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| Status |
Public on Oct 01, 2013 |
| Title |
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We describe an assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, as a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol with 500–50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. We discovered classes of DNA-binding factors that strictly avoided, could tolerate or tended to overlap with the nucleosome. Using ATAC-seq maps of human CD4+ T cells from a proband obtained on consecutive days, we demonstrated the feasibility of analyzing an individual’s epigenome on a timescale compatible with clinical decision-making.
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|
| Overall design |
We examined chromatin structure using ATAC-seq in 2 cell types (GM12878 cell line, purified CD4+ T cells).
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| |
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| Contributor(s) |
Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ |
| Citation(s) |
24097267 |
| Submission date |
Jun 07, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
William J Greenleaf |
| E-mail(s) |
wjg@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Street address |
279 Campus Dr West, Beckman Center
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA207663 |
| SRA |
SRP024293 |
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