Well-ST-seq: cost-effective and cellular level spatial transcriptomics with high RNA capture efficiency

Here, we developed spatially cellular-level RNA-capture probe arrays using miniaturized microfluidic and microarray technologies. By leveraging the predetermined and cost-effective probe fixation characteristics of this methodology, we significantly reduced the consumable cost of the probe array to $0.31/mm2 and fabrication time to approximately 2 hours. Furthermore, the fabrication process does not rely on large precision instruments. Notably, the efficiency of the transcript captured by the probe array is even comparable to conventional single-cell RNA sequencing. Based on this technology, we successfully mapped the transcriptome atlas and gained insights into spatial cell heterogeneity of the mouse hippocampus.