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| Status |
Public on Oct 05, 2016 |
| Title |
ATAC-Se1 to investigate the spatial choreography of the accessible genome |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
In order to completely understand the spatial choreography of the accessible genome in the 3D intact nucleus, we had developed a new technique termed assay of transposase accessible chromatin by visualization (ATAC-see). In brief, we had labeled the adaptor in hypersensitive Tn5 transposase with fluorophore dye and performed the Tn5 tagmentation on the fixed culture cells slide. We had performed ATAC-see in different types of cells and found out there are cell types specific spatial choreography of the accessible genome in the 3D intact nucleus, which is tightly linked to cell types specific function. Importantly, we could images the open chromatin distribution and do the sequencing on the exactly same sample, which offer a powerful tool to understand how the open chromatin organize in the 3D nucleus and how the open chromatin regulate gene expression.
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| Overall design |
We had compared the ATAC-seq libraries under different conditions such as with different Tn5s (Illumina Nextera Tn5, home-made Tn5 with and without Atto labeled on the adaptors in GM12878 cells), with and without fixation (in HT1080 cells ) and the cells growing on different materials (growing HT1080 cells on slide and suspensions cells in the tubes). In addition, we had performed ATAC-seq in human neutrophil.
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| Contributor(s) |
Chen X, Shen Y, Chang HY |
| Citation(s) |
27749837 |
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| Submission date |
Dec 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xingqi Chen |
| E-mail(s) |
xingqi@stanford.edu
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| Organization name |
Stanford University
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| Lab |
Howard Chang's lab
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| Street address |
269 Campus Drive
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| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94305-5168 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (22)
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| Relations |
| BioProject |
PRJNA305986 |
| SRA |
SRP067388 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE76006_RAW.tar |
20.3 Gb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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