High Quality ATAC-Seq Data Recovered from Cryopreserved Breast Cell Lines and Tissue.

ABSTRACT: DNA accessibility to transcription regulators varies between cells and modulates gene expression patterns. Several "open" chromatin profiling methods that provide valuable insight into the activity of these regulatory regions have been developed. However, their application to clinical samples has been limited despite the discovery that the Analysis of Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) method can be performed using fewer cells than other techniques. Obtaining fresh rather than stored samples and a lack of adequate optimization and quality controls are major barriers to ATAC's clinical implementation. Here, we describe an optimized ATAC protocol in which we varied nuclear preparation conditions and transposase concentrations and applied rigorous quality contr

SUBMITTER: Fujiwara S 

PROVIDER: S-EPMC6345852 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature