ATAC-Seq Data Analysis: A Quick Overview

Now that we’ve established our computing environment and clarified our experimental design, it’s time to analyze the data. For this tutorial, we will analyze a publicly available dataset originally published as part of a study by Hovhannisyan et al. In that study, the authors used an integrated RNA-seq and ATAC-seq analysis to investigate the gene expression and chromatin accessibility changes in the model organism Saccharomyces cerevisiae (budding yeast), before and after hybridization with another distantly related yeast species, Saccharomyces uvarum.

The main objective of our ATAC-seq analysis today will be to identify differentially accessible chromatin regions of S. cerevisiae upon transition to the hybrid state. In other words, this analysis will reveal whether and to what extent the budding yeast changes its open chromatin profiles after hybridization with another yeast.

The experimental design of this study included three biological replicates of parental S. cerevisiae and three biological replicates of the hybrid S. cerevisiae x S. uvarum. Both organisms were grown under the same experimental conditions, and the experiments were performed concurrently by the same laboratory technician to avoid batch effects.

After the transposase integration, the obtained genetic material was sequenced by Illumina HiSeq 2500 machine using paired-end 50 base-pair long reads. All replicates were sequenced for at least 60 million paired-end reads (i.e. 30 million reads in each read direction per sample) to achieve high coverage data according to the recommendations mentioned above. In fact, when scaling from human to yeast, 60 million reads for human data would be proportional to having 0.24 million reads for yeast. Thus, considering the small size of the yeast genome compared to the human one, the amount of ATAC-seq data obtained in this study is abundant.

Cited works

Hovhannisyan, Hrant, Ester Saus, Ewa Ksiezopolska, Alex J. Hinks Roberts, Edward J. Louis, and Toni Gabaldón. 2020. “Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization.” Frontiers in Genetics 11 (May): 404.