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Integrating single-cell transcriptomes, chromatin accessibility, and multiomics analysis of mesoderm-induced embryonic stem cells

Here, we present workflows for integrating independent transcriptomic and chromatin accessibility datasets and analyzing multiomics. First, we describe steps for integrating independent transcriptomic and chromatin accessibility measurements. Next, we detail multimodal analysis of transcriptomes and...

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Detalles Bibliográficos
Autores principales: Ko, Kyung Dae, Jiang, Kan, Dell’Orso, Stefania, Sartorelli, Vittorio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10199178/
https://www.ncbi.nlm.nih.gov/pubmed/37192048
http://dx.doi.org/10.1016/j.xpro.2023.102307
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author Ko, Kyung Dae
Jiang, Kan
Dell’Orso, Stefania
Sartorelli, Vittorio
author_facet Ko, Kyung Dae
Jiang, Kan
Dell’Orso, Stefania
Sartorelli, Vittorio
author_sort Ko, Kyung Dae
collection PubMed
description Here, we present workflows for integrating independent transcriptomic and chromatin accessibility datasets and analyzing multiomics. First, we describe steps for integrating independent transcriptomic and chromatin accessibility measurements. Next, we detail multimodal analysis of transcriptomes and chromatin accessibility performed in the same sample. We demonstrate their use by analyzing datasets obtained from mouse embryonic stem cells induced to differentiate toward mesoderm-like, myogenic, or neurogenic phenotypes. For complete details on the use and execution of this protocol, please refer to Khateb et al.(1)
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spelling pubmed-101991782023-05-21 Integrating single-cell transcriptomes, chromatin accessibility, and multiomics analysis of mesoderm-induced embryonic stem cells Ko, Kyung Dae Jiang, Kan Dell’Orso, Stefania Sartorelli, Vittorio STAR Protoc Protocol Here, we present workflows for integrating independent transcriptomic and chromatin accessibility datasets and analyzing multiomics. First, we describe steps for integrating independent transcriptomic and chromatin accessibility measurements. Next, we detail multimodal analysis of transcriptomes and chromatin accessibility performed in the same sample. We demonstrate their use by analyzing datasets obtained from mouse embryonic stem cells induced to differentiate toward mesoderm-like, myogenic, or neurogenic phenotypes. For complete details on the use and execution of this protocol, please refer to Khateb et al.(1) Elsevier 2023-05-15 /pmc/articles/PMC10199178/ /pubmed/37192048 http://dx.doi.org/10.1016/j.xpro.2023.102307 Text en 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
Ko, Kyung Dae
Jiang, Kan
Dell’Orso, Stefania
Sartorelli, Vittorio
Integrating single-cell transcriptomes, chromatin accessibility, and multiomics analysis of mesoderm-induced embryonic stem cells
title Integrating single-cell transcriptomes, chromatin accessibility, and multiomics analysis of mesoderm-induced embryonic stem cells
title_full Integrating single-cell transcriptomes, chromatin accessibility, and multiomics analysis of mesoderm-induced embryonic stem cells
title_fullStr Integrating single-cell transcriptomes, chromatin accessibility, and multiomics analysis of mesoderm-induced embryonic stem cells
title_full_unstemmed Integrating single-cell transcriptomes, chromatin accessibility, and multiomics analysis of mesoderm-induced embryonic stem cells
title_short Integrating single-cell transcriptomes, chromatin accessibility, and multiomics analysis of mesoderm-induced embryonic stem cells
title_sort integrating single-cell transcriptomes, chromatin accessibility, and multiomics analysis of mesoderm-induced embryonic stem cells
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10199178/
https://www.ncbi.nlm.nih.gov/pubmed/37192048
http://dx.doi.org/10.1016/j.xpro.2023.102307
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