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Publication
Microscopic examination of spatial transcriptome using Seq-Scope.
Authors Cho CS, Xi J, Si Y, Park SR, Hsu JE, Kim M, Jun G, Kang HM, Lee JH
Submitted By Submitted Externally on 12/3/2021
Status Published
Journal Cell
Year 2021
Date Published 6/1/2021
Volume : Pages 184 : 3559 - 3572.e22
PubMed Reference 34115981
Abstract Spatial barcoding technologies have the potential to reveal histological details
of transcriptomic profiles; however, they are currently limited by their low
resolution. Here, we report Seq-Scope, a spatial barcoding technology with a
resolution comparable to an optical microscope. Seq-Scope is based on a
solid-phase amplification of randomly barcoded single-molecule oligonucleotides
using an Illumina sequencing platform. The resulting clusters annotated with
spatial coordinates are processed to expose RNA-capture moiety. These
RNA-capturing barcoded clusters define the pixels of Seq-Scope that are
~0.5-0.8 µm apart from each other. From tissue sections, Seq-Scope visualizes
spatial transcriptome heterogeneity at multiple histological scales, including
tissue zonation according to the portal-central (liver), crypt-surface (colon)
and inflammation-fibrosis (injured liver) axes, cellular components including
single-cell types and subtypes, and subcellular architectures of nucleus and
cytoplasm. Seq-Scope is quick, straightforward, precise, and easy-to-implement
and makes spatial single-cell analysis accessible to a wide group of biomedical
researchers.




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