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Related Concept Videos

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

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
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High-throughput SuperSAGE for digital gene expression analysis of multiple samples using next generation sequencing.

Hideo Matsumura1, Kentaro Yoshida, Shujun Luo

  • 1Iwate Biotechnology Research Center, Kitakami, Japan. hideoma@shinshu-u.ac.jp

Plos One
|August 12, 2010
PubMed
Summary

We developed High-Throughput (HT-) SuperSAGE, a digital gene expression profiling method using next-generation sequencing. This technique offers sensitive, reproducible, and accurate analysis of many samples in a single run.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Transcriptomics

Background:

  • SuperSAGE is a digital gene expression profiling technique.
  • It isolates 26-bp tag fragments from expressed transcripts.
  • High-throughput analysis of multiple samples is challenging.

Purpose of the Study:

  • To establish a High-Throughput (HT-) SuperSAGE protocol.
  • To enable pooled library analysis of multiple samples in a single sequencing run.
  • To demonstrate the sensitivity, reproducibility, and accuracy of HT-SuperSAGE.

Main Methods:

  • Combined SuperSAGE technology with next-generation sequencing.
  • Incorporated index (barcode) sequences to differentiate samples.
  • Pooled libraries from multiple samples for single sequencing run analysis.

Main Results:

  • HT-SuperSAGE provides highly sensitive, reproducible, and accurate digital gene expression data.
  • Demonstrated successful application in analyzing laser-microdissected cells and biological replicates.
  • Showcased versatility with different tag extraction methods using anchoring enzymes.

Conclusions:

  • HT-SuperSAGE significantly increases throughput for digital gene expression analysis.
  • The protocol is robust and applicable to diverse biological samples and experimental designs.
  • This method facilitates large-scale transcriptomic studies.