txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility

Area of Science:

• Genomics
• Molecular Biology
• Epigenetics

Background:

• Single-cell ATAC-seq (scATAC-seq) is crucial for understanding cell-type-specific gene regulation.
• Existing methods face limitations in scalability and throughput.
• Accurate interpretation of scATAC-seq data is essential for biological discovery.

Purpose of the Study:

• To develop a high-throughput, large-scale single-cell ATAC-seq method.
• To profile a diverse range of human and mouse tissues at single-nucleus resolution.
• To identify and characterize technical artifacts in commonly used mouse models.

Main Methods:

• Integration of Tn5 transposase-based pre-indexing with 10× Genomics single-cell barcoding.
• Processing and profiling of up to 200,000 nuclei per reaction across multiple samples.
• Application of the method to diverse tissues including human cortex, mouse brain, and lung, as well as a CC16 knockout model.

Main Results:

• Successfully profiled 449,953 nuclei from various tissues.
• Identified significant, previously underappreciated technical artifacts in the CC16 knockout mouse model.
• Demonstrated that these artifacts, stemming from 129 mouse strain genetic material, cause cell-type-specific alterations in regulatory elements, confounding study interpretations.

Conclusions:

• The developed method enables unprecedented scale for single-cell ATAC-seq.
• Technical artifacts in mouse models can profoundly impact epigenetic interpretations.
• Careful consideration of genetic background is critical for accurate analysis of epigenomic data.