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Updated: Jul 15, 2025

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

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.

Biorxiv : the Preprint Server for Biology

|October 3, 2023

Summary

This summary is machine-generated.

Single-cell combinatorial fluidic indexing ATAC-sequencing (scifi-ATAC-seq) significantly increases throughput for analyzing regulatory elements. This novel method enables high-resolution genomic studies at a lower cost.

Keywords:

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

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

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Published on: November 13, 2017

Area of Science:

Genomics
Epigenetics
Single-cell analysis

Background:

Single-cell ATAC-seq is crucial for identifying regulatory elements genome-wide with cell-type resolution.
Existing single-cell ATAC-seq methods face limitations in throughput and cost.

Approach:

We developed single-cell combinatorial fluidic indexing ATAC-sequencing (scifi-ATAC-seq).
This technique integrates barcoded Tn5 pre-indexing with droplet-based single-cell ATAC-seq on the 10X Genomics platform.
scifi-ATAC-seq allows indexing of up to 200,000 nuclei from multiple samples in one reaction.

Key Points:

Achieves a ~20-fold increase in throughput compared to standard 10X Genomics workflows.
Facilitates large-scale genomic and epigenomic studies at single-cell resolution.
Maintains high cell-type resolution for regulatory element identification.

Conclusions:

scifi-ATAC-seq overcomes throughput limitations of current single-cell ATAC-seq methods.
Enables more comprehensive and cost-effective analysis of cis-regulatory elements.
Advances the field of single-cell epigenomics and regulatory genomics.