Paired-Tag Technology

What It Is

Flow diagram of Droplet Paired-Tag process

Paired-Tag is a single-cell multiomic library preparation method that simultaneously captures RNA expression and epigenetic marks—such as histone modifications, transcription factor (TF) binding, or chromatin remodelers. By combining these data streams in a single assay, Paired-Tag provides a comprehensive look at cellular regulation, enabling researchers to uncover critical insights into disease mechanisms, developmental processes, and more.

Who It’s For

Paired-Tag and 10X Multiome Data
  • Pre-Clinical Researchers (Academic & Industry): Explore gene regulation underlying disease progression, treatment resistance, or aging.
  • Core Facilities: A streamlined workflow compatible with standard single-cell platforms, perfect for research groups.
  • 10x Multiome Users: Easily integrate Paired-Tag into existing protocols with minimal modifications.

How It Works

Schematic workflow diagram of the Paired-Tag workflow
  1. Single-Cell Platform Integration: Paired-Tag works seamlessly with single-cell barcoding platforms like 10x Chromium®.
  2. Sample Prep & Assay: Use fresh or frozen tissue, cell lines, PBMCs, and organoids. Recommended starting material is 100,000 nuclei.
  3. Data Generation: Map RNA expression and epigenetic marks back to the same single cell with recovery rates matching platform specifications.
  4. Analysis & Interpretation: Fastq files can be analyzed with existing tools (e.g., CellRanger) and enhanced with our R workflows.

Why Paired-Tag?

IGV track of in-silico sorted cell types from PairedTag for H3K27ac and H3K27me3
  • Comprehensive Epigenetic Profiling: Directly measure histone states, TF binding, and chromatin remodeling.
  • Cell-Specific Insights: Identify rare cell populations without sorting, using RNA-based clustering.
  • Enhanced Discovery Power: Link gene expression to epigenetic signals for deeper insights.
  • Effortless Integration: Built for popular single-cell platforms like 10x Chromium®.

Performance & Throughput

Abstract illustration of different epigenetic states in single-cell research
  • Throughput: Match single-cell platform capacity (e.g., 10K–20K cells per run).
  • Data Depth: RNA coverage mirrors 10x Multiome outputs, with 3K–5K UMIs per cell for broad histone marks.
  • Sample Types: Fresh/frozen tissue, PBMCs, organoids, and cell lines.

Product & Service Options

Picture of Droplet Paired Tag reagent kit boxes
  • Paired-Tag Kits: Ready-to-use reagents for single-cell epigenetic profiling.
  • Full-Service Offerings: End-to-end sample processing and data analysis solutions.

Get Started

Ready to enhance your research with Paired-Tag? Contact us here to order kits or learn more about integrating this powerful technology into your workflows.