Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain

Xiaonan Fu, Li Sun, Runze Dong, Jane Y. Chen, Runglawan Silakit, Logan F. Condon, Yiing Lin, Shin Lin, Richard D. Palmiter, Liangcai Gu

Research output: Contribution to journalArticlepeer-review

32 Scopus citations


Methods for acquiring spatially resolved omics data from complex tissues use barcoded DNA arrays of low- to sub-micrometer features to achieve single-cell resolution. However, fabricating such arrays (randomly assembled beads, DNA nanoballs, or clusters) requires sequencing barcodes in each array, limiting cost-effectiveness and throughput. Here, we describe a vastly scalable stamping method to fabricate polony gels, arrays of ∼1-micrometer clonal DNA clusters bearing unique barcodes. By enabling repeatable enzymatic replication of barcode-patterned gels, this method, compared with the sequencing-dependent array fabrication, reduced cost by at least 35-fold and time to approximately 7 h. The gel stamping was implemented with a simple robotic arm and off-the-shelf reagents. We leveraged the resolution and RNA capture efficiency of polony gels to develop Pixel-seq, a single-cell spatial transcriptomic assay, and applied it to map the mouse parabrachial nucleus and analyze changes in neuropathic pain-regulated transcriptomes and cell-cell communication after nerve ligation.

Original languageEnglish
Pages (from-to)4621-4633.e17
Issue number24
StatePublished - Nov 23 2022


  • DNA array
  • DNA stamping
  • Pixel-seq
  • chronic pain
  • microcontact printing
  • olfactory bulb
  • parabrachial nucleus
  • polony gel
  • polony sequencing
  • spatial transcriptomics


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