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Series GSE83727 Query DataSets for GSE83727
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
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.
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.
Contributor(s) Gryder BE, Wen X
Citation(s) 28446439, 32744500
Submission date Jun 26, 2016
Last update date May 06, 2021
Contact name Nitin Roper
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
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (2)
GSM2214146 RH4 MYOD1 promoter 4C
GSM2214147 RH4 MYOD1 super enhancer 4C
This SubSeries is part of SuperSeries:
GSE83728 Epigenetic Lanscape and BRD4 Transcriptional Dependency of PAX3-FOXO1 Driven Rhabdomyosarcoma
BioProject PRJNA326876
SRA SRP077228

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE83727_RAW.tar 1.2 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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