How does SeekSpace achieve spatial localization?

Answer:
SeekSpace performs spatial localization through the integrated analysis of spatial barcodes and single-nucleus transcriptomics.

During the experiment, spatial barcodes on the chip surface are enzymatically released into local tissue regions. To associate these barcodes with individual nuclei, the workflow incorporates a non-ionic surfactant that partially permeabilizes the cell membrane by disrupting the lipid bilayer while largely preserving nuclear membrane integrity. This controlled permeabilization allows spatial barcodes to pass through the cell membrane and enter nuclei via nuclear pores.

Following barcode entry, a fixation step immobilizes the spatial barcodes within the nuclei.

Each nucleus typically accumulates a characteristic combination of spatial barcodes. During library preparation, these spatial barcodes are captured together with nuclear RNA molecules in the same single-nucleus transcriptomic workflow.

During downstream analysis, spatial positions are reconstructed by integrating spatial barcode enrichment patterns, barcode abundance distributions, single-nucleus transcriptomic clustering and histological image information.