Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SiRNA ELK1 depletion and EGF stimulation

ABSTRACT: ELK1 is a well-known target of the ERK branch (EGF-responsive) of the MAP kinase pathway. This transcription profiling experiment studied the effects of ELK1 depletion by siRNA and subsequent EGF stimulation.

ORGANISM(S): Homo sapiens

SUBMITTER: Leo Zeef

PROVIDER: E-MEXP-3407 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

ELK1 uses different DNA binding modes to regulate functionally distinct classes of target genes.

Odrowaz Zaneta Z Sharrocks Andrew D AD

PLoS genetics 20120510 5

Eukaryotic transcription factors are grouped into families and, due to their similar DNA binding domains, often have the potential to bind to the same genomic regions. This can lead to redundancy at the level of DNA binding, and mechanisms are required to generate specific functional outcomes that enable distinct gene expression programmes to be controlled by a particular transcription factor. Here we used ChIP-seq to uncover two distinct binding modes for the ETS transcription factor ELK1. In o ...[more]

PMID: 22589737

Similar Datasets

Transcription profiling by array of siRNA silencing of GABPA in MCF10A cells

Project description:The ETS transcription factor GABPA controls cell migration in breast epithelial cells through targeting a cohort of genes, independently from another family member ELK1, and thereby achieves biological specificity. Here, both direct and indirect target genes for GABPA are identified by siRNA silencing of GABPA. Therefore, although ELK1 and GABPA ultimately control the same biological process, they do so by regulating distinct cohorts of target genes associated with actin cytoskeletal functions and cell migration control.

2013-07-15 | E-MEXP-3682 | biostudies-arrayexpress

RNA-seq of MCF10A cells at 4 time points in 3 hours following EGF addition

Project description:Sequencing the nuclear RNA in MCF10A cells by RNA-seq at the 4 time points, 0, 30, 90, and 180 minutes following EGF addition.

2021-11-11 | E-MTAB-9881 | biostudies-arrayexpress

A Splice Variant of HER2 Activates Key Signaling Cascades and Evokes Mammary Tumors and Metastases

Project description:The Epidermal Growth Factor Receptor 2 (ERBB2 or HER2) is amplified and overexpressed in approximately 20% of invasive breast cancers and is associated with metastasis and poor prognosis. Here we describe the role of a constitutively active splice variant of HER2 (Delta-HER2) in human mammary epithelial cells. Overexpression of Delta-HER2 in human mammary cells decreased apoptosis and increased proliferation and expression of epithelial-to-mesenchymal markers. It also induced invasion in three-dimensional cultures and promoted tumorigenicity and metastasis in vivo. In contrast, similar overexpression of wild-type HER2 failed to evoke the same effects. Unbiased protein-tyrosine phosphorylation profiling revealed a significant increase in phosphorylation of several key signaling proteins upon Delta-HER2 expression, some of which not previously shown to belong to the HER2 pathway. In addition, microarray analysis revealed the expression of a set of genes specifically associated with Delta-HER2 expression. We found those genes to be highly expressed in ER-negative, high grade and metastatic primary breast tumors. Altogether, these results provide new insights into the function of a tumorigenic splice variant of HER2 and the signaling cascade deriving from its activity RNA was extracted from MCF10A expressing empty vector, WT-HER2 or Delta-HER2 (n=3).

2013-10-22 | E-GEOD-42781 | biostudies-arrayexpress

Proteomic breast cancer data set for exploring somatic mutations

Project description:MCF7, SKBR3 (breast cancer) and MCF10 (non-tumorigenic) cell extracts were explored by LC-MS/MS for the identification of protein-level mutations.

2019-07-25 | PXD014458 | Pride

Transcription profiling by array of human female interstitial cystitis urothelial cells after inducing differentiation

Project description:Purpose: Evaluate gene expression profiles after inducing differentiation in cultured interstitial cystitis (IC) and control urothelial cells. Materials and Methods: Bladder biopsies were taken from IC patients and controls (women having surgery for stress incontinence). Primary cultures were grown in Keratinocyte Growth Medium with supplements. To induce differentiation, in some plates the medium was changed to DMEM-F12 with supplements. RNA was analyzed with Affymetrix chips. Three nonulcer IC patients were compared with three controls. Results: After inducing differentiation, 302 genes with a described function were altered at least 3-fold with p <0.01 in both IC and control cells. Functions of the162 upregulated genes included cell adhesion (e.g. claudins, occludin, cingulin); urothelial differentiation, retinoic acid pathway and keratinocyte differentiation (e.g. skin cornified envelope components). The 140 downregulated genes included genes associated with basal urothelium (e.g. p63, integrins ?4, ?5 and ?6, basonuclin 1 and extracellular matrix components), vimentin, metallothioneins and members of the Wnt and Notch pathways. Comparing IC vs. control cells after differentiation, only seven genes with a described function were altered at least 3-fold with p <0.01. PI3, SERPINB4, CYP2C8, EFEMP2 and SEPP1 were decreased in IC; AKR1C2 and MKNK1 were increased in IC. Conclusions: Differentiation-associated changes occurred in both IC and control cells. Comparing IC vs. control revealed very few differences. This study may have included IC patients with minimal urothelial deficiency and/or selected the cells that were most robust in culture. Also, the abnormal urothelium in IC may be due to post-translational changes and/or the bladder environment. Experiment Overall Design: Human female urothelial cell cultures, differentiated vs. non-differentiated,interstitial cystitis vs. control

2008-10-25 | E-GEOD-11839 | biostudies-arrayexpress

The CASP3 Prodomain Regulates Human Cell Survival and Proliferation

Project description:CASPASE-3 (CASP3) is well known for its proteolytic function that mediates multiple key cell death-initiated processes and other related cellular processes. However, the possibility that CASP3 may also possess important additional non-catalytic functions in mammalian cells has remained largely unexplored. We now report the results of CASP3 knockdown, rescue, proteomic analysis and flow cytometry experiments initially in normal and malignant human mammary cells and later shown to extent to all other human cell types tested. The results reveal a new role of the CASP3 prodomain in regulating the cell cycle progression, survival, proliferation, and protein aggregate accumulation in all cells tested. The generality of these findings suggests that the ancestral pro-survival role of CASP3 in yeast persisted throughout evolution via a conservation of its prodomain, predating its later acquisition of an inherent catalytic property and subsequently preserved cell death control functions.

2024-01-17 | PXD045234 | Pride

ELK1 ChIP-seq

Project description:Chromatin immunoprecipitation of ELK1 in MCF10A cells detected by SOLiD sequencing

2012-08-20 | E-MTAB-830 | biostudies-arrayexpress

Overexpression of PHF8 promotes an EMT-related gene signature in MCF10A cells

Project description:PHF8 exerts distinct functions in different types of cancer. However, the mechanisms underlying its specific functions in each case remain obscure. To establish whether overexpression of PHF8 regulates the TGF-Î² induced the epithelial-mesenchymal transition (EMT), we treated MCF10A-Mock (control) and MCF10A-PHF8wt (overexpressing wild-type PHF8) cells with TGF-Î²1 for 0, 24, 48 and 72 hours and performed RNA-seq in biological duplicates. Our data indicated that EMT gene signatures were significantly enriched in MCF10A-PHF8 cells with TGF-Î²1 treatment at all time points, strongly indicating that PHF8 overexpression induces a sustained EMT signaling program. mRNA profiles of MCF10A-Mock (control) and MCF10A-PHF8 with TGF-Î²1 treatment for 0, 24, 48 and 72 hours were generated by RNA-seq, in duplicate, using HiSeq2500 instrument.

2016-10-26 | E-GEOD-74377 | biostudies-arrayexpress

Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells

Project description:Background: Higher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been charted between normal and breast cancer tissues, changes in higher-order chromatin organization during tumorigenesis have not been fully explored. To probe the differences in higher-order chromatin structure between mammary epithelial and breast cancer cells, we performed Hi-C analysis on MCF-10A mammary epithelial and MCF-7 breast cancer cell lines. Results: Our studies reveal that the small, gene-rich chromosomes chr16 through chr22 in the MCF-7 breast cancer genome display decreased interaction frequency with each other compared to the inter-chromosomal interaction frequency in the MCF-10A epithelial cells. Interestingly, this finding is associated with a higher occurrence of open compartments on chr16-22 in MCF-7 cells. Pathway analysis of the MCF-7 up-regulated genes located in altered compartment regions on chr16-22 reveals pathways related to repression of WNT signalling. There are also differences in intra-chromosomal interactions between the cell lines; telomeric and sub-telomeric regions in the MCF-10A cells display more frequent interactions than are observed in the MCF-7 cells. Conclusions: We show evidence of an intricate relationship between chromosomal organization and gene expression between epithelial and breast cancer cells. Importantly, this work provides a genome-wide view of higher-order chromatin dynamics and a resource for studying higher-order chromatin interactions in two cell lines commonly used to study the progression of breast cancer. Hi-C experiments were conducted in MCF-7 and MCF-10A parental cells. The RNA-seq data associated with this study is deposited under the GEO accession number GSE71862.

2015-09-02 | E-GEOD-66733 | biostudies-arrayexpress

Transcriptional profiling of 7SK knockdown in mouse embryonic stem cells

Project description:Transcriptome profiling of mouse embryonic stem cells following antisense knockdown of the non-coding RNA 7SK.

2013-09-09 | E-MTAB-1585 | biostudies-arrayexpress