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Construction of transcriptional regulatory networks using total RNA-seq data
Total RNA sequencing allows capturing of long non-coding and circular RNA along with mRNA. Additional sequencing of micro RNA (miRNA), using libraries with shorter fragments, provides the means to characterize miRNA-driven transcriptional regulation. Here, we present a protocol for processing total...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8403681/ https://www.ncbi.nlm.nih.gov/pubmed/34485938 http://dx.doi.org/10.1016/j.xpro.2021.100769 |
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author | Chouvarine, Philippe Hansmann, Georg |
author_facet | Chouvarine, Philippe Hansmann, Georg |
author_sort | Chouvarine, Philippe |
collection | PubMed |
description | Total RNA sequencing allows capturing of long non-coding and circular RNA along with mRNA. Additional sequencing of micro RNA (miRNA), using libraries with shorter fragments, provides the means to characterize miRNA-driven transcriptional regulation. Here, we present a protocol for processing total RNA and miRNA sequencing data to quantify circular RNA, long non-coding RNA, mRNA, and miRNA. Further, the protocol combines the quantification data with miRNA target annotation to construct likely transcriptional regulatory networks, which can be validated in the subsequent studies. For complete details on the use and execution of this protocol, please refer to Chouvarine et al. (2021). |
format | Online Article Text |
id | pubmed-8403681 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-84036812021-09-02 Construction of transcriptional regulatory networks using total RNA-seq data Chouvarine, Philippe Hansmann, Georg STAR Protoc Protocol Total RNA sequencing allows capturing of long non-coding and circular RNA along with mRNA. Additional sequencing of micro RNA (miRNA), using libraries with shorter fragments, provides the means to characterize miRNA-driven transcriptional regulation. Here, we present a protocol for processing total RNA and miRNA sequencing data to quantify circular RNA, long non-coding RNA, mRNA, and miRNA. Further, the protocol combines the quantification data with miRNA target annotation to construct likely transcriptional regulatory networks, which can be validated in the subsequent studies. For complete details on the use and execution of this protocol, please refer to Chouvarine et al. (2021). Elsevier 2021-08-25 /pmc/articles/PMC8403681/ /pubmed/34485938 http://dx.doi.org/10.1016/j.xpro.2021.100769 Text en © 2021 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Protocol Chouvarine, Philippe Hansmann, Georg Construction of transcriptional regulatory networks using total RNA-seq data |
title | Construction of transcriptional regulatory networks using total RNA-seq data |
title_full | Construction of transcriptional regulatory networks using total RNA-seq data |
title_fullStr | Construction of transcriptional regulatory networks using total RNA-seq data |
title_full_unstemmed | Construction of transcriptional regulatory networks using total RNA-seq data |
title_short | Construction of transcriptional regulatory networks using total RNA-seq data |
title_sort | construction of transcriptional regulatory networks using total rna-seq data |
topic | Protocol |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8403681/ https://www.ncbi.nlm.nih.gov/pubmed/34485938 http://dx.doi.org/10.1016/j.xpro.2021.100769 |
work_keys_str_mv | AT chouvarinephilippe constructionoftranscriptionalregulatorynetworksusingtotalrnaseqdata AT hansmanngeorg constructionoftranscriptionalregulatorynetworksusingtotalrnaseqdata |