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

Area of Science:

• Molecular Biology
• Genomics
• Epigenetics

Background:

• DNA accessibility to regulatory elements influences gene expression.
• Open chromatin profiling methods like ATAC-seq offer insights into regulatory regions.
• Clinical implementation of ATAC-seq is hindered by sample requirements and optimization challenges.

Purpose of the Study:

• To optimize the ATAC-seq protocol for clinical sample applicability.
• To assess the feasibility of using fresh, flash-frozen, and cryopreserved breast cells and tissues.
• To ensure high-quality data generation from small cell numbers.

Main Methods:

• Varied nuclear preparation conditions and transposase concentrations.
• Implemented rigorous quality control measures.
• Tested the optimized protocol on fresh, flash-frozen, and cryopreserved breast cells and tissues.

Main Results:

• High-quality ATAC-seq data was obtained from a small number of cells.
• Genomic distribution of reads and enrichment at transcription start sites were comparable between fresh and cryopreserved samples.
• Transcription factor footprint analyses showed similarity between fresh and cryopreserved samples.

Conclusions:

• The optimized ATAC-seq protocol is suitable for clinical samples, including fine needle aspirates and biopsy tissues.
• This method facilitates chromatin accessibility analysis in patient samples, expanding translational research and personalized medicine.
• Clinically relevant epigenetic features can be identified using this approach.