Microscopic examination of spatial transcriptome using Seq-Scope.

Cell
Chun-Seok ChoJun Hee Lee

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.

References

Aug 1, 1992·Liver·F CalleaF Bonino
Nov 1, 1989·The American Journal of Surgical Pathology·D S Levine, R C Haggitt
Apr 12, 2005·Biophysical Journal·Jean-François Mercier, Gary W Slater
Jan 11, 2007·Journal of Microscopy·S Bolte, F P Cordelières
Nov 7, 2008·Nature·David R BentleyAnthony J Smith
Jun 22, 2010·Journal of Hepatology·Cornelia S ViebahnGeorge C T Yeoh
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Dec 6, 2014·American Journal of Physiology. Gastrointestinal and Liver Physiology·Laurent DolléLeo A van Grunsven
Dec 30, 2015·Cell Reports·Keren Bahar HalpernShalev Itzkovitz
Jul 28, 2016·Mucosal Immunology·J Spencer, L M Sollid
Sep 3, 2017·Biotechnology Journal·Audra J Storm, Paul A Jensen
Nov 17, 2017·Nature·Adam L HaberAviv Regev
Feb 10, 2018·Methods in Molecular Biology·Rupesh Kanchi RaviMahdieh Khosroheidari
Aug 10, 2018·Nature·Gioele La MannoPeter V Kharchenko
Dec 12, 2018·Nature Biotechnology·Etienne BechtEvan W Newell
Apr 3, 2019·Nature Reviews. Gastroenterology & Hepatology·Shani Ben-Moshe, Shalev Itzkovitz
Sep 11, 2019·Nature Methods·Sanja VickovicPatrik L Ståhl
Feb 13, 2020·Frontiers in Immunology·Lang DouYifang Gao
Mar 20, 2020·Sub-cellular Biochemistry·George H Sack
Apr 4, 2020·Nature Reviews. Gastroenterology & Hepatology·Romain DonneChantal Desdouets
May 5, 2020·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Michaela AspJoakim Lundeberg
Jul 16, 2020·BMC Genomics·Joseph BergenstråhleJoakim Lundeberg
Sep 12, 2020·Microscopy Research and Technique·Maria MazzariniAnna Rita Migliaccio
Oct 27, 2020·American Journal of Physiology. Endocrinology and Metabolism·Sung Rye ParkJun Hee Lee
Dec 9, 2020·Nature Biotechnology·Robert R StickelsFei Chen
Jan 8, 2021·Nature Methods·Vivien Marx

❮ Previous
Next ❯

Citations

Jul 25, 2021·International Journal of Molecular Sciences·Charles Gwellem AnchangAndreas Ramming
Aug 13, 2021·Nature·Anjali RaoItai Yanai
Oct 3, 2021·Genome Research·Ruben DriesGuo-Cheng Yuan
Oct 16, 2021·BJOG : an International Journal of Obstetrics and Gynaecology·E R Barrozo, K M Aagaard

❮ Previous
Next ❯

Related Concepts

Related Feeds

Cell eTOC

Cell is a scientific journal publishing research across a broad range of disciplines within the life sciences field. Discover the latest research from Cell here.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Related Papers

BioRxiv : the Preprint Server for Biology
Franziska Frederike Annalena HildebrandtJ. Ankarklev
BioRxiv : the Preprint Server for Biology
Sanja VickovicPatrik L Staahl
International Journal of Biological Sciences
Ying ZhouQinyu Ge
BioRxiv : the Preprint Server for Biology
Y. DengRong Fan
© 2021 Meta ULC. All rights reserved