High-Spatial-Resolution Multi-Omics Atlas Sequencing of Mouse Embryos via Deterministic Barcoding in Tissue
Cold Spring Harbor Laboratory, 2020
Online
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SUMMARYWe 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 ligationin situyielded 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 10μm 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.HighlightsDeterministic barcoding in tissue enables NGS-based spatial multi-omics mapping.DBiT-seq identified spatial patterning of major tissue types in mouse embryos.DBiT-seq revealed fine features such as retinal pigmented epithelium and microvascular endothelium at the cellular level.Direct integration with scRNA-seq data allows for rapid cell type identification.
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High-Spatial-Resolution Multi-Omics Atlas Sequencing of Mouse Embryos via Deterministic Barcoding in Tissue
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Autor/in / Beteiligte Person: | Tebaldi, Toma ; Zhang, Di ; Norris, Eileen ; Pan, Alisia ; Xiao, Yang ; Liu, Yang ; Guo, Cindy C. ; Deng, Yanxiang ; Fan, Rong ; Enninful, Archibald ; Kim, Dong-Joo ; Halene, Stephanie ; Yang, Mingyu ; Li, Jiatong ; Su, Graham ; Bai, Zhiliang |
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Veröffentlichung: | Cold Spring Harbor Laboratory, 2020 |
Medientyp: | unknown |
DOI: | 10.1101/2020.08.01.232496 |
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