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Series GSE116868 Query DataSets for GSE116868
Status Public on Feb 27, 2019
Title Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques [MB157_ChIP-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Purpose: To investigate the impact of oncogenic Notch on the 3D genome organization of cancer cells.
Methods: We generated cohesin HiChIP and 1D epigenomic data sets in two different Notch-dependent cancer cell types, triple-negative breast cancer (TNBC) and mantle cell lymphoma (MCL), in the Notch-on and -off states.
Results: We report here that Notch transcription complexes control their direct target genes through two distinct regulatory modes: either through existing loops or by facilitating new long-range regulatory interactions. This combination of pre-existing and Notch-promoted loops coalesce enhancers and promoters to form highly interacting clusters, termed “3D cliques”. Notch preferentially activates enhancers and promotes looping interactions within highly connected 3D cliques that regulate key oncogenes.
Conclusions: These observations suggest a general mechanism that oncogenic transcription factors can exploit to regulate the transcriptional outputs of cancer cells.
Overall design ChIP-seq, RNA-seq and HiChIP in Notch-on, -off, -recovery conditions in TNBC and MCL cell lines to profile Notch transcriptional complex binding, histone modification, Notch target genes and contact between regulatory elements.
Contributor(s) Zhou Y, Petrovic J, Faryabi R
Citation(s) 30745086
Submission date Jul 10, 2018
Last update date May 05, 2021
Contact name YEQIAO ZHOU
Phone (215)573-8220
Organization name University of Pennsylvania
Department Pathology
Lab Faryabi
Street address 421 Curie Boulevard
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (25)
GSM3263143 MB157_GSI_H3K27ac_ChIPseq_rep1
GSM3263144 MB157_GSI_H3K27ac_ChIPseq_rep2
GSM3263145 MB157_WO_H3K27ac_ChIPseq_rep1
This SubSeries is part of SuperSeries:
GSE116876 Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques
BioProject PRJNA480472
SRA SRP152956

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Supplementary file Size Download File type/resource
GSE116868_RAW.tar 9.2 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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