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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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Related Experiment Video

Updated: May 27, 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

Analyzing ChIP-seq data: preprocessing, normalization, differential identification, and binding pattern

Cenny Taslim¹, Kun Huang, Tim Huang

¹Department of Molecular Virology, Immunology & Medical Genetics, The Ohio State University, Columbus, OH, USA.

Methods in Molecular Biology (Clifton, N.J.)

|December 2, 2011

Summary

This summary is machine-generated.

This study presents a guideline for analyzing chromatin immunoprecipitation followed by sequencing (ChIP-seq) data. The method enhances accuracy and efficiency for studying genome-wide protein-DNA interactions.

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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

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Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a key technique for mapping protein-DNA interactions genome-wide.
ChIP-seq offers improved accuracy, coverage, and speed compared to older ChIP-chip methods.

Purpose of the Study:

To provide a comprehensive, step-by-step guideline for analyzing ChIP-seq data.
To enable robust identification and characterization of protein-DNA binding sites.

Main Methods:

Data preprocessing and quality control.
Nonlinear normalization for inter-sample comparability.
Statistical analysis using mixture modeling and local false discovery rates (fdrs) for differential binding site identification.
Binding pattern characterization.

Main Results:

A detailed workflow for ChIP-seq data analysis is described.
The guideline facilitates accurate identification of differential binding sites.
The presented methods allow for comprehensive characterization of protein-DNA binding patterns.

Conclusions:

The developed guideline offers a robust framework for ChIP-seq data analysis.
This approach enhances the reliability and interpretability of genome-wide protein-DNA interaction studies.
The methodology supports efficient and accurate discovery of regulatory elements.