29 Result(s)
within
Protocol
Da** Chen
Gene Expression
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Protocol
A Label-Free Electrochemical Biosensor for Sensitive Detection of 5-Hydroxymethylcytosine
The 5-hydroxymethylcytosine (5-hmC) is regarded as sixth base in the genome and closely linked to a series of physiological and pathological processes. Nevertheless, the sensitive detection of 5-hmC and effici...
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Electrochemical Assay for Continuous Monitoring of Dynamic DNA Methylation Process
DNA methylation is an important mode of epigenetic modification, which plays key roles in many cellular processes. Within the last decades, various methods have been proposed for quantitative analysis of methy...
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Characterization of Circular RNAs
Accumulated lines of evidence have revealed that a large number of circular RNAs are produced in transcriptomes from fruit fly to mouse and human. Unlike linear RNAs shaped with 5′ cap and 3′ tail, circular RN...
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Illuminating lncRNA Function Through Target Prediction
Most of the transcribed human genome codes for noncoding RNAs (ncRNAs), and long noncoding RNAs (lncRNAs) make for the lion’s share of the human ncRNA space. Despite growing interest in lncRNAs, because there ...
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CRISPR/Cas9 Guide RNA Design Rules for Predicting Activity
A critical stage in performing gene editing experiments using the CRISPR/Cas9 system is the design of guide RNA (gRNA). In this chapter, we conduct a review of the current gRNA design rules for maximizing on-t...
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Synthesis and Evaluation of Caged siRNAs with Single cRGD Modification for Photoregulating RNA Interference
We designed and synthesized caged siRNAs with photolabile linker and single cRGD peptide modifications for the photoregulation of gene expression. Photolabile linker and cRGD were inserted at 5′ terminus of si...
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Protocol
Engineering T Cells Using CRISPR/Cas9 for Cancer Therapy
Recent advances in the development of gene editing technologies, especially the CRISPR/Cas 9 system, have substantially enhanced our ability to make precise and efficient changes in the genomes of various cell...
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MiR-302-Mediated Somatic Cell Reprogramming and Method for Generating Tumor-Free iPS Cells Using miR-302
Human induced pluripotent stem cells (iPSCs) by four factors have the risks of teratoma formation and potential tumorigenicity. To overcome this major hurdle, we examined the mechanism(s) by which the cell cyc...
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Live-Cell Imaging of Long Noncoding RNAs Using Molecular Beacons
Long noncoding RNAs (lncRNAs) are a family of non-protein-coding RNA transcripts greater than 200 nucleotides in length that have been regarded as crucial modulators of gene expression in various biological an...
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Degradome Sequencing in Plants
Degradome sequencing provides large amounts of data regarding RNA degradation. The degradome library construction described here is modified from the 5′-rapid amplification of cDNA ends (5′-RACE), and each deg...
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Analysis of Methylation Status of Plant MicroRNAs
Small noncoding RNAs of 20–30 nucleotides in length are key mediators of gene silencing. 2′-O-Methylation on the 3′ terminal nucleotide of several types of small RNAs, including microRNAs (miRNAs) and small in...
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Targeted Delivery with Imaging Assessment of siRNA Expressing Nanocassettes into Cancer
Molecular therapy using small interfering RNA (siRNA) shows great promise in the development of novel therapeutics for cancer. Although various approaches have been developed for in vivo delivery of siRNAs int...
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Protocol
Magnetic Resonance Spectroscopy of siRNA-Based Cancer Therapy
Small interfering RNA (siRNA) is routinely used as a biological tool to silence specific genes, and is under active investigation in cancer treatment strategies. Noninvasive magnetic resonance spectroscopy (MR...
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High-Throughput RNA-Seq for Allelic or Locus-Specific Expression Analysis in Arabidopsis-Related Species, Hybrids, and Allotetraploids
With the next generation sequencing technology, RNA-Seq (RNA sequencing) becomes one of the most powerful tools in quantification of global transcriptomes, discovery of new transcripts and alternative isoforms...
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Evaluating the MicroRNA Targeting Sites by Luciferase Reporter Gene Assay
MicroRNAs are post-transcriptional regulators that control mRNA stability and the translation efficiency of their target genes. Mature microRNAs are approximately 22-nucleotide in length. They mediate post-tra...
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Quantitative NanoProteomics Approach for Protein Complex (QNanoPX) Using Gold Nanoparticle-Based DNA Probe
Affinity purification by pulldown methods using target-bound gel beads provides a powerful approach for purifying endogenous protein complexes. Such methods can be improved by using nanoparticle-based probe, c...
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Use of Histone Deacetylase Inhibitors to Examine the Roles of Bromodomain and Histone Acetylation in p300-Dependent Gene Expression
The bromodomain is an evolutionarily conserved motif harbored by many transcription regulators and nearly all nuclear histone acetyltransferases including the transcriptional coactivator p300. The function of ...
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Protocol
Application of Intronic MicroRNA Agents in Cosmetics
MicroRNAs (miRNA) are short, single-stranded, noncoding RNAs that regulate a number of cellular processes through their capability to silence the expression of target proteins. Using miRNAs to target and reduc...
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Fluorescence Anisotropy Microplate Assay to Investigate the Interaction of Full-Length Steroid Receptor Coactivator-1a with Steroid Receptors
Estrogens, acting via estrogen receptor (ER) play key roles in growth, differentiation, and gene regulation in the reproductive, central nervous, and skeletal systems. ER-mediated gene transcription contribute...
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Histone Deacetylase Inhibitor Valproic Acid as a Small Molecule Inducer to Direct the Differentiation of Pluripotent Stem Cells
Pluripotent stem cells can be directed into myogenic differentiation by small molecular inducers, which preferentially activate muscle-specific transcription networks. Here we describe how to efficiently direc...
