ATAC-seq Assay with Low Mitochondrial DNA Contamination from Primary Human CD4+ T Lymphocytes

Overview

This article presents a modified protocol for performing ATAC-seq on activated CD4+ human lymphocytes. The new lysis buffer significantly reduces mitochondrial DNA contamination, enhancing the efficiency of the assay.

Key Study Components

Area of Science

• Neuroscience
• Cell Biology
• Genomics

Background

• ATAC-seq is a technique used to study chromatin accessibility.
• Mitochondrial DNA contamination can skew sequencing results.
• Activated CD4+ T cells are crucial for immune response studies.
• Minimizing sample loss is essential for high-quality ATAC-seq results.

Purpose of Study

• To present a refined ATAC-seq protocol for human lymphocytes.
• To reduce mitochondrial contamination in sequencing data.
• To validate the protocol across various cell types.

Methods Used

• Introduction of a new lysis buffer to minimize contamination.
• Validation of the protocol in human primary PBMCs and monocytes.
• Application of the method to mouse dendritic cells and melanoma cell lines.
• Demonstration of handling small cell numbers from precious samples.

Main Results

• Mitochondrial DNA reads were reduced from 50% to less than 3%.
• The protocol allows for a 50% decrease in sequencing costs.
• Validated effectiveness across multiple cell types.
• Demonstrated handling of small cell samples with basic equipment.

Conclusions

• The modified ATAC-seq protocol enhances data quality.
• It is applicable to a wide range of cell types.
• This approach can facilitate more efficient chromatin accessibility studies.

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