E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data
Summary: 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 expression...
Saved in:
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2025-09-01
|
| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166725003958 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1839613519435137024 |
|---|---|
| author | Hua Yu Yunjie Liu Zhouming Zhang Guanglei Xie Jingyu Liu Yijia Liu Siyue He Zhiwei Peng Lu Lu Fei Li Xi Wang |
| author_facet | Hua Yu Yunjie Liu Zhouming Zhang Guanglei Xie Jingyu Liu Yijia Liu Siyue He Zhiwei Peng Lu Lu Fei Li Xi Wang |
| author_sort | Hua Yu |
| collection | DOAJ |
| description | Summary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| format | Article |
| id | doaj-art-c0ae2e8f0eff4cab8ac9cf45c2f77203 |
| institution | Matheson Library |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-c0ae2e8f0eff4cab8ac9cf45c2f772032025-07-27T04:56:29ZengElsevierSTAR Protocols2666-16672025-09-0163103989E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq dataHua Yu0Yunjie Liu1Zhouming Zhang2Guanglei Xie3Jingyu Liu4Yijia Liu5Siyue He6Zhiwei Peng7Lu Lu8Fei Li9Xi Wang10The 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; Corresponding authorThe First Affiliated Hospital, School of Basic Medical Sciences and Institute of Biomedical Innovation, Jiangxi Medical College, Nanchang University, Nanchang 330031, ChinaQueen Mary School, Nanchang University Nanchang 330031, ChinaWestlake Genomics and Bioinformatics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China; Westlake Institute for Advanced Study, Hangzhou 310024, ChinaThe First Affiliated Hospital, School of Basic Medical Sciences and Institute of Biomedical Innovation, Jiangxi Medical College, Nanchang University, Nanchang 330031, ChinaThe First School of Clinical Medicine of Nanchang University, Nanchang 330031, ChinaThe First Affiliated Hospital, School of Basic Medical Sciences and Institute of Biomedical Innovation, Jiangxi Medical College, Nanchang University, Nanchang 330031, ChinaThe First Affiliated Hospital, School of Basic Medical Sciences and Institute of Biomedical Innovation, Jiangxi Medical College, Nanchang University, Nanchang 330031, ChinaCollege of Computer Science, Jiangxi University of Chinese Medicine, Nanchang 330004, ChinaThe 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, ChinaWestlake Genomics and Bioinformatics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China; Westlake Institute for Advanced Study, Hangzhou 310024, China; Corresponding authorSummary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166725003958BioinformaticsRNAseqSequence analysis |
| spellingShingle | Hua Yu Yunjie Liu Zhouming Zhang Guanglei Xie Jingyu Liu Yijia Liu Siyue He Zhiwei Peng Lu Lu Fei Li Xi Wang E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data STAR Protocols Bioinformatics RNAseq Sequence analysis |
| title | E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data |
| title_full | E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data |
| title_fullStr | E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data |
| title_full_unstemmed | E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data |
| title_short | E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data |
| title_sort | e3rc a step by step computational protocol for exploring enhancer rna expression and regulation using conventional rna seq data |
| topic | Bioinformatics RNAseq Sequence analysis |
| url | http://www.sciencedirect.com/science/article/pii/S2666166725003958 |
| work_keys_str_mv | AT huayu e3rcastepbystepcomputationalprotocolforexploringenhancerrnaexpressionandregulationusingconventionalrnaseqdata AT yunjieliu e3rcastepbystepcomputationalprotocolforexploringenhancerrnaexpressionandregulationusingconventionalrnaseqdata AT zhoumingzhang e3rcastepbystepcomputationalprotocolforexploringenhancerrnaexpressionandregulationusingconventionalrnaseqdata AT guangleixie e3rcastepbystepcomputationalprotocolforexploringenhancerrnaexpressionandregulationusingconventionalrnaseqdata AT jingyuliu e3rcastepbystepcomputationalprotocolforexploringenhancerrnaexpressionandregulationusingconventionalrnaseqdata AT yijialiu e3rcastepbystepcomputationalprotocolforexploringenhancerrnaexpressionandregulationusingconventionalrnaseqdata AT siyuehe e3rcastepbystepcomputationalprotocolforexploringenhancerrnaexpressionandregulationusingconventionalrnaseqdata AT zhiweipeng e3rcastepbystepcomputationalprotocolforexploringenhancerrnaexpressionandregulationusingconventionalrnaseqdata AT lulu e3rcastepbystepcomputationalprotocolforexploringenhancerrnaexpressionandregulationusingconventionalrnaseqdata AT feili e3rcastepbystepcomputationalprotocolforexploringenhancerrnaexpressionandregulationusingconventionalrnaseqdata AT xiwang e3rcastepbystepcomputationalprotocolforexploringenhancerrnaexpressionandregulationusingconventionalrnaseqdata |