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

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.

Publications

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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...

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

Assess open regions of chromatin at single nucleotide resolution

ATAC-seq services include:

Standard analysis

Additional analysis on request:

Differential accessibility analysis:

Annotation in genomic regions:

Gene ontology terms analysis:

Pathway analysis:

Visualization of specific genomic regions:

Additional information

How to properly cite our product/service in your work

Events

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

Assess open regions of chromatin at single nucleotide resolution

ATAC-seq services include:

Standard analysis

Additional analysis on request:

Differential accessibility analysis:

Annotation in genomic regions:

Gene ontology terms analysis:

Pathway analysis:

Visualization of specific genomic regions:

Additional information

How to properly cite our product/service in your work

Bioinformatics Data Mining Service

ChIP-seq Profiling Service

Total RNA-seq Service

Events