Genetics / Genomics JoVE (Open Access) Citable · DOI

Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells

Name: Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells
Uploaded: 2026-06-21
Duration: 8 min 34 s
Description: Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) is a technique of choice for studying protein-DNA interactions. ChIP-seq ...

DOI: 10.3791/52150-v

What you'll learn

✓ Automate chromatin immunoprecipitation (ChIP) using robotic liquid handling systems
✓ Generate epigenetic profiles from as few as 10,000 cells
✓ Reduce labor, cost, and time in ChIP-seq library preparation
✓ Map in vivo protein-DNA interactions at scale

Protocol

Methods for mapping in vivo protein-DNA interactions are becoming crucial for every aspect of genomic research but they are laborious, costly, and time consuming. Here a commercially available robotic liquid handling system that automates chromatin immunoprecipitation for mapping in vivo protein-DNA interactions with limited amounts of cells is presented.

Difficulty

advanced

Total time

~2–3 days per batch (automation reduces hands-on time to ~4–6 hours)

Model organism

HeLa cells

Biosafety

BSL-1

Steps

Set up robotic chromatin immunoprecipitation workflow

Configure the commercially available liquid handling system for automated ChIP assay. Load samples, reagents, and consumables according to protocol specifications.

▶ 01:40

Execute automated library preparation for sequencing

Run the robotic system through chromatin fragmentation, immunoprecipitation, DNA extraction, and library construction steps with minimal manual intervention.

▶ 05:48

Analyze generated epigenetic profiles from low cell numbers

Evaluate ChIP-seq results demonstrating successful epigenetic mapping from 10,000 HeLa cells and assess data quality and consistency.

▶ 07:38

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