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bioRxiv · 10.1101/788992

High-Spatial-Resolution Multi-Omics Atlas Sequencing of Mouse Embryos via Deterministic Barcoding in Tissue

Liu, Y.·Yang, M.·Deng, Y.·Su, G.·Guo, C. C.·Zhang, D.·Kim, D.·Bai, Z.·Xiao, Y.·Fan, R.
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Abstract

We present DBiT-seq -Deterministic Barcoding in Tissue for spatial omics sequencing - for co-mapping of mRNAs and proteins in a formaldehyde-fixed tissue slide via NGS sequencing. Parallel microfluidic channels were used to deliver DNA barcodes to the surface of a tissue slide and crossflow of two sets of barcodes A1-50 and B1-50 followed by ligation in situ yielded a 2D mosaic of tissue pixels, each containing a unique full barcode AB. Application to mouse embryos revealed major tissue types in early organogenesis as well as fine features like microvasculature in a brain and pigmented epithelium in an eye field. Gene expression profiles in 10m pixels conformed into the clusters of single-cell transcriptomes, allowing for rapid identification of cell types and spatial distributions. DBiT-seq can be adopted by researchers with no experience in microfluidics and may find applications in a range of fields including developmental biology, cancer biology, neuroscience, and clinical pathology. In BriefMicrofluidic deterministic barcoding of mRNAs and proteins in tissue slides followed by high-throughput sequencing enables the construction of a high-spatial-resolution multi-omics atlas at the genome scale. Application to mouse embryos (E10-12) identified major tissue types in early organogenesis and revealed fine tissue features such as retinal pigmented epithelium and endothelial microvasculature at the cellular level. HighlightsO_LIDeterministic barcoding in tissue enables NGS-based spatial multi-omics mapping. C_LIO_LIDBiT-seq identified spatial patterning of major tissue types in mouse embryos. C_LIO_LIDBiT-seq revealed fine features such as retinal pigmented epithelium and microvascular endothelium at the cellular level. C_LIO_LIDirect integration with scRNA-seq data allows for rapid cell type identification. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/788992v2_ufig1.gif" ALT="Figure 1"> View larger version (77K): org.highwire.dtl.DTLVardef@41d937org.highwire.dtl.DTLVardef@11bdc46org.highwire.dtl.DTLVardef@1aa143org.highwire.dtl.DTLVardef@51755c_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Liu, Y., Yang, M., Deng, Y., Su, G., Guo, C. C., Zhang, D., Kim, D., Bai, Z., Xiao, Y., Fan, R.. 2019-10-01. High-Spatial-Resolution Multi-Omics Atlas Sequencing of Mouse Embryos via Deterministic Barcoding in Tissue. https://doi.org/10.1101/788992

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