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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...

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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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CistromeFinder for ChIP-seq and DNase-seq data reuse.

Hanfei Sun1, Bo Qin, Tao Liu

  • 1Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 20092, China.

Bioinformatics (Oxford, England)
|March 20, 2013
PubMed
Summary
This summary is machine-generated.

CistromeFinder is a new data portal that makes it easier for researchers to find and use public Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing data. This resource aids in understanding gene regulation and epigenetics.

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

Published on: March 22, 2018

Area of Science:

  • Genomics
  • Epigenetics
  • Molecular Biology

Background:

  • High-throughput sequencing assays like Chromatin immunoprecipitation and DNase I hypersensitivity are crucial for understanding transcriptional and epigenetic regulation.
  • Reuse of this valuable data by the research community has been historically challenging.
  • A need exists for centralized, curated, and easily accessible repositories of this data.

Purpose of the Study:

  • To develop and introduce CistromeFinder, a comprehensive data portal.
  • To facilitate the querying, evaluation, and visualization of publicly available Chromatin immunoprecipitation and DNase I hypersensitivity assay data.
  • To enhance data accessibility and usability for experimental biologists.

Main Methods:

  • Creation of a centralized database, CistromeFinder.
  • Inclusion of 6378 samples across 4391 datasets, covering 313 factors and 102 cell types.
  • Implementation of a consistent analysis and quality control pipeline for all datasets.

Main Results:

  • CistromeFinder provides access to a large collection of curated sequencing data.
  • The portal enables users to evaluate data quality before in-depth analysis.
  • Integrated tools for visualization (UCSC Genome Browser), primer design (Primer3Plus), and data submission (CistromeMap) are included.

Conclusions:

  • CistromeFinder significantly improves the accessibility and utility of crucial genomic and epigenomic datasets.
  • The portal empowers researchers to better understand transcriptional and epigenetic regulation through data reuse.
  • Community engagement through comments is facilitated for ongoing data improvement.