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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...

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Updated: Sep 30, 2025

Detection of a CDH1 Rare Transcript Variant in Fresh-frozen Gastric Cancer Tissues by Chip-based Digital PCR

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ChIP-seq.

Tae Hoon Kim, Job Dekker

Cold Spring Harbor Protocols

|May 3, 2018

Summary

This summary is machine-generated.

ChIP-seq is a standard genome-wide analysis method. It uses next-generation sequencing and ligation-mediated PCR (LM-PCR) to identify protein binding sites, even with small DNA amounts.

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Area of Science:

Genomics
Molecular Biology
Biotechnology

Background:

Chromatin immunoprecipitation sequencing (ChIP-seq) is the standard for genome-wide ChIP analysis.
Next-generation sequencing (NGS) platforms generate millions of sequence reads.
Protein binding sites are identified by analyzing ChIP sequence read densities along the genome.

Purpose of the Study:

To describe the standard ChIP-seq protocol using the Illumina Genome Analyzer.
To highlight the necessity of DNA amplification despite small ChIP DNA requirements.
To present a method for parallel ChIP-chip analysis.

Main Methods:

ChIP DNA is amplified using ligation-mediated PCR (LM-PCR).
The protocol involves linker ligation and two rounds of size selection.
Purified ChIP DNA is sequenced using the Illumina Genome Analyzer.

Main Results:

The described protocol enables genome-wide identification of protein binding sites.
This method is effective even with limited ChIP DNA input.
Parallel ChIP-chip analysis is feasible.

Conclusions:

The standard ChIP-seq protocol effectively identifies protein binding sites genome-wide.
LM-PCR amplification is crucial for current NGS platforms in ChIP-seq.
The protocol supports parallel ChIP-chip analysis, offering versatility.