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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...
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...
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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Semiconductor Sequencing for Preimplantation Genetic Testing for Aneuploidy
09:03

Semiconductor Sequencing for Preimplantation Genetic Testing for Aneuploidy

Published on: August 25, 2019

A quality control system for profiles obtained by ChIP sequencing.

Marco-Antonio Mendoza-Parra1, Wouter Van Gool, Mohamed Ashick Mohamed Saleem

  • 1Department of Cancer Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, BP 10142, 67404 Illkirch Cedex, France.

Nucleic Acids Research
|September 17, 2013
PubMed
Summary
This summary is machine-generated.

A new quality control (QC) system addresses weaknesses in analyzing next-generation sequencing (NGS) data, particularly for chromatin immunoprecipitation sequencing (ChIP-seq) and other enrichment assays. This system enhances comparative analyses of genome-wide profiles.

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Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform
09:30

Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform

Published on: August 17, 2022

Area of Science:

  • Genomics and Bioinformatics
  • Molecular Biology
  • Epigenetics

Background:

  • Comparative analysis of genome-wide profiles from next-generation sequencing (NGS) lacks robust quality control (QC) systems.
  • This limitation particularly affects chromatin immunoprecipitation sequencing (ChIP-seq) and other enrichment-based assays like RNA-seq.
  • Effective QC is crucial for multidimensional comparisons of epigenetic marks, protein-DNA interactions, and RNA profiles.

Purpose of the Study:

  • To develop and present a novel approach for associating global and local quality control (QC) indicators with NGS data.
  • To establish a QC system applicable to ChIP-seq and various other enrichment-based NGS studies.
  • To enable improved data mining and comparative QC analyses of publicly available datasets.

Main Methods:

  • Development of an integrated QC system combining global and local indicators.
  • Application of the QC system to diverse NGS enrichment-based assays, including ChIP-seq.
  • Certification of over 5600 publicly available datasets using the developed QC system.

Main Results:

  • The presented QC approach successfully integrates global and local indicators for ChIP-seq and related NGS studies.
  • A comprehensive database of over 5600 certified public datasets is now available for data mining and comparative analysis.
  • The QC system demonstrates its utility in assessing and improving the reliability of genome-wide profiling data.

Conclusions:

  • The developed QC system provides a critical framework for evaluating the quality of NGS-based genome-wide profiling data.
  • This approach significantly enhances the reliability and comparability of data from ChIP-seq and other enrichment assays.
  • The availability of certified datasets facilitates robust meta-analyses and further discoveries in epigenomics and transcriptomics.