Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain
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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.
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High-resolution methods Seq-Scope, Stereo-seq and PIXEL-seq provide submicrometer resolution and highly efficient transcriptome-capture efficiency up to ~23 unique transcripts per μm2.
“Recently, several ultra-high-resolution technologies such as Seq-Scope61, Stereo-seq62 and polony-indexed library sequencing (PIXEL-seq)63 have been developed, which could prove ideal for identification and characterization of senescent cells and their interactions with the environment. In addition to providing submicrometer resolution, which is comparable to that of optical microscopy, these meth”
From Spatial mapping of cellular senescence: emerging challenges and opportunities (2023) · cites this paper as [63]
The Introduction identifies this paper as the report of Pixel-seq and describes high-resolution tissue mapping with efficient RNA capture; the mouse olfactory-bulb Results likewise report high capture efficiency. But the Results describe Pixel-seq’s assay feature resolution as 1 μm, while the submicrometer figure refers to gel-to-gel replication. Our copy does not report ~23 unique transcripts per μm² or establish that figure for all three named methods; pages are not provided in the indexed copy. (LLM, conf=0.86)
Experimental — accuracy not yet measuredPIXEL-seq uses DNA arrays called 'polony gels' that capture tissue RNA from a single-cell layer touching the gel, improving single-cell resolution.
“Furthermore, PIXEL-seq uses DNA arrays called ‘polony gels’, which capture tissue RNA from a single-cell layer touching the gel, similar to confocal microscopy, and restrain template diffusion, thus improving single-cell resolution63.”
From Spatial mapping of cellular senescence: emerging challenges and opportunities (2023) · cites this paper as [63]
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Mapping Cell Atlases at the Single‐Cell Level
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Decoding Human Biology and Disease Using Single-Cell Omics Technologies
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- Authors
- Fu, X., Sun, L., Dong, R., Chen, J. Y., Silakit, R., Condon, L. F., Lin, Y., Lin, S., Palmiter, R. D., & Gu, L.
- Affiliations
- University of Washington (US)
- Howard Hughes Medical Institute (US)
- Washington University in St. Louis (US)
- Corresponding author
- Gu, Liangcai
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2022-11
- Volume
- 185
- Issue
- 24
- Pages
- 4621-4633.e17
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC9691594
- OpenAlex
- W4308834910
- Cited by
- 161
- References
- 58
- Citations by year
- 2026: 42 · 2025: 43 · 2024: 46 · 2023: 29 · 2022: 1
- FWCI
- 9.72
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 387 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of Mental Health (R41MH130299)
- National Institute on Drug Abuse (R21DA051194, R21DA051555, R01DA024908)
- National Cancer Institute (UG3CA268096)
- National Institute of General Medical Sciences (R35GM128918)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Keywords
- spatial transcriptomics, single-cell spatial transcriptomics, chronic pain, neuropathic pain, parabrachial nucleus, nerve ligation, intercellular communication
- MeSH terms
- Animals, DNA, Gels, RNA, Mice, Chronic Pain, Transcriptome
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