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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...
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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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An Easy Method for Plant Polysome Profiling
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Published on: August 28, 2016

Transcript profiling in Arabidopsis with genome tiling microarrays.

Diana Coman1, Wilhelm Gruissem, Lars Hennig

  • 1Plant Biotechnology, Department of Biology, ETH Zurich, Zurich, Switzerland.

Methods in Molecular Biology (Clifton, N.J.)
|August 27, 2013
PubMed
Summary
This summary is machine-generated.

This study presents a standardized workflow for analyzing Arabidopsis gene expression using whole-genome tiling microarrays. The AGRONOMICS1 array enables strand-specific analysis and integrates with existing data, simplifying transcriptome profiling.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Microarray technology is a standard for genome-wide expression analysis.
  • Whole-genome tiling microarrays offer flexible and comprehensive expression profiling.
  • Analyzing the plant transcriptome requires robust and adaptable experimental workflows.

Purpose of the Study:

  • To describe a detailed, standardized workflow for Arabidopsis transcriptome analysis using tiling arrays.
  • To provide guidance on critical steps from experimental design to data analysis.
  • To highlight the capabilities of the AGRONOMICS1 array for strand-specific expression profiling.

Main Methods:

  • Utilized whole-genome tiling microarrays for expression profiling.
  • Developed a standardized experimental and data analysis workflow.
  • Employed the AGRONOMICS1 array for strand-specific transcriptome analysis.

Main Results:

  • Established a comprehensive workflow for Arabidopsis transcriptome assessment.
  • The AGRONOMICS1 array allows for single-array, strand-specific expression analysis.
  • The protocol is adaptable to other tiling arrays and integrates with existing ATH1 data.

Conclusions:

  • The described workflow facilitates efficient and detailed transcriptome analysis in Arabidopsis.
  • AGRONOMICS1 arrays provide enhanced capabilities for genomic expression studies.
  • This standardized approach supports integration with existing knowledge bases and requires no specialized hardware.