El. knyga: Functional Analysis of Long Non-Coding RNAs: Methods and Protocols

Bioinformatics Approaches for Functional Prediction of Long Non-Coding RNAs.- Visualization of lncRNA and mRNA Structure Models within the Integrative Genomics Viewer.- RNA Coding Potential Prediction Using Alignment-Free Logistic Regression Model.- Classification of Long Non-Coding RNAs by K-mer Content.- Genome-Wide Computational Analysis and Validation of Potential Long Non-Coding RNA-Mediated DNA-DNA:RNA Triplexes in the Human Genome.- Using INFERNO to Infer the Molecular Mechanisms Underlying Non-Coding Genetic Associations.- A Bioinformatic Pipeline to Integrate GWAS and eQTL Datasets to Identify Disease Relevant Human Long Non-Coding RNAs.- AnnoLnc: A One-Stop Portal to Systematically Annotate Novel Human Long Non-Coding RNAs.- Annotation of Full-Length Long Non-Coding RNAs with Capture Long-Read Sequencing (CLS).- Single-Cell Analysis of Long Non-Coding RNAs (lncRNAs) in Mouse Brain Cells.- Detection and Characterization of Ribosome-Associated Long Non-Coding RNAs.- Analysis ofAnnotated and Unannotated Long Non-Coding RNAs from Exosome Subtypes Using Next-Generation RNA Sequencing.- DMS-MaPseq for Genome-Wide or Targeted RNA Structure Probing In Vitro and In Vivo.- Labeling and Purification of Temporally Expressed RNAs during the S-Phase of the Cell Cycle in Living Cells.- A Quick Immuno-FISH Protocol for Detecting RNAs, Proteins, and Chromatin Modifications.- M(R)apping RNA-Protein Interactions.- In Vivo Administration of Therapeutic Antisense Oligonucleotides.- CRISPR-Mediated Mutagenesis of Long Non-Coding RNAs.- In Vivo CRISPR/Cas9-Based Targeted Disruption and Knock-In of a Long Non-Coding RNA.- Genome-Scale Perturbation of Long Non-Coding RNA Expression Using CRISPR Interference.- In Vivo Functional Analysis of Non-Conserved Human lncRNAs Using a Humanized Mouse Model.