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ATACseq is a technique used to identify open versus closed chromatin regions (depleted on nucleosomes and high chromatin structure) in a context specific way (in particular cell types from controls and patients). The output of ATACseq is similar to the information provided by the well-established DNase I hypersensitivity but the former one has the advantage of reduced number of cells to be implemented (50,000 cells). This enables to apply it in clinical samples and allows comparison of the chromatin landscape between healthy and diseased individuals. High-density sequencing using Hiseq output will also allow to develop footprints for transcription binding sites. Overlapping of ATACseq information in cells from patients with other annotation information such as K27Ac, K4me1,K4me3, RNAseq, DHS, eQTLs...will help to prioritise those SNPs within loci identified to be associated to disease in different GWAS which may have a functional role in regulation of gene expression. These candidate SNPs will be suitable for later confirmation using the high-throughput chromosome conformation capture technique known as Capture-C.
| Project ID | ATAC-seq |
|---|---|
| Status | Ongoing |
| Dates | 2014-2017 |
| Publication | Unpublished |
| Ethics | Psoriasis and ankylosing spondylitis patients recruitment |
| Sample information | |
|---|---|
| Organism | Homo sapiens |
| Organism part | Blood and skin |
| Cell type | T cells (CD4+ and CD8+), monocytes, keratinocytes and others; K562 (collaboration with the Core) |
| Experimental conditions | healthy controls and patients |
| Phenotype | Psoriasis and ankylosing spondylitis patients |
| Sample source | ATACseq_001 folder contains Miseq NGS data from blood-isolated human monocytes using CD14+ Miltenyi magnetic beads and cultured in RPMI 20% FBS for 24 hours |
| Sequencing project ID | Data type | Platform | Repository name *1 | Repository ID *2 | Data release status | Analysis *3 | Script Repository |
|---|---|---|---|---|---|---|---|
| XXX | ATAC sequencing | Illumina Miseq | rescomp1: /well/jknight/Irina/ATAC | ??? | NA | analysis with PineChrom, ATAC-Seq pipeline | https://github.com/jknightlab/ATACseq_pipeline |
| P150493 | ATAC sequencing | Illumina Hiseq2500 | rescomp1: /well/bsgjknight | ??? | NA | analysis with PineChrom and Core's ATAC pipeline | https://github.com/jknightlab/ATACseq_pipeline/tree/master/Core_manuscript |
| P160086 | ATAC sequencing AS and psoriasis | Illumina HiSeq400 | on rescomp: /well/jknight/ATACseq_all_projects/AS | ??? | NA | PineChrom | https://github.com/jknightlab/ATACseq_pipeline |
| P160135 | ATAC sequencing AS and psoriasis | Illumina HiSeq400 | on rescomp: /well/jknight/ATACseq_all_projects/AS | ??? | NA | PineChrom | https://github.com/jknightlab/ATACseq_pipeline |
- *1 - Name of public data repository to which data has been submitted
- *2 - ID assigned by repository
- *3 - Brief description of analysis. Include links to scripts in Git repository and pages describing results where possible.
| Contact information | |
|---|---|
| Contact1, name and email | Irina Pulyakhina, [email protected] |
| Contact2, name and email | Alicia Lledo Lara, [email protected] |
| Contact3, name and email | Anna Sanniti, [email protected] |
| Contact4, name and email | Julian Knight, [email protected] |