Among the services that the Applied Bioinformatics Laboratories offer is assay for transposase-accessible chromatin through sequencing, or ATAC-seq. ATAC-seq can provide chromatin accessibility across the genome. It can identify open chromatin sites and show the interaction between locations of open chromatin, DNA-binding proteins, nucleosomes, and compaction of chromatin at the nucleotide level.

Request an ATAC-Seq Service

To request this service from us, please provide the following:

• a sample sheet with the corresponding conditions for the samples
• the organism(s) of the particular study
• the link to the generated FASTQ data (obtained from NYU Langone’s Genome Technology Center or another sequencing facility)

You receive the following from us:

• a comprehensive report
• quality assessment (read quality, alignment statistics, and enrichment plots)
• individual bigWig files for visualization using a genome browser
• principal component analysis plot for assessment of sample similarities
• BED files of identified chromatin accessibility peaks
• distribution of identified peaks in genomic regions of interest (promoters, introns, exons, etc.)
• annotated peak tables and differential binding analysis (logarithm of fold change, statistics, and normalized peak intensity value of each sample)

Additional or Customized Analyses

We also provide the following analyses:

• gene-ontology term and pathway enrichment analysis
• binding motif discovery
• integration with gene expression (using RNA-seq data, if available)
• customized plots

Each of these may be subject to an additional charge.

Additional Resources

Below you can find links to the computational pipelines that we typically use for our analyses:

• HiC-bench platform (atacseq–standard pipeline)
• Seq-N-Slide pipeline (ATAC route)