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| Status |
Public on Apr 27, 2017 |
| Title |
Chromatin looping evidence between PAX3-FOXO1 bound super enhancer and MYOD1 promoter [4C-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
Circular chromatin confirmation capture in rhabdomyosarcoma cells was performed with viewpoints at the PAX3-FOXO1 bound super enhancer upstream of MYOD1, and also at the MYOD1 promoter, to find support for looping between these two genetic elements almost 80 thousand base pairs apart.
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| Overall design |
4C-seq was performed on fixed cells, which were exposed to 4-bp cutter DpnII for the primary restriction enzyme, re-ligated in dilute conditions, followed by reversal of crosslinks and purification. Csp6I was used to reduce template to sizes amenable to inverse PCR for viewpoint amplification. 4C samples of RMS cell line (RH4) were amplified at anchors within the viewpoint.
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| Contributor(s) |
Gryder BE, Wen X |
| Citation(s) |
28446439, 32744500 |
| Submission date |
Jun 26, 2016 |
| Last update date |
May 06, 2021 |
| Contact name |
Javed Khan |
| E-mail(s) |
khanjav@mail.nih.gov
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| Phone |
2407606135
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| Organization name |
NCI, NIH
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| Department |
Genetics Branch
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| Lab |
Javed Khan
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| Street address |
37 Convent Dr.
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE83728 |
Epigenetic Lanscape and BRD4 Transcriptional Dependency of PAX3-FOXO1 Driven Rhabdomyosarcoma |
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| Relations |
| BioProject |
PRJNA326876 |
| SRA |
SRP077228 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE83727_RAW.tar |
1.2 Mb |
(http)(custom) |
TAR (of BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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