117 Result(s)
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Protocol
CRISPR-Cas9 Correction of Duchenne Muscular Dystrophy in Mice by a Self-Complementary AAV Delivery System
Duchenne muscular dystrophy (DMD) is a fatal neuromuscular disorder, caused by mutations in the DMD gene coding dystrophin. Applying clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-a...
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Protocol
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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Protocol
A Review of High-Dimensional Mediation Analyses in DNA Methylation Studies
DNA methylation alterations have been widely studied as mediators of environmentally induced disease risks. With new advances in technique, epigenome-wide DNA methylation data (EWAS) have become the new standa...
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Protocol
Workflow to Mine Frequent DNA Co-methylation Clusters in DNA Methylome Data
The advances in high-throughput nucleotide sequencing technology revolutionized biomedical research. Vast amount of genomic data rapidly accumulates in a daily basis, which in turn calls for the development of...
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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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Protocol
Pseudogene Profiling for Cancer Subtype Classification
Although long thought of as “gene relics,” pseudogenes have recently gained research and medical interests because of their potential impacts on cellular pathways and of their clinical relevance. Studies have ...
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Protocol
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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Protocol
Analysis of Mutations in K-ras and p53 Genes in Sputum and Plasma Samples
Sputum and plasma can provide noninvasive materials to investigate biomarkers for cancer detection and diagnosis. Mutations in the K-ras oncogene and p53 suppressor gene have been frequently found in sputum an...
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Protocol
Telomere and G-Quadruplex Colocalization Analysis by Immunofluorescence Fluorescence In Situ Hybridization (IF-FISH)
Four-stranded G-quadruplexes consists of tracks of guanines that are stabilized by Hoogsteen base pairing. The formation of G-quadruplexes in genomic DNA contribute to numerous biological processes in vivo, in...
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Protocol
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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Protocol
Characterization of Co-transcriptional Formation of G-Quadruplexes in Double-Stranded DNA
In vitro transcription of double-stranded DNA (dsDNA) induces a formation of two types of G-quadruplexes, intramolecular DNA G-quadruplexes or DNA:RNA hybrid G-quadruplexes, in clusters of guanine tracts. The ...
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Protocol
Synthesis and Evaluation of Novel Neamine–Nucleoside Conjugates as Potential Antibiotic Targets for Escherichia coli 16S Ribosomal RNA
Based on the nucleobase rich character of the binding pocket of A-site 16S ribosomal RNA of Escherichia coli, it was proposed that the neamine moiety of synthesized Neamine–nucleoside conjugates could bind to the...
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Protocol
Decoding the Atlas of RNA Modifications from Epitranscriptome Sequencing Data
Over 100 types of chemical modifications have been identified in protein-coding and noncoding RNAs (ncRNAs). However, the prevalence, regulation, and function of diverse RNA modifications remain largely unknow...
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Protocol
Fast and Quantitative Identification of Ex Vivo Precise Genome Targeting-Induced Indel Events by IDAA
Recent developments in gene targeting methodologies such as ZFNs, TALENs, and CRISPR/Cas9 have revolutionized approaches for gene modifications in cells, tissues, and whole animals showing great promise for tr...
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Protocol
An Improved Genome Engineering Method Using Surrogate Reporter-Coupled Suicidal ZFNs
Using engineered nucleases such as zinc-finger nucleases (ZFNs) and TALE nuclease (TALEN) to accomplish genome editing often causes high cellular toxicity because of the consistent expression of artificial nuc...
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Protocol
QuickRNASeq: Guide for Pipeline Implementation and for Interactive Results Visualization
Sequencing of transcribed RNA molecules (RNA-Seq) has been used wildly for studying cell transcriptomes in bulk or at the single-cell level (Wang et al., Nat Rev Genet, 10:57–63, 2009; Ozsolak and Milos, Nat R...
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Protocol
Isolation of Extracellular RNA from Serum/Plasma
Extracellular RNAs are initiating increased interest due to their potentials in serving as novel biomarkers, mediators of intercellular communication, and therapeutic applications. As a newly emerging field, o...
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Protocol
Application of TALE-Based Approach for Dissecting Functional MicroRNA-302/367 in Cellular Reprogramming
MicroRNAs are small 18–24 nt single-stranded noncoding RNA molecules involved in many biological processes, including stemness maintenance and cellular reprogramming. Current methods used in loss-of-function s...
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Protocol
Discovering circRNA-microRNA Interactions from CLIP-Seq Data
Circular RNAs (circRNAs) represent an abundant group of noncoding RNAs in eukaryotes and are emerging as important regulatory molecules in physiological and pathological processes. However, the precise mechani...
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Protocol
An Adaptive Laboratory Evolution Method to Accelerate Autotrophic Metabolism
Adaptive laboratory evolution (ALE) is an approach enabling the development of novel characteristics in microbial strains via the application of a constant selection pressure. This method is also an efficient ...
