Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ectopic expression of wild-type Cop Fry in MDA-MB-231 cells

ABSTRACT: We identified the wt Cop allele of the predicted Fry gene as a mammary carcinoma susceptibility gene. This gene has not been characterized in mammals, so for part of our analysis we conducted microarray experiments to look at the changes in gene expression which occur when the wt Cop Fry allele is ectopically expressed in the MDA-MB-231 breast cancer cell line (a cell line which we identified as having low FRY mRNA expression). We used microarrays to identify the Fry interactome and identified that Fry affects the expression of gene networks that maintain normal cellular and tissue architecture, organization, differentiation of epithelial cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE36441 | GEO | 2014/12/31

SECONDARY ACCESSION(S): PRJNA153185

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Expression of FRY-targeting shRNA in MCF10A cells

Project description:We identified the predicted FRY gene as a candidate mammary carcinoma susceptibility gene. This gene has not been characterized in mammals, so for part of our analysis we conducted microarray experiments to look at the changes in gene expression which occur when FRY-targeting shRNA is expressed in the nontumorigenic MCF10A mammary epithelial cell line (a cell line which we identified as having higher FRY mRNA expression than breast cancer cell lines). We used microarrays to identify the FRY interactome and identified that FRY affects the expression of gene networks that maintain normal cellular and tissue architecture, organization, differentiation of epithelial cells.

2014-12-31 | GSE35928 | GEO

Panicum virgatum strain:COP | cultivar:COP

Project description:Panicum virgatum COP Resequencing genome sequencing

| PRJNA334728 | ENA

Alfa2-COP is involved in early secretory traffic in Arabidopsis and it is required for plant growth

Project description:The loss-of-function mutants of alfa1-COP (alfa1-COP-1) and alfa2-COP (alfa2-COP1), the two alfa-COP isoforms of Arabidopsis. Unlike in alfa1-COP mutant, the alfa2-COP mutant displays defects in plant growth, including small rosettes, stems and roots and mislocalization of p24a5, a protein containing a C-terminal dylisine motif involved in COPI binding. In addition, it exhibited abnormal morphology of the Golgi apparatus. Global expression analyses of the alfa2-COP mutant versus wild-type Arabidopsis plants reveal altered expression of plant cell wall-associated genes. A high expression of the COPII sec31A isoform was observed in the alfa2-COP mutant that also occurs in a mutant of an upstream gene of COPI assembly, the ARF-GEF GNL1

2016-12-01 | GSE81049 | GEO

Hi-CoP, a simple and robust assay for detecting interactions of regulatory regions

Project description:First we developed a new, simple, and robust assay called CoP (Column Purified chromatin) for profiling of accessible regions by directly purifying fragmentized crosslinked chromatin with DNA purification column. The CoP chromatin regions by CoP-seq are consistent with the accessible regions detected by ATAC-seq and FARIE-seq. Then we integrated CoP-seq and Hi-C technique (Hi-CoP) for interactions of accessible chromatin regions which represent active cis-regulatory elements in cells. Our data showed that Hi-CoP assay can robustly detect interactions of regulatory regions.

2020-01-29 | GSE144412 | GEO

Revealing nascent RNA processing dynamics with nano-COP

Project description:During maturation, eukaryotic precursor RNAs undergo processing events including intron splicing, 3’-end cleavage, and polyadenylation. Here, we describe nanopore analysis of CO-transcriptional Processing (nano-COP), a method for probing the timing and patterns of RNA processing. An extension of native elongating transcript sequencing (NET-seq), which quantifies transcription genome-wide through short-read sequencing of nascent RNA 3’ ends, nano-COP uses long-read nascent RNA sequencing to observe global patterns of RNA processing. First, nascent RNA is stringently purified through a combination of 4-thiouridine metabolic labeling and cellular fractionation. In contrast to cDNA or short-read–based approaches relying on reverse transcription or amplification, the sample is sequenced directly through nanopores to reveal the native context of nascent RNA. nano-COP identifies both active transcription sites and splice isoforms of single RNA molecules during synthesis, providing insight into patterns of intron removal and the physical coupling between transcription and splicing. The nano-COP protocol yields data within 3 days.

2021-01-06 | GSE154079 | GEO

Comparative genomic hybridization of 3 rat strains BN, SS and COP

Project description:Nimblegen RN34_WG array for BN, SS and COP rats

2008-04-13 | E-MEXP-1517 | biostudies-arrayexpress

FRY Impacts Breast Cancer Malignancy by Inducing an Enrichment of Genes with Tumor-Suppressive Functions and Affecting EMT Potential of Breast Cancer Cells

Project description:Breast cancer is a disease with diverse phenotypes, and while the progression of breast cancer from a localized lesion to metastatic disease is well understood clinically. Our previous study genetically linked the FRY gene with differential susceptibility to mammary carcinogenesis; however, little is known about the mechanistic insights of FRY in mammalian cells and breast cancer progression. Through RNA-Seq analysis of series of constructed cell lines based on highly malignant triple-negative human breast cancer cells MDA-MB-231, we show that enhanced FRY induces massive changes in gene expression, which favor signalings and molecules with tumor-suppressive functions and engage in promoting cell differentiation, maintaining the normal and histopathological characteristics of epithelial cells, and in regulating EMT potential of breast cancer cells. As a result, the proliferation, migration and invasion potentials of breast cancer cells are significantly inhibited both in vitro and in xenograft tumor models. Importantly, consistent with FRY’s anti-tumor progression role, decreased FRY protein levels are correlated with poorly differentiated and aggressive tumor phenotypes in the analysis of two clinically annotated breast cancer cohorts. Our results identify FRY’s potent tumor-suppressive role at the gene transcription and molecular function levels, providing a novel biomarker for breast cancer prognosis and a target for therapeutic intervention.

2019-05-01 | GSE112910 | GEO

Transcription profiling of heart left ventricles from 15 week old inbred COP, DA, and F1(COP x DA) offspring with respect to aerobic running capacity (low, high, and intermediate performers respectively)

Project description:We used high density oligonucleotide arrays to measure the relative expression levels of ~27,000 probe sets in the left ventricles of inbred rat strains; DA (high performing), Copenhagen (COP, low performing), as well as F1(COPxDA) rats bred from these tw

2007-09-13 | E-GEOD-1795 | biostudies-arrayexpress

Transcription profiling of rat strains Cop AND F334 mammary gland treated WITH N-nitrosomethylurea (NMU), TIME series

Project description:Gene expression profiles in mammary glands of different rat strains are genetically defined. Experiment Overall Design: 18 Cop rats with or without N-nitrosomethylurea (NMU) treatment at 6h, 1d, and 30 d compared to 18 F344 rats with or without NMU treatment at 6h, 1d, and 30 day

2008-04-07 | E-GEOD-10641 | biostudies-arrayexpress

Revealing nascent RNA processing dynamics with nano-COP

Project description:Revealing nascent RNA processing dynamics with nano-COP

| PRJNA645078 | ENA