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Related Concept Videos

In-situ Hybridization02:31

In-situ Hybridization

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In situ hybridization (ISH) is a technique used to detect and localize specific DNA or RNA molecules in cells, tissue, or tissue sections using a labeled probe. The technique was first used in 1969 for the investigation of nucleic acids. It is currently an essential tool in scientific research and clinical settings, especially for diagnostic purposes.
Types of probes and labels
A probe is a complementary strand of DNA or RNA that binds to corresponding nucleotide sequences in a cell. Many...
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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: Aug 9, 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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Improved in situ sequencing for high-resolution targeted spatial transcriptomic analysis in tissue sections.

Xinbin Tang1, Jiayu Chen1, Xinya Zhang1

  • 1School of Medicine and School of Biomedical Sciences, Huaqiao University, Quanzhou, Fujian 362021, China.

Journal of Genetics and Genomics = Yi Chuan Xue Bao
|February 16, 2023
PubMed
Summary
This summary is machine-generated.

Improved in situ sequencing (IISS) enhances spatial transcriptomics by using novel probing and barcoding for high-resolution gene expression analysis in tissues. This method offers greater signal intensity and specificity for mapping cellular communication and developmental trajectories.

Keywords:
Gene expression profilingImagingIn situ sequencingSingle cellSpatial transcriptomics

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Spatial transcriptomics reveals gene expression patterns within tissue microenvironments.
  • In situ sequencing (ISS) is a targeted technique for multiplexed spatial gene expression profiling.
  • Existing ISS methods can be limited by signal intensity and specificity.

Purpose of the Study:

  • To present an improved in situ sequencing (IISS) method for high-resolution spatial gene expression profiling.
  • To enhance signal intensity and specificity in targeted spatial transcriptomics.
  • To enable detailed analysis of tissue transcriptional landscapes.

Main Methods:

  • Developed an improved combinatorial probe anchor ligation chemistry with a 2-base encoding strategy.
  • Integrated advanced image analysis pipelines for high-resolution data processing.
  • Applied IISS to fresh frozen and formalin-fixed paraffin-embedded (FFPE) tissue sections.

Main Results:

  • Achieved higher signal intensity and improved specificity for barcode interrogation in situ.
  • Demonstrated single-cell level spatial gene expression analysis capabilities.
  • Successfully applied IISS to diverse tissue types, including FFPE samples.

Conclusions:

  • IISS provides a streamlined and robust platform for targeted spatial transcriptomics.
  • The method facilitates the construction of developmental trajectories and cell-cell communication networks.
  • IISS advances the study of gene expression localization in complex biological systems.