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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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ATAC-Seq Optimization for Cancer Epigenetics Research

ATAC-Seq Optimization for Cancer Epigenetics Research

Published on: June 30, 2022

A simple ATAC-seq protocol for population epigenetics.

Ronaldo de Carvalho Augusto^1,2, Oliver Rey¹, Céline Cosseau¹

¹Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France.

Wellcome Open Research

|February 2, 2021

Summary

This summary is machine-generated.

This study presents a simplified Assay for Transposase Accessible Chromatin with High-throughput Sequencing (ATAC-seq) protocol. It effectively monitors population chromatin changes in response to environmental factors, even in small organisms.

Keywords:

ATAC-seq Daphnia pulex Schistosoma mansoni epigenetics epigenomics

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Area of Science:

Epigenetics
Genomics
Molecular Biology

Background:

Population epigenomics studies require efficient methods to analyze chromatin accessibility.
Environmental factors can induce significant changes in chromatin structure.
Existing ATAC-seq protocols may not be suitable for small organisms or large-scale population studies.

Purpose of the Study:

To develop and validate a streamlined protocol for generating sequence-ready libraries for population epigenomics.
To demonstrate the utility of this protocol in monitoring chromatin structure alterations in response to environmental cues.
To provide a user-friendly method applicable to small biological samples.

Main Methods:

A simplified Assay for Transposase Accessible Chromatin with High-throughput Sequencing (ATAC-seq) protocol was developed.
The protocol focuses on generating sequence-ready libraries for epigenomic analysis.
Alignment results were analyzed to assess chromatin accessibility and structure changes.

Main Results:

The protocol successfully generates sequence-ready libraries for population epigenomics.
Chromatin structure changes in populations exposed to environmental cues were monitored.
The method is effective for small organisms like daphnia and schistosome worms (~10,000 cells).

Conclusions:

The streamlined ATAC-seq protocol is a valuable tool for population epigenomics.
It enables the monitoring of environmentally induced chromatin changes in diverse small organisms.
The protocol requires minimal molecular biology expertise, increasing accessibility for researchers.