Generating transcriptional regulatory networks from time-ordered stem cell differentiation RNA sequencing data

We describe steps to 1) identify ascending and descending monotonic key genes from time-ordered stem cell differentiation expression data, 2) construct time-ordered transcriptional regulatory networks, and 3) infer the involvement of transcription factors along the differentiation process. For compl...

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Detalles Bibliográficos
Autores principales: Tsai, Yu-Shuen, Chang, Yao-Ming, Lim, Yang-Mooi, Cheong, Soon-Keng, Chung, I-Fang, Wong, Chee-Yin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9420390/
https://www.ncbi.nlm.nih.gov/pubmed/36042881
http://dx.doi.org/10.1016/j.xpro.2022.101541
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author Tsai, Yu-Shuen
Chang, Yao-Ming
Lim, Yang-Mooi
Cheong, Soon-Keng
Chung, I-Fang
Wong, Chee-Yin
author_facet Tsai, Yu-Shuen
Chang, Yao-Ming
Lim, Yang-Mooi
Cheong, Soon-Keng
Chung, I-Fang
Wong, Chee-Yin
author_sort Tsai, Yu-Shuen
collection PubMed
description We describe steps to 1) identify ascending and descending monotonic key genes from time-ordered stem cell differentiation expression data, 2) construct time-ordered transcriptional regulatory networks, and 3) infer the involvement of transcription factors along the differentiation process. For complete details on the use and execution of this protocol, please refer to Wong et al. (2020).
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spelling pubmed-94203902022-08-29 Generating transcriptional regulatory networks from time-ordered stem cell differentiation RNA sequencing data Tsai, Yu-Shuen Chang, Yao-Ming Lim, Yang-Mooi Cheong, Soon-Keng Chung, I-Fang Wong, Chee-Yin STAR Protoc Protocol We describe steps to 1) identify ascending and descending monotonic key genes from time-ordered stem cell differentiation expression data, 2) construct time-ordered transcriptional regulatory networks, and 3) infer the involvement of transcription factors along the differentiation process. For complete details on the use and execution of this protocol, please refer to Wong et al. (2020). Elsevier 2022-08-19 /pmc/articles/PMC9420390/ /pubmed/36042881 http://dx.doi.org/10.1016/j.xpro.2022.101541 Text en © 2022 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
Tsai, Yu-Shuen
Chang, Yao-Ming
Lim, Yang-Mooi
Cheong, Soon-Keng
Chung, I-Fang
Wong, Chee-Yin
Generating transcriptional regulatory networks from time-ordered stem cell differentiation RNA sequencing data
title Generating transcriptional regulatory networks from time-ordered stem cell differentiation RNA sequencing data
title_full Generating transcriptional regulatory networks from time-ordered stem cell differentiation RNA sequencing data
title_fullStr Generating transcriptional regulatory networks from time-ordered stem cell differentiation RNA sequencing data
title_full_unstemmed Generating transcriptional regulatory networks from time-ordered stem cell differentiation RNA sequencing data
title_short Generating transcriptional regulatory networks from time-ordered stem cell differentiation RNA sequencing data
title_sort generating transcriptional regulatory networks from time-ordered stem cell differentiation rna sequencing data
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9420390/
https://www.ncbi.nlm.nih.gov/pubmed/36042881
http://dx.doi.org/10.1016/j.xpro.2022.101541
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