Enhancer Rnas: Methods and Protocols (Hardcover, 2017)

Cellular Fractionation and Isolation of Chromatin-associated RNA.- Knockdown of Nuclear-located Enhancer RNAs and Long ncRNAs using Locked Nucleic Acid GapmeRs.- Visualization of Enhancer-derived Non-coding RNA.- UV-RNA Immunoprecipitation (UV-RIP) Protocol in Neurons.- Mapping Long non-coding RNA Chromatin Occupancy using Capture Hybridization Analysis of RNA Targets (CHART).- Detecting long-range Enhancer-promoter Interactions by Quantitative Chromosome Conformation Capture.- Deciphering Noncoding RNA and Chromatin Interactions: Multiplex Chromatin Interaction Analysis by Paired-End Tag Sequencing (mChIA-PET).- Identification of Transcribed Enhancers by Genome-wide Chromatin Immunoprecipitation Sequencing.- Global Run-On sequencing (GRO-seq).- Computational Approaches for Mining GRO-seq Data to Identify and Characterize Active Enhancers.- Evaluating the Stability of mRNAs and Non-coding RNAs.- A Novel Method to Quantify RNA-protein Interactions in situ using FMTRIP and Proximity Ligation.- In silico Promoter Recognition from deepCAGE data.- Bioinformatics Pipeline for Transcriptome Sequencing Analysis.- CRISPR/Cas-9 Genome Editing in Embryonic Stem Cells.- Targeted Gene Activation Using RNA-Guided Nucleases