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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.
Why study Open Chromatin?
- Gain mechanistic insight into gene regulation, cellular response to treatment or disease
- Identify which transcription factors are driving cell fate, disease, or response
- Primary tissues or cells such as pancreatic Beta cells
- Limited patient samples
- 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;
- Cell preparation
- Transposase reaction
- Library amplification
- Sequencing on an Illumina platform
- Bioinformatic analysis
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:
- Human and animal tissues (including xenografts and human biopsies)
- Primary cells (including T and B cells)
- FACS sorted cells
- Most rare cell populations
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Figure 1: Active Motif’s ATAC-Seq assay reliably detects regions of open chromatin.
Figure 2: Active Motif’s ATAC-Seq assay distinguishes sample groups by identifying chromatin regions that are differentially open.
Figure 3: Identifying important transcription factor binding sites using ATAC-Seq
Figure 4: Distribution of Histone Modifications Relative to ATAC-Seq Peaks at Annotated Promoters
Figure 5: Distribution of Histone Modifications Relative to ATAC-Seq Peaks Outside of Annotated Promoters
Figure 6: Active Motif’s ATAC-Seq data generated from tissues
Figure 7: Active Motif’s ATAC-Seq data shows high reproducibility
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.
Figure 1: Active Motif’s optimized ATAC-Seq protocol results in increased FRiP scores.
Figure 2: Active Motif’s optimized ATAC-Seq protocol results in increased number of peaks.
References for ATAC-Seq & Omni ATAC-Seq publications
- Buenrostro, J.D. et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position, Nature Methods. 2013; 10:1213-1218.
- Corces, M.R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues, Nature Methods. 2017; 14:959-962.