Related Experiment Video
Updated: Sep 13, 2025
Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation
Published on: June 21, 2016
E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional
Hua Yu1, Yunjie Liu2, Zhouming Zhang3
1The First Affiliated Hospital, School of Basic Medical Sciences and Institute of Biomedical Innovation, Jiangxi Medical College, Nanchang University, Nanchang 330031, China; Jiangxi Provincial Key Laboratory of Hematological Diseases, Department of Hematology, Nanchang University, Nanchang 330031, China; Jiangxi Provincial Key Laboratory of Tumor Biology, Nanchang University, Nanchang 330031, China.
None:
Here, we present a computational framework, E3RC, for exploring enhancer RNA (eRNA) expression and regulation using conventional RNA sequencing (RNA-seq) data. Using a public dataset as an example, we describe step-by-step guidelines for identifying eRNAs and characterizing their expressional changes and transcriptional regulation across multiple developmental stages of mouse preimplantation embryos. For complete details on the use and execution of this protocol, please refer to Yu et al.1.
Related Concept Videos
03:21RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
02:40The Eukaryotic Promoter Region
02:24Ribosome Profiling
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...