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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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Related Experiment Video

Updated: Oct 24, 2025

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue

Published on: November 21, 2018

Quantitative ChIP-seq by Adding Spike-in from Another Species.

Kongyan Niu¹, Rui Liu², Nan Liu¹

¹Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.

|August 16, 2021

Summary

This summary is machine-generated.

Comparing epigenomes across experiments using chromatin immunoprecipitation followed by sequencing (ChIP-seq) is difficult. This study presents a new protocol and computational workflow for accurate, quantitative epigenome comparisons in animal tissues.

Keywords:

Drosophila Epigenome H3K27me3 Quantitative ChIP-seq Spike-in

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Last Updated: Oct 24, 2025

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue

Published on: November 21, 2018

Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq

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Published on: February 26, 2015

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

Published on: May 5, 2023

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a standard technique for analyzing protein-DNA interactions and epigenomic profiling.
Quantitative comparison of epigenome-wide data from independent ChIP-seq experiments presents significant challenges due to technical variability.

Purpose of the Study:

To develop and validate an experimental protocol and computational workflow for quantitative and comparative epigenome assessment.
To enable robust analysis of epigenomic data across multiple independent ChIP-seq experiments using animal tissues.

Main Methods:

Development of a standardized ChIP-seq experimental protocol.
Creation of a computational workflow for data processing and quantitative analysis.
Application of the protocol and workflow to animal tissue samples.

Main Results:

The combined protocol and workflow enable reliable quantitative comparisons of epigenomes.
Demonstrated successful application in assessing epigenomic variations in animal tissues.
Overcame key challenges in inter- ChlP-seq experiment comparability.

Conclusions:

The presented methodology facilitates accurate, quantitative epigenome-wide comparisons.
This approach enhances the utility of ChIP-seq for studying epigenetic regulation in animal models.
Provides a valuable tool for reproducible epigenomic research.