BenchDrop-seq: a microfluidics-free platform for benchtop single-cell long-read RNA sequencing

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Single-cell long-read RNA sequencing (scLong-RNA-seq) provides direct measurement of full-length transcripts.
• Current scLong-RNA-seq methods face challenges in scalability due to microfluidics, specialized equipment, and high costs.

Purpose of the Study:

• To develop a practical and accessible benchtop platform for scLong-RNA-seq.
• To enable high-throughput, isoform-resolved transcriptomic measurements from individual cells.

Main Methods:

• BenchDrop-seq utilizes particle-templated partitioning for single-cell barcoding.
• The platform integrates with Oxford Nanopore sequencing for full-length transcript capture.
• An open-source analysis pipeline facilitates barcode recovery, alignment, and quantification.

Main Results:

• BenchDrop-seq demonstrates high barcode recovery and accurate gene quantification.
• The platform successfully identifies cell-type-specific transcript usage in heterogeneous tissues.
• Isoform-resolved measurements are achieved from thousands of cells using standard lab equipment.

Conclusions:

• BenchDrop-seq establishes a practical framework for scLong-RNA-seq, reducing experimental barriers.
• The platform enables routine single-cell experiments with transcript-level analysis capabilities.
• This advancement makes advanced transcriptomic analyses more accessible to researchers.