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Related Concept Videos

Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
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.
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...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...

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Related Experiment Video

Updated: Jun 22, 2026

qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping
07:00

qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping

Published on: May 25, 2015

CSReport: A New Computational Tool Designed for Automatic Analysis of Class Switch Recombination Junctions Sequenced

François Boyer1,2, Hend Boutouil1,2, Iman Dalloul1,2

  • 1Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.

Journal of Immunology (Baltimore, Md. : 1950)
|April 19, 2017
PubMed
Summary

CSReport is a new software tool that automates the analysis of immunoglobulin class switch recombination (CSR) junctions. This tool accurately analyzes large datasets from high-throughput sequencing, accelerating B cell function research.

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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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A Reporter Based Cellular Assay for Monitoring Splicing Efficiency
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A Reporter Based Cellular Assay for Monitoring Splicing Efficiency

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Last Updated: Jun 22, 2026

qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping
07:00

qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping

Published on: May 25, 2015

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

Published on: October 5, 2018

A Reporter Based Cellular Assay for Monitoring Splicing Efficiency
08:53

A Reporter Based Cellular Assay for Monitoring Splicing Efficiency

Published on: September 15, 2021

Area of Science:

  • Immunology
  • Bioinformatics
  • Computational Biology

Background:

  • B cells are crucial for humoral immunity, producing memory B cells and antibody-secreting plasma cells.
  • B cell activation involves terminal maturation and immunoglobulin (Ig) isotype class switch recombination (CSR) in secondary lymphoid organs.
  • CSR generates unique IgH loci through recombination between switch (S) regions, providing insights into B cell mechanisms.

Purpose of the Study:

  • To develop an automated software tool, CSReport, for analyzing large datasets of CSR junction sequences.
  • To support the analysis of CSR junctions generated by high-throughput sequencing (HTS) protocols, specifically Ion Torrent technology.
  • To facilitate and accelerate basic and clinical research on B cell functions through efficient CSR junction analysis.

Main Methods:

  • Designed and implemented CSReport, a software program for analyzing CSR recombination junctions.
  • Assessed CSReport's accuracy using simulated CSR junction datasets.
  • Applied CSReport to analyze Sμ-Sα and Sμ-Sγ1 junctions from CH12F3 cells and primary murine B cells.

Main Results:

  • CSReport accurately identifies junction segment breakpoints on reference sequences.
  • The software characterizes junction structures, including blunt-ended junctions, insertions, and microhomology.
  • CSReport demonstrated accuracy in analyzing CSR junction sequences from HTS-based protocols.

Conclusions:

  • CSReport provides an accurate and automated tool for analyzing large-scale CSR junction sequence data.
  • The software facilitates unprecedented analysis of large junction libraries, offering a unified framework for CSR studies.
  • CSReport significantly accelerates the study of immunoglobulin class switch recombination and B cell functions.