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Protocols

protocols
Protocol

RNA Pull-Down Protocol of CircRNA Research

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.

protocols
Protocol

Protocol for Studying RSV Transcription using Minigenome Systems

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.

protocols
Protocol

CRISPRCas9 Library Screening Protocol

Experiment Tags: CRISPRCas9 Library Screening, CRISPRCas9

Experiment Summary: In this protocol, we briefly describe the CRISPR/Cas9 library screening process to simplify and facilitate high-throughput screening.

protocols
Protocol

Assay for Transposase-Accessible Chromatin with High-Throughput Sequencing (ATAC-Seq) Protocol for Zebrafish Embryos

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.

protocols
Protocol

Virus Binding and Internalization Protocol for Adeno-associated Virus

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.

protocols
Protocol

Preparation of Circular RNA In Vitro Protocol

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.

protocols
Protocol

Antisense Oligo Pulldown of Circular RNA for Downstream Analysis Protocol

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).

protocols
Protocol

Test MicroRNA Target with in vitro Cell Culture Luciferase Assay Protocol

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.

protocols
Protocol

Protocol for Constructing Glycine Oxidase Mutant Libraries by Random Mutagenesis

Experiment Tags: Glycine Oxidase Mutant Libraries, Random Mutagenesis

Experiment Summary: This protocol describes the construction of a glycine oxidase mutant library by random mutagenesis and the use of a phage T7 lysis-based approach for high-throughput screening of oxidase activity, among other things.

protocols
Protocol

LncRNA Pulldown Combined with Mass Spectrometry to Identify the Novel lncRNA-Associated Proteins Protocol

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.

* For research use only. Not intended for any clinical use.
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