Spatial omics

Pixel-seq

In situ reading “omic” states of single cells in morphologically intact tissues is highly desirable for discovering physiological, pathological, and pharmacological changes. Pixel-seq uses polony gels, arrays of ~1-micrometer clonal DNA clusters bearing unique barcodes, to spatially capture and sequence RNAs, proteins (via DNA tagged affinity reagents), or other molecules in tissues.

We use high-density polony gels showing a continuous DNA distribution with minimal feature-to-feature gaps, which is distinct from those amplified in Illumina nonpatterned flowcells showing a discrete, peak-shape distribution. For spatial transcriptomic mapping, the continuous, even distribution of poly(T) probes can minimize variations in RNA capture efficiency across the array.

Although polonies are connected, they often do not interpenetrate due to a "polony exclusion" effect, similar to the formation a clear boundary between competing glass species (photo taken in Seattle Magnuson Park):

After barcoded transcripts (cDNAs) are sequenced and then mapped back to the barcode map, they are spatially aggregated into cell masks to obtain single-cell data for clustering and other downstream analyses:

Pixel-seq protocol link.