Diagenode

ATAC-seq service (Assay for Transposase-Accessible Chromatin)

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Catalog Number
Format
G02060000

ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) allows for assessing genome-wide chromatin accessibility. The technology is based on the use of the transposase Tn5 which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing.

Assess open regions of chromatin at single nucleotide resolution

  • Gain insight into gene regulation and understand open chromatin signatures
  • Determine nucleosome positions at single nucleotide resolution
  • Uncover transcription factor (TF) occupancy
  • Benefit from comprehensive service – tagmentation, library preparation, sequencing, and analysis

  • Description

    ATAC-seq services include:

    Sample tagmentation

    • Lysis
    • TDE1 digestion

    Library preparation

    • Library amplification
    • Library purification
    • QC on the ATAC-seq library (DNA concentration, analysis of library profile)
    • Library pooling

    Deep sequencing

    • Samples are sequenced on an Illumina ® platform, paired-end 2x75bp
    • 100 million raw reads on average are obtained per sample when pooling 3samples/lane (Hi-seq 4000). Sequencing depth will be adjusted to project dependent criteria.
  • Bioinformatic analysis

    Standard analysis

    Quality check, alignment to reference genome, identification of enriched regions (peak calling) are included.

    Provided files:

    • Report with sequencing statistics
    • Raw data in FASTQ format
    • FastQC reports
    • Alignment files in BAM format
    • Peak files in BED format

    Additional analysis on request:

    Differential binding analysis:

    Identification and annotation (human, mouse, rat, drosophila) of differential chromatin accessibility between samples.

    Provided files:

    • Report with summary of differential accessibility analysis and plots
    • Files containing differentially accessibility sites or unique peaks and breakdown of those in annotated regions: introns, exons, promoters, 1-to-5 kb upstream-TSS and intergenic regions for human, mouse, rat and drosophila.

    Annotation in genomic regions:

    Annotation of ATAC-Seq peaks with genomic regions: introns, exons, promoters, 1-to-5 kb upstream-TSS and intergenic regions for human, mouse, rat and drosophila.

    Gene ontology terms analysis:

    Enrichment analysis on gene sets. Gene Ontology terms that are overrepresented in differentially bound regions may indicate the underlying biological processes involved.

    Pathway analysis:

    Identify biochemical pathways in which genes associated with differentially methylated regions (or individual differentially methylated CpGs) may be overrepresented.  

    Visualization of specific genomic regions:

    Visualization of results (i.e. sequencing data, peaks) at specific genomic regions (e.g. genes, promoters) in publication-ready images (human, mouse, rat).

    Additional information

    Generated files will be available for download during 1 month and stored for an additional period of 3 months on Diagenode’s servers. Additional long-term storage of data is available upon request.  Original samples are stored at Diagenode during 12 months after project completion, but will be discarded once this time is exceeded. Return shipment of samples is available upon request.

  •  Documents
    Full services brochure BROCHURE
    Diagenode's full services brochure
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  •  Publications

    How to properly cite this product in your work

    Diagenode strongly recommends using this: ATAC-seq service (Assay for Transposase-Accessible Chromatin) (Diagenode Cat# G02060000). Click here to copy to clipboard.

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