Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

51 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Requirement for the Mediator kinase module for activation of super-enhancer associated genes in colon cancer cells

ABSTRACT: RNA sequencing of HCT116 colon cancer cells following single and combined depletions of Mediator kinase module subunits CDK8, CDK19, MED12, MED13 and MED13L and the BET family protein BRD4. The results provide insight into the shared and specific functions of kinase module subunits and BRD4 in regulation of expression of transcriptional programs including genes associated with cancer acquired super-enhancers.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Eva Domenech-Moreno

PROVIDER: E-MTAB-5873 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of the primary patient-derived GBM cell line G797 following siRNA-mediated knockdown and pcDNA3.1-Neomycin-mediated overexpression of the lncRNA HOXA10-AS

Project description:We used a machine-learning framework to systematically discover prognostic long non-coding RNAs (lncRNAs) in 9,446 patient tumors of 30 types. We identified 166 prognostic lncRNAs whose transcript abundance correlated with patient risk and improved the performance of common clinical variables and molecular tumor subtypes. In lower-grade gliomas, discrete activation of HOXA10-AS indicated poor patient prognosis, neurodevelopmental pathway activation and a transcriptomic similarity to glioblastomas. To understand the role of HOXA10-AS in the hallmark pathways of glioma, we used RNA-seq to profile the patient-derived G797 glioma cells with siRNA-mediated HOXA10-AS knockdown (KD) and pcDNA3.1-Neomycin-mediated overexpression (OE) phenotypes. Both KD and OE were validated using RT-PCR. We found a pronounced transcriptional response to HOXA10-AS deregulation with 1,715 and 408 differentially expressed protein-coding genes detected in KD and OE cells, respectively (FDR < 0.05, absolute FC > 1.2), including 23 genes detected in both experiments, as well as known genes involved in glioma biology and Hippo signaling. Our study underscores the pan-cancer potential of the non-coding transcriptome for developing molecular biomarkers and innovative therapeutic strategies.

2021-10-02 | E-MTAB-10944 | biostudies-arrayexpress

Barcoded mRNA-seq of murine brown preadipocytes (IBA) upon transcriptomic perturbation

Project description:Loss of function assays were performed in differentiating IBAs using short hairpin RNAs (shRNAs) against a set of candidate transcription factors: NFIA, DBP, HOXA4, ZFP467, SOX18, ELF3, YBX2 and PPARa. Gene expression profiles of the perturbed and non perturbed (controls including non transduced cells, cells transduced with scrambled and GFP constructs) transcriptomes were measured at Day 6 of differentiation using a novel multiplex, bulk mRNA-seq barcoding method which employs a 3' sequencing approach. This method allowed the measurement of the deviation of the perturbed transcriptome from the non-perturbed transcriptome.

2017-09-21 | E-MTAB-5161 | biostudies-arrayexpress

Ubiquitin-dependent turnover of MYC promotes loading of the PAF complex on RNA Polymerase II to drive transcriptional elongation (RNA-seq)

Project description:The MYC transcription factor is an unstable protein and its turnover is controlled by the ubiquitin system. Ubiquitination enhances MYC-dependent transactivation, but the underlying mechanism remains unresolved. Here we show that proteasomal turnover of MYC is dispensable for recruitment of RNA polymerase II (RNAPII), but is required to promote transcriptional elongation at MYC target genes. Degradation of MYC stimulates histone acetylation and recruitment of BRD4 and P-TEFb to target promoters, leading to phosphorylation of RNAPII CTD and the release of elongating RNAPII. In the absence of degradation, the RNA polymerase II-associated factor (PAF) complex associates with MYC via interaction of its CDC73 subunit with a conserved domain in the amino-terminus of MYC ("MYC box I"), suggesting that a MYC/PAF complex is an intermediate in transcriptional activation. Since histone acetylation depends on a second highly conserved domain in MYCs amino-terminus ("MYC box II"), we propose that both domains co-operate to transfer elongation factors onto paused RNAPII. RNA-Seq Experiments were performed in a primary breast epithelial cell line (IMEC).The cell line expressed doxycycline-inducible versions of MYC (WT;Kless,Swap=WTN-KC). Where indicated cells were transfected with siRNAs (siCtrl;siSKP2). Where indicated cells were treaed with the proteasome inhibitor MG132 or EtOH as solvent control. DGE was performed by comparing Dox-treated populations expressing either Dox-inducible MYC or a vector control or comparing Dox-induced cells with EtOH (solvent control) treated cells.

2016-01-04 | E-GEOD-70000 | biostudies-arrayexpress

Regulation of the KEAP1/NRF2 oxidative stress response pathway by BRD4 in prostate and colorectal cancer

Project description:To identify genes regulated by BRD4 and to provide insight into new mechanisms de-regulated by BRD4, such as the response to oxidative stress, we integrated BRD4-binding regions with BRD4 gene expression data. For this analysis we performed BRD4 chromatin immunoprecipitation experiments and BRD4 knock down experiments followed by RNA-Seq analyses. By integration of both gene lists we identified top candidate genes regulated by BRD4. HEK cells have been investigated for genomewide BRD4 binding sites and expression changes after knock down of BRD4. Illumina sequencing was used to gather data of the type ChIP Seq and mRNA Seq.

2014-02-28 | E-GEOD-50491 | biostudies-arrayexpress

RNA-seq analysis of vorinostat-resistant HCT116 cells following gene knockdown of potential vorinostat-resistance candidate genes

Project description:Potential vorinostat-resistance candidate genes were identified using RNA interference screening in vorinostat-resistant HCT116 cells (HCT116-VR) using a synthetic lethal approach. In order to understand the mechanisms by which these genes contributed to vorinostat response, transcriptomic analysis was conducted on HCT116-VR cells and those with siRNA-mediated knockdown of each of the vorinostat resistance candidate genes. There are 45 samples in total, from triplicate independent biological experiments of 15 samples each. The negative control to which all gene knockdowns are compared is the mock transfection control (mock).

2014-07-07 | E-GEOD-56788 | biostudies-arrayexpress

RNA-seq of JAK2VF and DNMT3A mutant Myelofibrosis patients

Project description:Determination of differentially expressed genes from peripheral blood of Myelofibrosis patients with JAK2VF and JAK2VF and DNMT3A mutations

2018-12-01 | E-MTAB-7255 | biostudies-arrayexpress

RNA-seq of Jak2VF LSK cells transduced with Dnmt3a-Cas9-GFP lentivirus vs. emp-Cas9-GFP controls 8 weeks post transplantation

Project description:Determination of differentially expressed genes from in vivo hematopoietic stem cell progenitors (LSK) in Jak2VF-emp-Cas9 and Jak2VF-Dnmt3a-Cas9 8 weeks post transplantation.

2018-10-29 | E-MTAB-6644 | biostudies-arrayexpress

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

RNA-seq of Jak2VF LSK cells transduced with Dnmt3a-Cas9-GFP lentivirus vs. emp-Cas9-GFP controls one week and five weeks post methylcellulose plating

Project description:Determination of differentially expressed genes in culture-derived hematopoietic stem cell progenitors (LSK) between Jak2VF-emp-Cas9 and Jak2VF-Dnmt3a-cas9.

2018-10-29 | E-MTAB-6635 | biostudies-arrayexpress

RNAseq analysis of colon and ileum tissue from naive wild type, MR1-/- and IL-17A-/- mice

Project description:Determination of differentially expressed genes in the proximal colon and distal ileum tissue in MR1 and IL-17A deficiency at steady-state. Tissue from naïve mice was harvested, total RNA extracted and subjected to RNASeq analysis.

2018-03-31 | E-MTAB-6547 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data