Matrix-seq: An adjustable-resolution spatial transcriptomics via microfluidic matrix-based barcoding [article]

Haifeng Zhao, Geng Tian, Aihua Hu
2022 bioRxiv   pre-print
Spatial transcriptomics technology complements the spatial information lost in single-cell RNA sequencing, which enables visualization and quantitative analysis of transcriptomics of cells in tissue sections. Although this technology is a promising tool to study complex biological processes, its popularization is limited by cumbersome barcoding steps. We presented a microfluidics-based barcoding strategy called Matrix-seq, which gets rid of both precision instruments and the in situ indexing.
more » ... e deterministic barcoding matrix is fabricated by the crossflow of Barcode-X and Barcode-Y. The overlapping areas (spot) formed deterministic barcoding primers (Barcode-X-Y) via the ligation reaction. Matrices with different spot size (ranging from 10 to 50 μm), which was decided by the width of microchannels, were fabricated and then applied to a mouse main olfactory bulb section and a mouse brain section. While maintaining high performance and resolution, this technology greatly reduces the technical threshold and cost of spatial barcoding. As a result, Matrix-seq can be rapidly applied in various fields including developmental biology, neuroscience and clinical pathology.
doi:10.1101/2022.08.05.502952 fatcat:7kqnirxfencmtdajznxxeipk5y