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Experiment Tags: CircRNAs, RNA Pull-Down, RNA-Protein Interactions
Experiment Summary: In this protocol, we introduce a method to study RNA-protein interactions, which will facilitate researchers to carry out circRNA related experiments.
Experiment Tags: RSV Transcription, Minigenome, Polymerase, Luciferase Assay, Real-Time Quantitative PCR Assay
Experiment Summary: In this protocol, we detail two different methods of detecting viral RNA synthesis: a firefly luciferase assay for rapid and sensitive measurement of RSV polymerase activity; and a real-time quantitative PCR method for determination of specific effects on the transcription of individual viral genes and the polar transcription gradient of RSV.
Experiment Tags: TAC-Seq, Chromatin Accessibility, Genome Wide, Zebrafish, Tn5 Transposase
Experiment Summary: In this article, we describe the application of ATAC-seq in zebrafish embryos, thus illustrating the applicability of this method to the entire vertebrate population.
Experiment Tags: Adeno-Associated Virus, Binding, Internalization, Virus Entry, Virus, Cell Surface
Experiment Summary: In this protocol, we describe a quantitative PCR (qPCR) based method to determine the amount of vector bound to the cell surface and the amount of subsequent virus internalization based on viral genome quantification.
Experiment Tags: Circular RNA, In Vitro Transcription, Ligase, Phosphorylation, Polyacrylamide Gel Electrophoresis
Experiment Summary: This protocol describes a simple and straightforward way to obtain single-stranded circular RNA sequences in vitro.
Experiment Tags: CircRNAs, CircRNA Pulldown, Antisense Oligo, Biotin Pulldown, RT-qPCR, miRNA, RNA-Binding Proteins
Experiment Summary: In this detailed protocol, the circRNA of interest (e.g., circHipk2) was captured using a biotin-labeled antisense oligo (ASO) targeting the circHipk2 backsplice junction sequence followed by pulldown with streptavidin-conjugated magnetic beads. The specific enrichment of circRNA was analyzed using reverse transcription quantitative PCR (RT-qPCR).
Experiment Tags: MicroRNA, 3'UTR (3’UTR), Luciferase Assay, In Vitro
Experiment Summary: This protocol is to be used to test the binding and activity of miRNA on putative UTR target sequences. It is based on the expression of Luciferase as a reporter gene fused to the UTR sequence in the presence of plasmids containing pre-miRNA of interest or synthetic miRNA to test in an in vitro cell culture assay.
Experiment Tags: Long Noncoding RNAs, RNA-Protein Interaction, Mass Spectrometry
Experiment Summary: This article provides a detailed protocol for the assay with hands-on tips for the LnRNA pulldown assay, which is commonly used to identify protein partners of the cellular environment that interact with InRNA.
Experiment Tags: Base-Editing, CRISPR-Cas9
Experiment Summary: This article provides optimized protocols (including experimental design, methods, and analyses) for designing base editing constructs for basic research.
Experiment Tags: Inflammation, Peritonitis, Sepsis, In Vivo Imaging, Myeloperoxidase
Experiment Summary: This protocol allows studying of inflammatory response induced by LPS that affect neutrophil infiltration by tracking myeloperoxidase (MPO) activity in vivo.
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