Multiplexed and Ultralow-Input ChIP-seq Enabled by Tagmentation-Based Indexing and Facile Microfluidics.

Area of Science:

• Molecular Biology
• Genomics
• Biotechnology

Background:

• The epigenome regulates gene expression crucial for development and disease.
• Chromatin immunoprecipitation (ChIP) is vital for profiling genome-wide epigenetic modifications like histone marks.
• Existing ChIP methods face challenges with low cell input and high-throughput analysis.

Purpose of the Study:

• To introduce microfluidic ChIPmentation (mu-CM) for epigenome profiling of low cell numbers.
• To enable simultaneous processing and indexing of multiple samples for ChIP analysis.
• To facilitate cell-type-specific epigenomic studies using limited tissue samples.

Main Methods:

• Development of a microfluidic device for simultaneous processing of eight samples.
• Application of tagmentation-based ChIPmentation for sample indexing.
• Merging indexed samples for unified library preparation and sequencing.
• Demultiplexing sequencing reads to obtain individual sample histone modification profiles.

Main Results:

• Successfully profiled epigenomes from samples as low as 20 cells.
• Demonstrated the capability of mu-CM to handle multiple samples concurrently.
• Achieved accurate histone modification profiling for each individual sample post-demultiplexing.

Conclusions:

• Microfluidic ChIPmentation (mu-CM) is an effective technology for epigenome profiling with limited cell input.
• mu-CM is well-suited for cell-type-specific studies and analysis of low-abundance tissues.
• This approach enhances throughput and reduces the cell number requirement for ChIP-based epigenomic studies.