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ATAC-Seq

Genome-wide profiles of open chromatin regions from < 100,000 cells

What our customers are saying about us ...

"I am studying the epigenetic regulation of heart failure. I have had a very good experience with Active Motif Epigenetic services and I will continue research with Active Motif in the future. I received good support from both the Sales Department and the Tech Support Team to help me to go through all the aspects of the service."
Ning Feng, MD, PhD
University of Pittsburgh
View complete list of testimonials >

 

ATAC-Seq is based on transposase-mediated insertion of sequencing primers into open chromatin regions. This assay provides genome-wide profiles of open and accessible regions of chromatin that are indicative of active regulatory regions.
ATAC-Seq image

Why study Open Chromatin?

  1. Gain mechanistic insight into gene regulation, cellular response to treatment or disease
  2. Identify which transcription factors are driving cell fate, disease, or response
  3. Primary tissues or cells such as pancreatic Beta cells
  4. Limited patient samples
  5. Stratify patients or sample groups based on open chromatin signatures

ATAC-Seq can be a good alternative to ChIP-Seq if it is unknown whether epigenetics plays a role in the response of your cell system, if it is unclear which histone modification is the most important to study using ChIP-Seq or when cell numbers are limited.

The ATAC-Seq assay includes;

  1. Cell preparation
  2. Transposase reaction
  3. Library amplification
  4. Sequencing on an Illumina platform
  5. Bioinformatic analysis

Sample Types

Active Motif’s services team is the only group routinely generating ATAC-Seq data from tissues. Active Motif will accept the following sample types for this service:

  1. Human and animal tissues (including xenografts and human biopsies)
  2. Primary cells (including T and B cells)
  3. FACS sorted cells
  4. Most rare cell populations

To learn more, send us an Epigenetic Services Information Request. You can also download Active Motif’s Epigenetic Services Brochure.

 
Name Cat No. Price  
ATAC-Seq 25079 Request Quote
ATAC-Seq Data 1
Figure 1: Active Motif’s ATAC-Seq assay reliably detects regions of open chromatin.

DNAse-Seq, which has long been the gold standard for generating genome-wide profiles of open chromatin, is shown above in blue. The utility of DNAse-Seq has been limited since it requires tens of millions of cells and is technically challenging. Active Motif’s ATAC-Seq (shown above in green), uses only 50,000 cells and provides data that is comparable to DNAse-Seq.


ATAC-Seq Data 2
Figure 2: Active Motif’s ATAC-Seq assay distinguishes sample groups by identifying chromatin regions that are differentially open.

The example above shows ATAC-Seq data from 4 different samples, each performed in triplicate. Differentially open regions are highlighted in yellow.


ATAC-Seq Data 3
Figure 3: Gene Ontology using differential regions from ATAC-Seq

Open regions that lie near genes can be used to create gene lists for gene ontology analysis. In the example above, some of the top ontologies are related to B cell biology, revealing pathways that are relevant to this cell system.


ATAC-Seq Data 4
Figure 4: Identifying important transcription factor binding sites using ATAC-Seq

The underlying DNA sequence of differentially open chromatin regions can be analyzed to identify the most enriched transcription factor binding sites. In this cell system the two most enriched binding motifs are also relevant to B cell biology. Fra1 is quickly upregulated upon B cell activation and PU.1 is a key regulator of B cell fate specification.


ATAC-Seq Data 5
Figure 5: Distribution of Histone Modifications Relative to ATAC-Seq Peaks at Annotated Promoters

Comparison of ATAC-Seq data to different histone modification ChIP-Seq data sets reveals that ATAC-Seq peaks at promoters are most enriched for H3K4me3 and H3K9Ac.


ATAC-Seq Data 6
Figure 6: Distribution of Histone Modifications Relative to ATAC-Seq Peaks Outside of Annotated Promoters

ATAC-Seq peaks outside promoters are enriched for all active marks including the enhancer marks H3K27Ac and H3K4me1.


ATAC-Seq Data 7
Figure 7: Active Motif’s ATAC-Seq data generated from tissues

The images above show ATAC-Seq data generated using frozen mouse liver and lung tissue. The open chromatin profiles are similar to DNAse-Seq profiles generated by the ENCODE consortium.


ATAC-Seq Data 8
Figure 8: Active Motif’s ATAC-Seq data shows high reproducibility

The experiment above was performed using a cell line that was left untreated or treated under three different conditions and each condition was performed in triplicate. The correlation coefficients are presented in the heat map. Replicates have coefficients of at least 0.96. The heat map shows that the samples cluster into four distinct groups as expected.


ATAC-Seq Quality Measures

There are multiple ways to assess the quality of an ATAC-Seq data set. The two that are considered the most important are FRiP Score and Peak Number.

  • FRiP Score: Fraction of Reads in Peaks is the percentage of reads that overlap within called peaks. It is a measure of the enrichment of open regions and can also be considered as a measure of signal-to-noise, with signal being reads that map in peaks and noise being reads that map outside of peaks. FRiP scores will vary depending on cell type. FRiP scores of >30% are a good indication of success. However, lower FRiP scores are acceptable in more difficult samples as long as there is consistency across those samples.
  • Peak Number: Number of peaks identified in an ATAC-Seq data set. Data repository consortia like ENCODE recommend that data sets have more than 50,000 peaks identified. This however varies depending on the cell type, tissue and health of cells.
Active Motif’s optimized ATAC-Seq protocol results in increased FRiP scores
Figure 1: Active Motif’s optimized ATAC-Seq protocol results in increased FRiP scores.

Human embryonic progenitor cells (4D20.8 cell line and primary cells), human primary endothelial cells, human mesenchymal stem cells, and rat primary neonatal cardiomyocytes were processed with either the standard ATAC-Seq protocol* (blue), Omni ATAC-Seq protocol# (orange), or Active Motif’s ATAC-Seq protocol (purple). Active Motif’s ATAC-Seq protocol consistently gives higher FRiP scores in a variety of samples.

Active Motif’s optimized ATAC-Seq protocol results in increased number of peaks
Figure 2: Active Motif’s optimized ATAC-Seq protocol results in increased number of peaks.

Human embryonic progenitor cells (4D20.8 cell line and primary cells), human primary endothelial cells, human mesenchymal stem cells, and rat primary neonatal cardiomyocytes were processed with either the standard ATAC-Seq protocol* (blue), Omni ATAC-Seq protocol# (orange), or Active Motif’s ATAC-Seq protocol (purple). Samples processed with Active Motif’s ATAC-Seq protocol consistently identify more peaks in a variety of samples.

 

References for ATAC-Seq & Omni ATAC-Seq publications