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Related Concept Videos

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.
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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...

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Related Experiment Video

Updated: May 30, 2026

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing.

Eun-Joon Lee1, Lirong Pei, Gyan Srivastava

  • 1GHSU Cancer Center, Department of Biochemistry and Molecular Biology, Georgia Health Sciences University, Augusta, GA 30912, USA.

Nucleic Acids Research
|July 26, 2011
PubMed
Summary

This study introduces a targeted bisulfite sequencing method for analyzing DNA methylation in CpG islands and regulatory regions. The approach effectively identifies aberrant methylation patterns in cancer epigenomes, offering a scalable solution for large-scale sample analysis.

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Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain
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Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain

Published on: July 12, 2012

Related Experiment Videos

Last Updated: May 30, 2026

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain
13:11

Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain

Published on: July 12, 2012

Area of Science:

  • Genomics
  • Epigenetics
  • Cancer Biology

Background:

  • DNA methylation is crucial for gene regulation and its aberrant patterns are hallmarks of cancer.
  • Accurate and quantitative analysis of DNA methylation across the genome is essential for understanding cancer epigenomes.

Purpose of the Study:

  • To develop and validate a targeted bisulfite sequencing approach for enriching and analyzing CpG islands (CGIs) and promoter sequences.
  • To identify differentially methylated regions (DMRs) in breast cancer cell lines and investigate the role of DNA methyltransferases (DNMTs) in DNA methylation.

Main Methods:

  • Solution hybrid selection was used to enrich for CGIs and promoter sequences from the human genome.
  • Targeted high-throughput bisulfite sequencing was performed on enriched DNA samples.
  • Quantitative analysis of CpG methylation was conducted, and results were confirmed using PCR-based bisulfite sequencing.

Main Results:

  • The method enabled accurate, quantitative analysis of millions of CpGs in thousands of CGIs and regulatory regions.
  • 77-84% of CpGs were on or near capture probes, with 69-75% within CGIs.
  • Differentially methylated regions were identified in breast cancer cell lines, particularly on the X-chromosome.
  • DNMT1 knockout cell lines showed significantly decreased CpG methylation, highlighting the role of DNMT1.

Conclusions:

  • Targeted bisulfite sequencing is a powerful and scalable method for uncovering novel aberrant methylation in cancer epigenomes.
  • The approach provides quantitative DNA methylation information for targeted regions with high efficiency.
  • This technique facilitates the identification of potential biomarkers and therapeutic targets in cancer research.