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RNA-seq

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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Updated: Jun 3, 2026

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

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

Published on: October 5, 2018

Using CisGenome to analyze ChIP-chip and ChIP-seq data.

Hongkai Ji¹, Hui Jiang, Wenxiu Ma

¹The Johns Hopkins University, Baltimore, Maryland, USA.

Current Protocols in Bioinformatics

|March 15, 2011

Summary

This summary is machine-generated.

CisGenome is a software system for analyzing chromatin immunoprecipitation (ChIP) data, including ChIP-chip and ChIP-seq. It helps identify protein-DNA interactions, visualize binding signals, and discover transcription-factor binding motifs.

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Chromatin immunoprecipitation (ChIP) with genome tiling array hybridization (ChIP-chip) and sequencing (ChIP-seq) are high-throughput methods for profiling genome-wide protein-DNA interactions.
These techniques are crucial for studying transcription-factor binding sites and chromatin modifications.

Purpose of the Study:

To describe the integrated software system CisGenome for analyzing ChIP-chip and ChIP-seq data.
To outline the basic functions of CisGenome for various analytical tasks.

Main Methods:

Utilizing the CisGenome software system.
Applying functions for identifying genomic regions with protein-DNA interactions.
Employing visualization tools for binding signals.
Associating binding regions with nearby genes.
Searching for novel transcription-factor binding motifs.
Mapping existing DNA sequence motifs to specific genomic locations.

Main Results:

CisGenome provides a comprehensive platform for analyzing ChIP-chip and ChIP-seq data.
The software facilitates the identification and characterization of protein-DNA interactions across the genome.
Users can effectively visualize binding data, link interactions to genes, and identify regulatory motifs.

Conclusions:

CisGenome is a valuable tool for researchers studying genome-wide protein-DNA interactions using ChIP-based technologies.
The software streamlines the analysis of complex ChIP data, aiding in the discovery of regulatory elements and mechanisms.