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bioRxiv · 10.1101/2021.03.17.435795

Continuous Polony Gels for Tissue Mapping with High Resolution and RNA Capture Efficiency

Fu, X.·Sun, L.·Chen, J.·Dong, R.·Lin, Y.·Palmiter, R.·Lin, S.·Gu, L.
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Abstract

Current technologies for acquiring spatial transcript information from tissue sections rely on either RNA probes or spatial barcodes. The former methods require a priori knowledge for probeset formulation; the latter have yet to achieve single cell resolution and/or transcript capture efficiencies approaching dissociative, single-cell methods. Here, we describe a novel spatial transcriptome assay called polony (or DNA cluster)-indexed library-sequencing (PIXEL-seq). It improves upon other spatial barcoding methods by employing "continuous" polony oligos arrayed across a customized gel surface. In terms of assay performance, PIXEL-seq attains [≤] 1 {micro}m resolution and captures >1,000 unique molecular identifiers/10x10 {micro}m2. In other words, this global, naive platform achieves subcellular spatial transcriptome mapping while maintaining high transcript capture efficiencies.

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Fu, X., Sun, L., Chen, J., Dong, R., Lin, Y., Palmiter, R., Lin, S., Gu, L.. 2021-03-17. Continuous Polony Gels for Tissue Mapping with High Resolution and RNA Capture Efficiency. https://doi.org/10.1101/2021.03.17.435795

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