymerase chain reaction (qPCR) is a powerful tool for analyzing and quantifying gene expression, and its primer design is the first and most important step. In order to improve the eff...
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PCR Primer Design for the Rapidly Evolving SARS-CoV-2 Genome
Real-time quantitative PCR is currently the most widely used method for the human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) identification. Due to the rapid evolution of the SARS-Co...
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Application of Correlation Pre-Filtering Neural Network to DNA Methylation Data: Biological Aging Prediction
We introduce the CPFNN (Correlation Pre-Filtering Neural Network) for biological age prediction based on blood DNA methylation data. The model is built on 20,000 top correlated DNA methylation features and traine...
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Construction of Strong Promoters by Assembling Sigma Factor Binding Motifs
Development of strong promoters is of growing interest in the field of biotechnology and synthetic biology. Here we present a protocol for the construction of strong prokaryotic promoters that can be recognize...
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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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Using Open Chromatin Enrichment and Network Hi-C (OCEAN-C) to Identify Open Chromatin Interactions
The open chromatin enrichment and network Hi-C (OCEAN-C) was developed not only for identifying large-scale chromatin structures, including topologically associated domains (TADs) and A/B compartments, but als...
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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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Fast and Efficient Measurement of Clinical and Biological Samples Using Immunoassay-Based Multiplexing Systems
Immunoassay is one of the most commonly used biomedical techniques to detect the expression of an antibody or an antigen in a test sample. Enzyme-linked immunosorbent assay (ELISA) has been used for a variety ...
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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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Bioinformatic Application of Fluorescence-Based In Vivo RNA Regional Accessibility Data to Identify Novel sRNA Targets
Data from fluorescence-based methods that measure in vivo hybridization efficacy of unique RNA regions can be used to infer regulatory activity and to identify novel RNA: RNA interactions. Here, we document th...
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CRISPR/Cas9-Mediated Gene Tagging: A Step-by-Step Protocol
CRISPR/Cas9 provides a simple and powerful tool for modifying almost any DNA of interest. One promising application of the CRISPR/Cas9 system is for tagging genes with a fluorescence marker or tag peptides. Fo...
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One-Step Generation of Seamless Luciferase Gene Knockin Using CRISPR/Cas9 Genome Editing in Human Pluripotent Stem Cells
Human pluripotent stem cells (hPSCs) offer powerful platforms for studying mechanisms of human diseases and for evaluating potential treatments. Genome editing, particularly the CRISPR/Cas9-based method, is hi...
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Using Human Neural Progenitor Cell Models to Conduct Large-Scale Drug Screens for Neurological and Psychiatric Diseases
High-throughput drug screen (HTS) has become a viable approach for new treatment discovery in human diseases. Advances in gene editing technology and human pluripotent stem cell differentiation techniques have...
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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...
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Quantification of d- and l-2-Hydroxyglutarate in Drosophila melanogaster Tissue Samples Using Gas Chromatography-Mass Spectrometry
The fruit fly Drosophila melanogaster has emerged as an ideal system in which to study 2-hydroxyglutarate (2HG) metabolism. Unlike many mammalian tissues and cell lines, which primarily accumulate d- or l-2HG as ...
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Mass Spectroscopic Study of G-Quadruplex
Mass spectrometry (MS) is an analytical tool complimentary for being sensitive, accurate, and versatile in its application, such as the identification of multistranded nucleic acid assemblies, including G-quad...
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5-Methylcytosine Analysis by RNA-BisSeq
5-Methylcytosine (m5C) is a posttranscriptional RNA modification identified in both stable and highly abundant tRNAs and rRNAs, and in mRNAs. Many known or novel m5C sites have been validated by using advanced hi...
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Production of Genetically Engineered Porcine Embryos by Handmade Cloning
Genetic engineering is essential to realize the full potentials of pigs both as livestock and as animal models of human disease. With the development of new genetic engineering technologies, such as the cluste...
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The GFF3toolkit: QC and Merge Pipeline for Genome Annotation
The GFF3toolkit (https://github.com/NAL-i5K/GFF3toolkit) supported by the i5k Workspace@NAL provides a suite of tools to handle gene annotations in GFF3 format fro...
