• Protocol for single-cell spati...

Treffer: Protocol for single-cell spatial transcriptomic profiling of cultured cells and engineered tissues without embedding or sectioning.

Title:
Protocol for single-cell spatial transcriptomic profiling of cultured cells and engineered tissues without embedding or sectioning.
Authors:
Helms HR; Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, OR 97201, USA; Knight Cancer Precision Biofabrication Hub, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA., Bertassoni LE; Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, OR 97201, USA; Knight Cancer Precision Biofabrication Hub, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; Division of Oncological Sciences, School of Medicine, Oregon Health and Science University, Portland, OR 97201, USA; Division of Biomaterials and Integrative Biosciences, School of Dentistry, Oregon Health and Science University, Portland, OR 97201, USA. Electronic address: bertasso@ohsu.edu.
Source:
STAR protocols [STAR Protoc] 2025 Sep 19; Vol. 6 (3), pp. 104074. Date of Electronic Publication: 2025 Sep 11.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Cell Press Country of Publication: United States NLM ID: 101769501 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2666-1667 (Electronic) Linking ISSN: 26661667 NLM ISO Abbreviation: STAR Protoc Subsets: MEDLINE
Imprint Name(s):
Original Publication: [Cambridge, MA] : Cell Press, [2020]-
MeSH Terms:
Gene Expression Profiling*/methods , Single-Cell Analysis*/methods , Tissue Engineering*/methods , Transcriptome*/genetics, Humans ; Cells, Cultured ; Animals ; Cell Culture Techniques/methods
References:
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Science. 2014 Jan 3;343(6166):84-87. (PMID: 24336571)
Dev Cell. 2021 Jan 25;56(2):180-191. (PMID: 33453155)
Nat Methods. 2022 Feb;19(2):171-178. (PMID: 35102346)
Nat Rev Methods Primers. 2022 Dec 15;2:98. (PMID: 37461429)
Cell Chem Biol. 2021 Mar 18;28(3):338-355. (PMID: 33740435)
Artif Organs. 2022 Jul;46(7):E211-E243. (PMID: 35349178)
Nat Rev Mol Cell Biol. 2025 Jan;26(1):11-31. (PMID: 39169166)
Nat Biotechnol. 2024 Feb;42(2):293-304. (PMID: 37231261)
J Biol Chem. 2024 Oct;300(10):107637. (PMID: 39122004)
Contributed Indexing:
Keywords: Biotechnology and bioengineering; Cancer; Cell Biology; Cell culture; Cell-based Assays; Gene Expression; Genomics; Microscopy; Sequence analysis; Sequencing; Single Cell; Tissue Engineering
Entry Date(s):
Date Created: 20250912 Date Completed: 20250923 Latest Revision: 20251007
Update Code:
20251007
PubMed Central ID:
PMC12491524
DOI:
10.1016/j.xpro.2025.104074
PMID:
40938748
Database:
MEDLINE

Weitere Informationen

Spatial transcriptomics is a powerful tool for investigating how cellular composition and spatial relationships influence cell behavior. Here, we present a protocol for spatial transcriptomic profiling of 2D engineered tissues and cell cultures that are not compatible with standard embedding and sectioning. We detail steps for sample generation, fixation, and staining to integrate with Visium HD spatial technology. This protocol provides a flexible solution for sample generation for spatial transcriptomic analysis.
(Copyright © 2025 The Authors. Published by Elsevier Inc. All rights reserved.)

Declaration of interests The authors declare no competing interests.