GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE120770 Query DataSets for GSE120770
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.
Overall design Genome-wide 3D interaction profiles as mediated by H3K27ac histone marks, in Rhabdomyosarcoma (RMS) cell lines before and after HDAC inhibition
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
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)
GPL19415 Illumina NextSeq 500 (Homo sapiens; Mus musculus)
Samples (2)
GSM3414982 RH4 Entinostat AQuA-HiChIP
This SubSeries is part of SuperSeries:
GSE120771 Selective Disruption of Core Regulatory Transcription
BioProject PRJNA494423
SRA SRP163153

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE120770_RAW.tar 441.4 Mb (http)(custom) TAR (of HIC)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap