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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.
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...
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
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Related Experiment Video

Updated: Jun 6, 2026

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
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G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Published on: March 22, 2018

Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles.

Michal Mokry1, Pantelis Hatzis, Ewart de Bruijn

  • 1Cancer Genomics Center, Department of Medical Genetics, Hubrecht Institute and University Medical Center Utrecht, Utrecht, The Netherlands.

Plos One
|December 15, 2010
PubMed
Summary
This summary is machine-generated.

A new double-fragmentation ChIP-seq method improves chromatin yields for next-generation sequencing (NGS). This technique generates accurate genome-wide protein-DNA binding profiles from minimal immunoprecipitated material.

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Published on: January 27, 2016

Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • Chromatin fragments from immunoprecipitation often exceed optimal lengths for next-generation sequencing (NGS).
  • Larger fragments may contain biologically relevant information missed by standard protocols.
  • These oversized fragments represent a significant portion of immunoprecipitated material.

Purpose of the Study:

  • To develop an improved ChIP-seq procedure addressing limitations of fragment size.
  • To enhance the yield and quality of sequencing data from immunoprecipitated chromatin.
  • To enable the capture of biologically relevant data from larger chromatin fragments.

Main Methods:

  • A double-fragmentation ChIP-seq protocol was designed, involving a second shearing step after de-crosslinking.
  • This method concentrates chromatin fragments into the optimal size range for NGS.
  • The protocol was optimized for the AB/SOLiD platform but is adaptable to others.

Main Results:

  • The double-fragmentation approach increases chromatin yields for NGS.
  • It eliminates the need for laborious size-selection steps.
  • Biologically relevant genome-wide protein-DNA binding profiles were generated from low-input material (sub-nanogram) for TCF7L2/TCF4, TBP, and H3K4me3.

Conclusions:

  • The double-fragmentation ChIP-seq procedure is effective for generating high-quality protein-DNA binding profiles.
  • It enhances efficiency and data yield, particularly with limited starting material.
  • This method offers a valuable alternative for ChIP-seq applications across various sequencing platforms.