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

Nana Chen; Manik Vohra; Srinivas Vinod Saladi

doi:10.1016/j.xpro.2023.102233

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

STAR Protoc. 2023 Apr 17;4(2):102233. doi: 10.1016/j.xpro.2023.102233. Online ahead of print.

Authors

Nana Chen¹, Manik Vohra², Srinivas Vinod Saladi³

Affiliations

¹ Department of Otolaryngology, Head and Neck Surgery, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Head and Neck Lab, 20 Staniford Street 2W, Boston, MA 02114, USA. Electronic address: chennana1986@gmail.com.
² Department of Otolaryngology, Head and Neck Surgery, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Head and Neck Lab, 20 Staniford Street 2W, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
³ Department of Otolaryngology, Head and Neck Surgery, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Head and Neck Lab, 20 Staniford Street 2W, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address: srinivasvinod_saladi@meei.harvard.edu.

Abstract

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.

Keywords: Cancer; Genomics; Molecular Biology; Sequencing.