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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...

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Detalles Bibliográficos
Autores principales: Chouvarine, Philippe, Hansmann, Georg
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2021
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).
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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
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