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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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Related Experiment Video

Updated: Nov 7, 2025

Author Spotlight: Investigating mRNA Spatial Distribution in Drosophila Muscle Tissue
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Author Spotlight: Investigating mRNA Spatial Distribution in Drosophila Muscle Tissue

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Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH.

Chee-Huat Linus Eng1, Michael Lawson2, Qian Zhu3

  • 1Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.

Nature
|March 27, 2019
PubMed
Summary
This summary is machine-generated.

Researchers developed seqFISH+, a new method to image 10,000 genes in single cells. This high-resolution technique maps cell types and their spatial organization in the mouse brain for biological discovery.

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Area of Science:

  • Single-cell biology
  • Molecular imaging
  • Neuroscience

Background:

  • Accurate in situ transcriptome imaging is crucial but limited by optical resolution and transcript density.
  • Existing methods struggle to capture the full transcriptome within individual cells in their native tissue context.

Purpose of the Study:

  • To present an advanced sequential fluorescence in situ hybridization (seqFISH+) method for high-resolution, transcriptome-wide imaging in single cells.
  • To demonstrate the capability of seqFISH+ for mapping cellular organization and gene expression within intact tissues.

Main Methods:

  • Developed an evolved version of sequential fluorescence in situ hybridization (seqFISH+).
  • Applied seqFISH+ using a standard confocal microscope to image mRNA for 10,000 genes in mouse brain tissues (cortex, subventricular zone, olfactory bulb).

Main Results:

  • Achieved high-accuracy, sub-diffraction-limit resolution imaging of 10,000 genes per single cell.
  • Enabled unbiased identification of cell classes and their spatial organization within tissue.
  • Revealed subcellular mRNA localization and intercellular ligand-receptor interactions.

Conclusions:

  • seqFISH+ is a powerful technology for generating spatial cell atlases.
  • This method facilitates discovery-driven studies of biological processes in situ at the transcriptome level.