STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array

Area of Science:

• Neuroscience
• Genomics
• Biotechnology

Background:

• Single-cell RNA sequencing (scRNA-seq) is crucial for cell type discovery and understanding cellular diversity.
• Archived human brain samples present significant challenges for existing high-throughput scRNA-seq platforms.

Purpose of the Study:

• To introduce STRT-seq-2i, a new 9600-microwell array platform designed for high-throughput single-cell analysis.
• To demonstrate the platform's capability in analyzing challenging sample types, including frozen human brain nuclei.

Main Methods:

• Development of an addressable 9600-microwell array system (STRT-seq-2i).
• Integration of sampling methods (limiting dilution or FACS) with imaging capabilities.
• Application to fresh mouse cortical cells and frozen post-mortem human cortical nuclei.

Main Results:

• STRT-seq-2i achieves high throughput at a competitive cost.
• The platform demonstrates comparable performance to lower-throughput methods.
• Successful analysis of both fresh and frozen human brain samples was achieved.

Conclusions:

• STRT-seq-2i offers a flexible and efficient solution for single-cell RNA sequencing, particularly for challenging archived human brain samples.
• The platform's adaptability suggests potential for broader high-throughput biological applications.