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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...
RNA-seq03:21

RNA-seq

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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.

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Related Experiment Video

Updated: Jun 21, 2026

Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization
16:37

Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization

Published on: August 5, 2008

An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping.

Rajkumar Sasidharan1, Ashish Agarwal, Joel Rozowsky

  • 1Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA. rsasidharan@stanford.edu

BMC Research Notes
|July 28, 2009
PubMed
Summary
This summary is machine-generated.

Comparing transcriptome profiling technologies, tiling microarrays and massively parallel signature sequencing (MPSS), reveals significant overlap in identified transcripts. Careful analysis, accounting for data differences, shows better agreement, especially for protein-coding genes.

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Technical Demonstration of Whole Genome Array Comparative Genomic Hybridization
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Published on: August 5, 2008

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transcriptome profiling is crucial for understanding gene expression.
  • Tiling microarrays and high-throughput sequencing are the primary methods.
  • Next-generation sequencing technologies have generated excitement, necessitating comparative studies.

Purpose of the Study:

  • To develop a fair comparison approach for transcripts identified by tiling microarrays and MPSS sequencing data.
  • To evaluate the overlap and agreement between these two transcriptome profiling technologies.

Main Methods:

  • Utilized published rice and Arabidopsis datasets for comparative analysis.
  • Developed an approach to compare discrete sequencing data with continuous tiling array data.
  • Mapped probe intensities onto sequencing tags and analyzed intensity distributions.

Main Results:

  • Initial comparison showed a small overlap (22% in rice, 66% in Arabidopsis) due to data type differences.
  • Detailed analysis revealed this overlap was an underestimate.
  • Mapping probe intensities to sequencing tags showed similar distributions to exons.
  • Restricting comparison to protein-coding genes demonstrated a good overlap between technologies.

Conclusions:

  • A reasonable overlap exists between transcripts identified by tiling microarrays and MPSS sequencing.
  • Scoring and thresholding methods in tiling array analysis can distort the perceived overlap.
  • The developed approach provides a more accurate assessment of transcript identification agreement.