Protocol for Bulk-ATAC sequencing in head and neck squamous cell carcinoma

The transposase-accessible chromatin using sequencing (ATAC-seq) offers a simplified approach to detect chromatin changes in cancer cells after genetic intervention and drug treatment. Here, we present an optimized ATAC-seq protocol to elucidate chromatin accessibility changes at the epigenetic leve...

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Detalles Bibliográficos
Autores principales: Chen, Nana, Vohra, Manik, Saladi, Srinivas Vinod
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10323015/
https://www.ncbi.nlm.nih.gov/pubmed/37071527
http://dx.doi.org/10.1016/j.xpro.2023.102233
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author Chen, Nana
Vohra, Manik
Saladi, Srinivas Vinod
author_facet Chen, Nana
Vohra, Manik
Saladi, Srinivas Vinod
author_sort Chen, Nana
collection PubMed
description The transposase-accessible chromatin using sequencing (ATAC-seq) offers a simplified approach to detect chromatin changes in cancer cells after genetic intervention and drug treatment. Here, we present an optimized ATAC-seq protocol to elucidate chromatin accessibility changes at the epigenetic level in head and neck squamous cell carcinoma cells. We describe steps for cell lysate preparation, transposition, and tagmentation, followed by library amplification and purification. We then detail next-generation sequencing and data analysis. For complete details on the use and execution of this protocol, please refer to Buenrostro et al.,(1) Chen et al.,(2)
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spelling pubmed-103230152023-07-07 Protocol for Bulk-ATAC sequencing in head and neck squamous cell carcinoma Chen, Nana Vohra, Manik Saladi, Srinivas Vinod STAR Protoc Protocol The transposase-accessible chromatin using sequencing (ATAC-seq) offers a simplified approach to detect chromatin changes in cancer cells after genetic intervention and drug treatment. Here, we present an optimized ATAC-seq protocol to elucidate chromatin accessibility changes at the epigenetic level in head and neck squamous cell carcinoma cells. We describe steps for cell lysate preparation, transposition, and tagmentation, followed by library amplification and purification. We then detail next-generation sequencing and data analysis. For complete details on the use and execution of this protocol, please refer to Buenrostro et al.,(1) Chen et al.,(2) Elsevier 2023-04-17 /pmc/articles/PMC10323015/ /pubmed/37071527 http://dx.doi.org/10.1016/j.xpro.2023.102233 Text en © 2023 The Author(s) 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
Chen, Nana
Vohra, Manik
Saladi, Srinivas Vinod
Protocol for Bulk-ATAC sequencing in head and neck squamous cell carcinoma
title Protocol for Bulk-ATAC sequencing in head and neck squamous cell carcinoma
title_full Protocol for Bulk-ATAC sequencing in head and neck squamous cell carcinoma
title_fullStr Protocol for Bulk-ATAC sequencing in head and neck squamous cell carcinoma
title_full_unstemmed Protocol for Bulk-ATAC sequencing in head and neck squamous cell carcinoma
title_short Protocol for Bulk-ATAC sequencing in head and neck squamous cell carcinoma
title_sort protocol for bulk-atac sequencing in head and neck squamous cell carcinoma
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10323015/
https://www.ncbi.nlm.nih.gov/pubmed/37071527
http://dx.doi.org/10.1016/j.xpro.2023.102233
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