10x Single-cell ATAC Service – scATAC-seq | Verygenome

10x Single-Cell ATAC-Seq

10x single-cell ATAC sequencing (Assay for Transposase-Accessible Chromatin using sequencing) is an epigenetics technology on the 10x Genomics microfluidics and Tn5 transposase platform that profiles chromatin accessibility at single-cell resolution, locating open regions (promoters, enhancers) to reveal epigenetic gene-regulation mechanisms. Chromatin accessibility determines transcription-factor–DNA binding efficiency. Unlike bulk ATAC, it captures subpopulation- and even cell-level accessibility differences while linking cell type and phenotype—applied in development, oncology, neuroscience, and immunology.

Principle Introduction

Based on 'transposase-mediated fragmentation–single-cell barcoding–sequencing': Tn5 binds open chromatin, cuts fragments, and inserts adapters. Single cells, barcode beads, and Tn5 are encapsulated; fragmentation and adapter tagging occur in-droplet. After amplification and library prep, cell barcodes assign reads to single cells; genome alignment and peak calling locate open regions, with motif analysis and annotation linking accessibility to regulatory networks.

Literature

Published in Nature Communications, 'Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines' used 10x single-cell ATAC with transcriptomics to resolve heterogeneity within cancer cell lines. Multiple lines showed multiple epigenetic subpopulations with distinct open-chromatin regions linked to expression heterogeneity; accessibility differences concentrated in proliferation- and drug-resistance-related regulatory regions, with some subpopulations intrinsically resistant.

Sample Requirements

Single-cell suspension

1×10⁵–1×10⁶ cells/mL, ≥1 mL, serum-free + 0.04% BSA, 4°C; viability ≥85%, no EDTA buffer.

Fresh tissue

≥0.1 g, preservation buffer, 4°C (no freezing), 24 h.

Cell line

≥1×10⁶ cells, 4°C; note line, culture, treatment.

Frozen cells

pellet ≥5×10⁶, EDTA-free freezing medium, liquid N2, dry ice; viability ≥80%.

Embryo / organoid

intact embryo or organoid ≥0.05 g, 4°C, 12 h; note stage, culture.

Deliverables

Sample QC

viability, purity, chromatin integrity, library fragment size, sequencing pre-QC.

Raw data

Fastq, QC (Q30, GC, duplication), barcode stats, peak calling.

Analysis

clustering, subpopulation open-region annotation, differential accessibility volcano, TF motif enrichment, regulatory network.

FAQ

What are the possible reasons and improvement strategies for generating few peaks in single‑cell ATAC‑seq experiments?

Causes: Low viability, poor transposase efficiency, impurities. Improve via low temp, optimize Tn5, density‑gradient cleanup.

How to address the issue of no detectable subpopulation differences from ATAC‑seq data?

Increase depth, enrich targets, tune peak/clustering params, use known markers.

How to realize data linkage between ATAC‑seq and transcriptome at single‑cell level?

10x multiomics shares cell barcode; map open regions to expression, build epigenetic–transcription network.

Single-Cell Omics