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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 1, 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

The analysis of ChIP-Seq data.

Wenxiu Ma¹, Wing Hung Wong

¹Department of Computer Science, Stanford University, Stanford, California, USA.

Methods in Enzymology

|May 24, 2011

Summary

This summary is machine-generated.

Chromatin immunoprecipitation sequencing (ChIP-seq) maps protein-DNA interactions genome-wide. This tutorial simplifies ChIP-seq data analysis for researchers using the CisGenome software package.

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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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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Chromatin immunoprecipitation sequencing (ChIP-seq) is crucial for studying genome-wide protein-DNA interactions.
Applications include analyzing transcription, regulation, and histone modifications.
Accurate mapping of binding loci aids understanding of development and disease.

Purpose of the Study:

To provide a comprehensive tutorial on preparing, preprocessing, and analyzing ChIP-seq datasets.
To address the challenges experimental investigators face with complex ChIP-seq data analysis.
To present a revised version of the CisGenome software package for standard ChIP-seq analysis tasks.

Main Methods:

Review of basic ChIP-seq experimental design.
In-depth tutorial utilizing the CisGenome software package.
Illustration of statistical and computational issues with real data examples.

Main Results:

The tutorial covers essential steps for ChIP-seq data analysis.
CisGenome software is revised to streamline common analysis tasks.
Statistical and computational challenges are highlighted and discussed.

Conclusions:

This work simplifies ChIP-seq data analysis for experimental researchers.
The CisGenome package facilitates efficient processing of ChIP-seq datasets.
Understanding ChIP-seq analysis is vital for advancing research in development and disease.