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Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition

A novel technology called DisCo has been developed for processing low-input samples (less than 500 cells) in single-cell RNA sequencing (scRNA-seq). Traditional scRNA-seq methods are designed for larger cell inputs, making them inefficient and costly for small tissue samples. DisCo employs a deterministic mRNA-capture bead and cell co-encapsulation droplet system, utilizing machine vision and multilayer microfluidics to achieve precise particle and cell positioning, as well as droplet sorting control. This enables the continuous processing of low-input single-cell suspensions with high capture efficiency (>70%) and speeds of up to 350 cells per hour.

 

To showcase DisCo’s capabilities, researchers analyzed 31 individual intestinal organoids at various developmental stages, revealing extensive heterogeneity within organoids, including distinct subtypes like a regenerative fetal-like Ly6a+ stem cell population and an uncharacterized ‘gobloid’ subtype mainly composed of precursor and mature goblet cells. Additionally, DisCo demonstrated its ability to process low-input, in vivo-derived tissues by analyzing individual mouse intestinal crypts, uncovering crypts with a composition similar to spheroids, primarily containing regenerative stem cells. This highlights DisCo’s unique power in providing high-resolution insights into cellular heterogeneity in small tissue samples.

Keywords: Organoid