ArticleScientific reports2019
A microfluidic platform towards automated multiplexed in situ sequencing.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 34 citations in OpenAlex.
- Spatial profiling of gene editing by in situ sequencing in mice and macaques.Nature biomedical engineering · 2026Article
- Engineering next-generation microfluidic technologies for single-cell phenomics.Nature genetics · 2025Review
- Polymerase Chain Reaction Chips for Biomarker Discovery and Validation in Drug Development.Micromachines · 2025Review
- Thermal-plex: fluidic-free, rapid sequential multiplexed imaging with DNA-encoded thermal channels.Nature methods · 2024Article
- NIPMAP: niche-phenotype mapping of multiplex histology data by community ecology.Nature communications · 2023Article
- A multi-depth spiral milli fluidic device for whole mount zebrafish antibody staining.Biomedical microdevices · 2023Article
- Single-Cell Analysis in Immuno-Oncology.International journal of molecular sciences · 2023Review
- Spatiotemporal dissection of tumor microenvironment via in situ sensing and monitoring in tumor-on-a-chip.Biosensors & bioelectronics · 2023Article
- Mechanisms of breast cancer metastasis.Clinical & experimental metastasis · 2022Review
- Automated multimodal fluorescence microscopy for hyperplex spatial-proteomics: Coupling microfluidic-based immunofluorescence to high resolution, high sensitivity, three-dimensional analysis of histological slides.Frontiers in oncology · 2022Article
- Rolling Circle Amplification in Integrated Microsystems: An Uncut Gem toward Massively Multiplexed Pathogen Diagnostics and Genotyping.Accounts of chemical research · 2021Review
- Applicability of spatial transcriptional profiling to cancer research.Molecular cell · 2021Review
- Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy.Nature reviews. Clinical oncology · 2021Review
- Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets.Russian journal of bioorganic chemistry · 2021Article
- Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue.Nucleic acids research · 2020Article
- Automated identification of the mouse brain's spatial compartments from in situ sequencing data.BMC biology · 2020Article
- High-Resolution Transcriptomic and Proteomic Profiling of Heterogeneity of Brain-Derived Microglia in Multiple Sclerosis.Frontiers in molecular neuroscience · 2020Review
- Microfluidics-assisted multiplexed biomarker detection for in situ mapping of immune cells in tumor sections.Microsystems & nanoengineering · 2019Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Advancements in multiplexed in situ RNA profiling techniques have given unprecedented insight into spatial organization of tissues by enabling single-molecule quantification and sub-micron localization of dozens to thousands of RNA species simultaneously in cells and entire tissue sections. However, the lack of automation of the associated complex experimental procedures represents a potential hurdle towards their routine use in laboratories. Here, we demonstrate an approach towards automated generation and sequencing of barcoded mRNA amplicons in situ, directly in fixed cells. This is achieved through adaptation of a microfluidic tool compatible with standard microscope slides and cover glasses. The adapted tool combines a programmable reagent delivery system with temperature controller and flow cell to perform established in situ sequencing protocols, comprising hybridization and ligation of gene-specific padlock probes, rolling circle amplification of the probes yielding barcoded amplicons and identification of amplicons through barcode sequencing. By adapting assay parameters (e.g. enzyme concentration and temperature), we achieve a near-identical performance in identifying mouse beta-actin transcripts, in comparison with the conventional manual protocol. The technically adapted assay features i) higher detection efficiency, ii) shorter protocol time, iii) lower consumption of oligonucleotide reagents but slightly more enzyme. Such an automated microfluidic tissue processor for in situ sequencing studies would greatly enhance its research potentials especially for cancer diagnostics, thus paving way to rapid and effective therapies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.