sci-L3Pipe

sci-L3Pipe enables high-throughput single-cell combinatorial indexing with linear amplification for sequencing diverse modalities including genome conformation capture and joint RNA/chromatin accessibility profiling.

Key Features:

• Three-level barcoding: Incorporates three-level combinatorial indexing for single-cell identification.
• Linear amplification: Addresses limitations of uniformity in single-cell genome amplification compared to exponential amplification methods.
• Modality extension: Adapts to new applications including template strand sequencing (sci-L3-Strand-seq), genome conformation capture (sci-L3-Hi-C), and joint profiling of RNA and chromatin accessibility (sci-L3-RNA/ATAC) with single-step protocol modifications.
• Multi-omics compatibility: Anticipated compatibility with DNA methylation (sci-MET) and chromatin-associated factors (CUT&Tag) profiling.

Scientific Applications:

• Sister chromatid exchange detection: Detects sister chromatid exchanges at single-cell resolution through sci-L3-Strand-seq.
• Genome compartmentalization analysis: Identifies genome compartmentalization patterns in thousands of single cells via sci-L3-Hi-C.
• Cell state characterization: Reveals cell state-specific features through joint RNA and chromatin accessibility profiling.

Methodology:

The pipeline builds upon the sci-L3 method with linear amplification and three-level barcoding, extending to new modalities with minimal single-step modifications to the original protocol.