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Related Concept Videos

RNA-seq03:21

RNA-seq

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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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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
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Related Experiment Video

Updated: Nov 19, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems.

Shahar Alon1,2,3, Daniel R Goodwin1,2, Anubhav Sinha1,2,4

  • 1Department of Media Arts and Sciences, MIT, Cambridge, MA, USA.

Science (New York, N.Y.)
|January 29, 2021
PubMed
Summary

Expansion sequencing (ExSeq) enhances RNA imaging resolution, enabling nanoscale mapping of gene expression. This technique reveals detailed RNA localization across various tissues and cell types.

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Area of Science:

  • Molecular Biology
  • Neuroscience
  • Genomics

Background:

  • Current multiplexed RNA imaging lacks nanoscale resolution, limiting transcript localization to subcellular compartments.
  • Accurate spatial transcriptomics is crucial for understanding cellular function and disease.

Purpose of the Study:

  • To adapt expansion microscopy for in situ RNA sequencing with nanoscale resolution.
  • To develop a method for highly multiplexed, long-read RNA sequencing applicable from subcellular to system scales.

Main Methods:

  • Adapted expansion microscopy for untargeted and targeted in situ RNA sequencing.
  • Applied expansion sequencing (ExSeq) to mouse brain, hippocampus, and human metastatic breast cancer biopsy.

Main Results:

  • Untargeted ExSeq provided readout of thousands of genes, including splice variants, in the mouse brain.
  • Targeted ExSeq generated nanoscale RNA maps in hippocampal neurons, revealing dendritic and spine-level transcript localization.
  • ExSeq identified cell-type-specific and layer-specific RNA patterns in the visual cortex and mapped tumor and immune cells in human cancer biopsies.

Conclusions:

  • Expansion sequencing (ExSeq) overcomes resolution limitations in RNA imaging.
  • ExSeq enables highly multiplexed mapping of RNA from nanoscale to system scale.
  • This technique offers unprecedented insights into spatial transcriptomics across diverse biological systems.