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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
What is Gene Expression?01:42

What is Gene Expression?

Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
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What is Gene Expression?01:42

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Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
What is Gene Expression?01:36

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A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then processed and...
Reporter Genes02:11

Reporter Genes

Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.
Commonly used reporter...
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Ribosome Profiling

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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Mapping Mammalian 3D Genome Interactions with Micro-C-XL
11:41

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High-resolution, three-dimensional mapping of gene expression using GeneExpressMap (GEM).

C J Flynn1, T Sharma, S W Ruffins

  • 1Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

Developmental Biology
|July 12, 2011
PubMed
Summary
This summary is machine-generated.

We developed GeneExpressMap (GEM), a tool for analyzing gene expression patterns in 3D using multiplex fluorescent whole mount in situ hybridization (F-WMISH). GEM enables single-cell resolution analysis, advancing developmental and gene network studies.

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Area of Science:

  • Developmental Biology
  • Genomics
  • Bioinformatics

Background:

  • Analyzing gene expression patterns is crucial for understanding developmental processes and gene regulatory networks.
  • High-resolution 3D mapping of gene expression in developing tissues is essential.
  • Multiplex fluorescent whole mount in situ hybridization (F-WMISH) combined with confocal microscopy is a leading method for this analysis.

Purpose of the Study:

  • To introduce GeneExpressMap (GEM), a novel image analysis tool.
  • To enable rapid, 3D, single-cell resolution analysis of multiplex F-WMISH data.
  • To demonstrate GEM's utility in analyzing gene expression in sea urchin embryos.

Main Methods:

  • Development of GeneExpressMap (GEM) software.
  • GEM utilizes proximity of hybridization signal to cell nuclei for signal assignment.
  • Application of GEM to analyze regulatory gene expression in sea urchin non-skeletogenic mesoderm.

Main Results:

  • GEM facilitates the rapid, 3D analysis of multiplex F-WMISH data at single-cell resolution.
  • The tool successfully assigns gene expression signals to individual cells.
  • Analysis of sea urchin embryo development revealed detailed gene expression patterns.

Conclusions:

  • GeneExpressMap (GEM) significantly enhances the capabilities of multiplex F-WMISH.
  • GEM is a valuable tool for gene network analysis and developmental studies.
  • The software provides high-resolution insights into spatial and temporal gene expression patterns.