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

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  •  描述
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目录号
格式
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
    • Tagmentation using Diagenode's Tagmentase (Tn5 transposase)

    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 and identification of enriched regions (peak calling).

    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 accessibility 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.

  •  文档
    Epigenomics Profiling Services FLYER
    Chromatin analysis DNA methylation services RNA-seq analysis     		Download
  •  出版物

    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.

    Using our products in your publication? Let us know!

    Disease related changes in ATAC-seq of iPSC-derived motor neuron lines from ALS patients and controls
    Tsitkov S. et al.
    Amyotrophic Lateral Sclerosis (ALS), like many other neurodegenerative diseases, is highly heritable, but with only a small fraction of cases explained by monogenic disease alleles. To better understand sporadic ALS, we report epigenomic profiles, as measured by ATAC-seq, of motor neuron cultures derived from a dive...

    Inflammatory stress-mediated chromatin changes underlie dysfunction in endothelial cells
    Liu H. et al.
    Inflammatory stresses underlie endothelial dysfunction and contribute to the development of chronic cardiovascular disorders such as atherosclerosis and vascular fibrosis. The initial transcriptional response of endothelial cells to pro-inflammatory cytokines such as TNF-alpha is well established. However, very few ...

    Answer ALS: A Large-Scale Resource for Sporadic and Familial ALS Combining Clinical Data with Multi-Omics Data from Induced Pluripotent Cell Lines
    Jeffrey Rothstein, James Berry, Clive Svendsen, Leslie Thompson, Steven Finkbeiner, Jennifer Van Eyk, Ernest Fraenkel, Merit Cudkowicz, Nicholas Maragakis, Dhruv Sareen, Raquel Norel, Victoria Dardov, Alyssa Coyne, Aaron Frank, Andrea Matlock
    Answer ALS is a comprehensive multi-omics approach to ALS to ascertain, at a population level, the various clinical-molecular- biochemical subtypes of sporadic ALS. This national program enrolled 1046 ALS and ALS/FTD patients along with a cohort of 100 matched control patients followed longitudinally over at least o...

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