Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genomic Profiling of MYC in 797 cells containing BRD4-NUT with JQ1 treatment

ABSTRACT: Genomic Profiling of MYC in 797 cells containing BRD4-NUT with JQ1 treatment

PROVIDER: PRJNA828125 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18810456.fastq.gz	Fastqsanger.gz
	SRR18810458.fastq.gz	Fastqsanger.gz
	SRR18810460.fastq.gz	Fastqsanger.gz
	SRR18810462.fastq.gz	Fastqsanger.gz
	SRR18810464.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

ChIP-seq analysis of BRD4-NUT and H3K27ac distribution in NUT Carcinoma cell line TC-797 treated with DMSO or Panobinostat

Project description:BRD4-NUT and H3K27ac are depleted from megadomains in NUT Carcinoma (NC) cell line TC-797 after treatment with Panobinostat.

2021-07-14 | GSE179692 | GEO

Genomic Profiling of MYC in 797 cells containing BRD4-NUT with JQ1 treatment

Project description:The oncogene cMYC (HGNC ID: HGNC:7553) is a critical genomic target of the BRD4-NUT (B4N) protein that defines many of the NUTM1-rearrangement cancer subtypes. B4N interacts with the EP300 lysine acetyltransferase (KAT) to create hyperacetylated “megadomains” that activate downstream genes such as MYC. However, it is less well understood how mis-regulation of MYC in turn affects its protein interactions and target genes. The goals of this study are to define the protein and genomic interactions of MYC in NUT carcinoma, and to test whether those change in response to B4N inactivation. We used CRISPR-Cas9 mediated knock-in of a BioTAP affinity tag to analyze MYC protein expressed from its normal chromosomal context. This allowed us to adapt a crosslinking purification method termed BioTAP-XL to preserve MYC integrity and chromatin association for genomic and mass spectrometry-based proteomic analyses. We found that MYC interacts primarily with NuA4 KAT subunits and that the interactions were maintained despite a decrease in MYC levels after JQ1 treatment. We propose that future analysis of MYC transcriptional regulation in NUT carcinoma, and likely other cancers, should prioritize how MYC recruits KAT complexes to modify the chromatin of its many gene targets.

2022-04-27 | GSE201033 | GEO

Differentiation of NUT midline carcinoma by epigenomic reprogramming

Project description:Knockdown of the oncogene, BRD4-NUT, in a rare cancer, termed NUTmidline carcinoma (NMC), results in morphologic features consistent with squamous differentiation. Treatment with the HDAC-inhibitor, TSA, appears to cause the same phenotype. Here, we use gene expression profiling to compare the changes in gene expression following BRD4-NUT knockdown and TSA treatment. RNA was extracted from two BRD4-NUT-expressing NMC cell lines, PER-403 and TC-797, 24h following siRNA knockdown versus control in duplicate. RNA was extracted from two BRD4-NUT-expressing NMC cell lines, PER-403 and TC-797, 24h following treatment with TSA versus etoh control in triplicate

2011-07-01 | E-GEOD-18668 | biostudies-arrayexpress

Oncogenic BRD4-NUT protein interactions

Project description:To investigate the mechanism that drives dramatic mistargeting of active chromatin in NUT midline carcinoma, we have identified protein interactions unique to the BRD4-NUT fusion oncoprotein compared to wild type BRD4. Using crosslinking, affinity purification, and mass spectrometry, we identified the EP300 acetyltransferase as uniquely associated with BRD4 through the NUT fusion in both NMC and non-NMC cell types. We also discovered ZNF532 among a small number of candidates associated with BRD4-NUT in NMC patient cells but not present in 293T cells.

2017-04-05 | PXD005786 | Pride

H3K9/14Ac in TC-797 genome

Project description:The goal is to localize "active" histone marks known to bind BRD4-NUT in the NMC genome. Characterization of the reference epigenome in humans by use of ChIP-Seq in the TC-797 human NMC cell line. ChIP-seq of untreated TC-797 cells using H3K9/14Ac antibodies versus IgG control.

2013-03-05 | E-GEOD-36512 | biostudies-arrayexpress

H3K9/14Ac in TC-797 genome

2013-03-05 | GSE36512 | GEO

Chip-seq BRD4NUT-BioTAP mapping in 293Trex and 797 cells

Project description:BRD4-NUT megadomains is an order of magnitude larger than super-enhancer regions and displays a more continuously enriched profile rather than appearing as a cluster of individual peaks. Chip-seq BRD4NUT-BioTAP mapping in 293Trex and 797 cells

2015-07-14 | E-GEOD-70869 | biostudies-arrayexpress

Chip-seq mapping of active chromatin marks in BRD4-NUT and different NMC cells

2015-07-14 | E-GEOD-70870 | biostudies-arrayexpress

Recovery and analysis of nascent RNA

Project description:Nascent transcription profiles are shown for scaled megadomains and 100kb flanking regions before BRD4-NUT induction (0h) and at different time points (2h, 3h, 7h) following induction in 293T cells. Increase of the transcription from 0h to 7h after induction. Average level of transcriptional activity is reduced within the megadomains and their flanking regions following JQ1 treatment of TC-797 cells. Profile of nascent RNA-seq is shown for cells without JQ1 treatment, and for cells 1hr, 2.5hr and 4hr following JQ1 treatment. Recovery and analysis of nascent RNA

2015-07-14 | E-GEOD-70871 | biostudies-arrayexpress

ChIP-seq analysis of BRD4-NUT and H3K27ac distribution in NUT Carcinoma cell line TC-797 treated with DMSO or Panobinostat

Project description:ChIP-seq analysis of BRD4-NUT and H3K27ac distribution in NUT Carcinoma cell line TC-797 treated with DMSO or Panobinostat

| PRJNA744553 | ENA