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Related Concept Videos

RNA-seq03:21

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Related Experiment Video

Updated: Nov 2, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

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Microscopic examination of spatial transcriptome using Seq-Scope.

Chun-Seok Cho1, Jingyue Xi2, Yichen Si2

  • 1Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

Cell
|June 11, 2021
PubMed
Summary
This summary is machine-generated.

Seq-Scope is a new spatial barcoding technology that achieves optical microscope resolution for transcriptomic profiling. This breakthrough enables detailed visualization of spatial transcriptome heterogeneity in tissues at single-cell and subcellular levels.

Keywords:
RNA captureSpatial transcriptomicscolonhigh resolutionhistologylivermolecular barcodingscRNA-seqspatial single cell analysissubcellular analysis

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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Current spatial barcoding technologies offer limited resolution, hindering detailed histological analysis of transcriptomic profiles.
  • High-resolution spatial transcriptomics is crucial for understanding tissue architecture and cellular heterogeneity.

Purpose of the Study:

  • To introduce Seq-Scope, a novel spatial barcoding technology with resolution comparable to optical microscopy.
  • To demonstrate Seq-Scope's capability in visualizing spatial transcriptome heterogeneity at various scales.

Main Methods:

  • Seq-Scope utilizes solid-phase amplification of randomly barcoded single-molecule oligonucleotides on an Illumina sequencing platform.
  • Spatial coordinates are assigned to barcoded clusters, which are then processed to expose RNA-capture moieties.
  • This creates pixels of approximately 0.5–0.8 μm, defining the technology's high resolution.

Main Results:

  • Seq-Scope visualizes spatial transcriptome heterogeneity across multiple histological scales, including tissue zonation (e.g., liver, colon) and inflammation-fibrosis axes.
  • The technology resolves cellular components, including single-cell types and subtypes, and subcellular architectures like the nucleus and cytoplasm.
  • Demonstrated high-resolution mapping of RNA distribution within tissue sections.

Conclusions:

  • Seq-Scope significantly advances spatial transcriptomic analysis by providing unprecedented resolution.
  • The technology is quick, straightforward, precise, and accessible, facilitating spatial single-cell analysis for biomedical researchers.
  • Enables detailed investigation of tissue organization and cellular interactions at a fine scale.