BART-Seq

BART-Seq performs targeted sequencing by assembling DNA barcodes onto invariant primer sets to enable highly sensitive, quantitative analysis of transcript cohorts or genomic regions across thousands of bulk samples or single cells.

Key Features:

• Multiplexing method: Generates extensive matrices of diverse DNA barcodes attached to invariant primer sets for large-scale sample indexing.
• Invariant primer sets: Uses primer sets that are pre-selected and optimized through in silico processes.
• High-throughput scalability: Capable of processing thousands of bulk samples or single cells in parallel.
• Quantitative sensitivity: Provides highly sensitive and quantitative measurements suitable for targeted assays.
• Dynamic range: Produces dynamic range measurements reported to surpass those of global transcriptomics techniques.
• Clinical variant detection: Has been applied for genetic screening, including identification of BRCA mutations in breast cancer patients.
• Demultiplexing pipeline: Demultiplexing implemented with Snakemake and supports parallel processing with customizable thread allocation.

Scientific Applications:

• Targeted transcriptomics and genomics: Analysis of transcript cohorts or specific genomic regions across thousands of samples.
• Single-cell developmental studies: Investigation of developmental states in single human pluripotent stem cells under different conditions or upon pathway activation such as Wnt/β-catenin.
• Clinical genetic screening: Targeted detection of clinically relevant mutations, exemplified by BRCA mutation identification in breast cancer patients.

Methodology:

In silico primer pre-selection and optimization, and a demultiplexing pipeline implemented with Snakemake supporting parallel processing and customizable thread allocation.