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Spatial transcriptomics using multiplexed deterministic barcoding in tissue.
Nat. Commun. 14:1523 (2023)
Spatially resolved transcriptomics of tissue sections enables advances in fundamental and applied biomedical research. Here, we present Multiplexed Deterministic Barcoding in Tissue (xDBiT) to acquire spatially resolved transcriptomes of nine tissue sections in parallel. New microfluidic chips were developed to spatially encode mRNAs over a total tissue area of 1.17 cm2 with a 50 µm resolution. Optimization of the biochemical protocol increased read and gene counts per spot by one order of magnitude compared to previous reports. Furthermore, the introduction of alignment markers allowed seamless registration of images and spatial transcriptomic spots. Together with technological advances, we provide an open-source computational pipeline to prepare raw sequencing data for downstream analysis. The functionality of xDBiT was demonstrated by acquiring 16 spatially resolved transcriptomic datasets from five different murine organs, including the cerebellum, liver, kidney, spleen, and heart. Factor analysis and deconvolution of spatial transcriptomes allowed for in-depth characterization of the murine kidney.
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Publication type
Article: Journal article
Document type
Scientific Article
Language
english
Publication Year
2023
HGF-reported in Year
2023
ISSN (print) / ISBN
2041-1723
e-ISSN
2041-1723
Journal
Nature Communications
Quellenangaben
Volume: 14,
Issue: 1,
Article Number: 1523
Publisher
Nature Publishing Group
Publishing Place
London
Reviewing status
Peer reviewed
Institute(s)
Helmholtz Pioneer Campus (HPC)
POF-Topic(s)
30201 - Metabolic Health
30204 - Cell Programming and Repair
30202 - Environmental Health
30204 - Cell Programming and Repair
30202 - Environmental Health
Research field(s)
Pioneer Campus
PSP Element(s)
G-510002-001
G-510005-001
G-510007-001
G-510005-001
G-510007-001
PubMed ID
36934108
Erfassungsdatum
2023-10-06