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ATAC Sequencing
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)