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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: Dec 7, 2025

CARIP-Seq and ChIP-Seq: Methods to Identify Chromatin-Associated RNAs and Protein-DNA Interactions in Embryonic Stem Cells

CARIP-Seq and ChIP-Seq: Methods to Identify Chromatin-Associated RNAs and Protein-DNA Interactions in Embryonic Stem Cells

Published on: May 25, 2018

An Optimized Protocol for ChIP-Seq from Human Embryonic Stem Cell Cultures.

Adrienne E Sullivan¹, Silvia D M Santos¹

¹Quantitative Cell Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK.

|October 1, 2020

Summary

This summary is machine-generated.

This study details an optimized chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq) protocol for human embryonic stem cells (hESCs). It includes quality control steps to ensure reliable genome-wide protein-binding data.

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Last Updated: Dec 7, 2025

CARIP-Seq and ChIP-Seq: Methods to Identify Chromatin-Associated RNAs and Protein-DNA Interactions in Embryonic Stem Cells

CARIP-Seq and ChIP-Seq: Methods to Identify Chromatin-Associated RNAs and Protein-DNA Interactions in Embryonic Stem Cells

Published on: May 25, 2018

Chromatin Immunoprecipitation ChIP Protocol for Low-abundance Embryonic Samples

Chromatin Immunoprecipitation ChIP Protocol for Low-abundance Embryonic Samples

Published on: August 29, 2017

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

Published on: August 13, 2020

Area of Science:

Molecular Biology
Genomics
Stem Cell Biology

Background:

Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is crucial for mapping genome-wide DNA-binding proteins.
General ChIP-seq workflows require sample-specific optimization for high-quality results.
Human embryonic stem cells (hESCs) present unique challenges for ChIP-seq protocols.

Purpose of the Study:

To present an optimized ChIP-seq protocol specifically for cultured hESCs.
To incorporate quality control measures for assessing sample integrity and enrichment specificity.
To facilitate accurate characterization of protein-DNA interactions in hESCs.

Main Methods:

Adaptation and optimization of the standard ChIP-seq workflow for hESC applications.
Implementation of pre-sequencing quality control checks for sample quality.
Inclusion of methods to identify and mitigate non-specific enrichment in "hyper-ChIPable" regions.

Main Results:

The optimized protocol yields high-quality ChIP-seq data from hESCs.
Quality control steps effectively assess sample quality and potential biases.
The protocol enables reliable genome-wide mapping of protein-DNA interactions in hESCs.

Conclusions:

This optimized ChIP-seq protocol provides a robust method for hESC research.
The integrated quality control measures enhance data reliability and reproducibility.
The protocol is essential for advancing our understanding of hESC epigenomics and gene regulation.