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| Status |
Public on Sep 27, 2019 |
| Title |
Selective Disruption of Core Regulatory Transcription [AQuA-HiChIP] |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
With emerging methods recently developed to capture protein-anchored 3D epigenome folding we herein report an experimental advance yielding a fundamental and systematic improvement in understanding the 3D genome: integrated normalization of orthologous chromatin for measurement of absolute changes in the landscape. With Absolute Quantification of chromatin Architecture (AQuA-HiChIP) global and local changes in the 3D epigenome can be measured, and the absolute differences in protein-anchored folding can be determined. These changes can be defined in a way that couples the relative occupancy of chromatin regulatory factors or histone marks to absolute quantification of 3D chromatin structure. While our method has intrinsic limitations, including restriction by the scope of available ChIP-grade antibodies with mouse/human cross-reactivity, the approach to measuring absolute components of chromatin folding will enable new insights into the topological determinants of transcriptional control and tissue-specific epigenetic memory.
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| |
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| Overall design |
Genome-wide 3D interaction profiles as mediated by H3K27ac histone marks, in Rhabdomyosarcoma (RMS) cell lines before and after HDAC inhibition
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| |
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| Contributor(s) |
Gryder BE, Wen X, Khan J |
| Citation(s) |
31285436 |
| Submission date |
Oct 02, 2018 |
| Last update date |
Dec 27, 2019 |
| Contact name |
Nitin Roper |
| E-mail(s) |
nitin.roper@nih.gov
|
| Phone |
2408583571
|
| Organization name |
NCI, NIH
|
| Department |
Developmental Therapeutics Branch
|
| Street address |
37 Convent Dr.
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (1) |
| GPL19415 |
Illumina NextSeq 500 (Homo sapiens; Mus musculus) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE120771 |
Selective Disruption of Core Regulatory Transcription |
|
| Relations |
| BioProject |
PRJNA494423 |
| SRA |
SRP163153 |
