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Updated: Jun 29, 2025

ATAC-Seq Optimization for Cancer Epigenetics Research

ATAC-Seq Optimization for Cancer Epigenetics Research

Published on: June 30, 2022

scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing.

Xuan Zhang¹, Alexandre P Marand^1,2, Haidong Yan¹

¹Department of Genetics, University of Georgia, Athens, GA, USA.

|April 8, 2024

Summary

We developed scifi-ATAC-seq, a new method for single-cell ATAC sequencing. This technique significantly increases throughput, enabling genome-wide analysis of regulatory elements in many more cells and samples.

Keywords:

ATAC-seq Chromatin accessibility Combinatorial fluidic indexing Massive-scale Single-cell

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Last Updated: Jun 29, 2025

ATAC-Seq Optimization for Cancer Epigenetics Research

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Published on: June 30, 2022

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

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An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Single-cell ATAC sequencing (scATAC-seq) is crucial for identifying cis-regulatory elements at single-cell resolution.
Existing scATAC-seq methods face limitations in throughput and cost, hindering large-scale studies.

Purpose of the Study:

To introduce scifi-ATAC-seq, a novel, high-throughput single-cell ATAC sequencing technique.
To overcome the throughput and cost limitations of current scATAC-seq methods.

Main Methods:

scifi-ATAC-seq combines combinatorial fluidic indexing with droplet-based single-cell ATAC sequencing.
A barcoded Tn5 pre-indexing step is integrated with the 10X Genomics platform.

Main Results:

scifi-ATAC-seq enables indexing of up to 200,000 nuclei in a single reaction.
This represents an approximately 20-fold increase in throughput compared to standard 10X Genomics workflows.

Conclusions:

scifi-ATAC-seq substantially enhances the scalability of single-cell ATAC sequencing.
This advancement facilitates comprehensive genome-wide analysis of regulatory elements across numerous cells and samples.