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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 Hybridization02:31

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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.
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Related Experiment Video

Updated: May 2, 2026

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay
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Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay

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Highly multiplexed subcellular RNA sequencing in situ.

Je Hyuk Lee1, Evan R Daugharthy, Jonathan Scheiman

  • 1Wyss Institute, Harvard Medical School, Boston, MA 02115, USA.

Science (New York, N.Y.)
|March 1, 2014
PubMed
Summary
This summary is machine-generated.

Fluorescent in situ RNA sequencing (FISSEQ) allows researchers to map gene expression and RNA localization within cells. This method enhances single-molecule detection for studying cellular processes in situ.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Cell Biology

Background:

  • Understanding spatial gene expression requires precise RNA localization within cells.
  • Current methods face limitations in optical resolution and signal noise for single-molecule detection.

Purpose of the Study:

  • To introduce fluorescent in situ RNA sequencing (FISSEQ) for high-resolution spatial transcriptomics.
  • To demonstrate FISSEQ's capability in analyzing RNA expression and localization in situ.

Main Methods:

  • Developed FISSEQ, a method involving in situ sequencing of cross-linked complementary DNA (cDNA) amplicons.
  • Applied FISSEQ to human primary fibroblasts using a simulated wound-healing assay.
  • Generated 30-base reads for 8102 genes in situ.

Main Results:

  • Successfully mapped RNA expression and localization in human fibroblasts.
  • FISSEQ demonstrated compatibility with tissue sections and whole-mount embryos.
  • Reduced limitations of optical resolution and noisy signals in single-molecule detection.

Conclusions:

  • FISSEQ provides a powerful platform for massively parallel detection of genetic elements in situ.
  • Enables investigation of cellular phenotype, gene regulation, and cellular environment.
  • Advances the study of spatial organization of gene expression at single-nucleotide resolution.