Home›Genetics / Genomics›Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells
Genetics / GenomicsJoVE (Open Access)Citable · DOI
Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells
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
1
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
2
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
3
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.