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Identification of dysregulated genes in 3D culture of BRIP1 knockdown cells

ABSTRACT: To identify down-stream target genes of BRIP1 during acinar morphogenesis of human mammary epithelial cells, we carried out microarray analysis of BRIP1 knockdown cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE33218 | GEO | 2013/10/21

SECONDARY ACCESSION(S): PRJNA149449

REPOSITORIES: GEO

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Identification of dysregulated genes in 3D culture of BRIP1 knockdown cells

Project description:To identify down-stream target genes of BRIP1 during acinar morphogenesis of human mammary epithelial cells, we carried out microarray analysis of BRIP1 knockdown cells. Changes in gene expression in 3D culture of non-target and BRIP1 shRNA-transduced cells were analyzed. Samples were harvested from three different clones of non-target and BRIP1 shRNA-transduced cells at three time points, 4, 8, and 12 days, after cell seeding in Matrigel.

2013-10-21 | E-GEOD-33218 | biostudies-arrayexpress

Expression profiling of MCF10A cells in 2D and 3D culture

Project description:In these microarray experiments, we characterize the gene expression of mammary epithelial cells (MCF10A cells) grown in either a traditional monolayer cell culture setting (2D) or on Matrigel, which induces single MCF10A cells to form organized acinar structures (3D). Morphogenesis of mammary epithelial cells into organized acinar structures in vitro is accompanied by widespread changes in gene expression patterns, including a substantial decrease in expression of Myc. The purpose of this study was to analyze the impact of morphogenesis and organization on gene expression with respect to changes in overall gene expression and Myc target gene expression. MCF10A cells were cultured in 2D for either 2 or 5 days (3 biological replicates each) or in 3D for 8 or 16 days (3 or 5 biological replicates, respectively)

2011-06-01 | E-GEOD-26148 | biostudies-arrayexpress

Expression profiling of MCF10A cells in 2D and 3D culture

2011-06-01 | GSE26148 | GEO

Changes in gene expression during acinar morphogenesis of normal-like human mammary epithelial cells in a 3D basement membrane cultures

Project description:In this study, we examined temporal changes in gene expression during acinar morphogenesis of normal-like human mammary epithelial cells (MCF-10A) in a three-dimensional (3D) basement membrane cultures. Changes in gene expression in 3D culture of MCF-10A cells were measured at 4, 8, and 12 days.

2013-12-01 | E-GEOD-33354 | biostudies-arrayexpress

Changes in gene expression during acinar morphogenesis of normal-like human mammary epithelial cells in a 3D basement membrane cultures

2013-12-01 | GSE33354 | GEO

Homo sapiens

Project description:Mutant p53 Disrupts Mammary Acinar Morphogenesis via the Mevalonate Pathway

| PRJNA145251 | ENA

E-GEOD-31812

Project description:Mutant p53 Disrupts Mammary Acinar Morphogenesis via the Mevalonate Pathway

2015-08-17 | E-GEOD-31812 | ExpressionAtlas

Gene expression profiling of PDX-derived lung squamous carcinoma cells (TUM622) grown in 2D vs. 3D culture

Project description:Tumorigenesis depends on intricate interactions between genetically altered tumor cells and their surrounding tumor microenvironment (TME). Investigation of tumor cell-TME interactions could be greatly facilitated by models that mimic human disease on both the genotypic and phenotypic levels. Three dimensional (3D) cultures represent an important means to study the impact of tumor cell-TME interactions on specific aspects of neoplastic phenotypes. Here, we developed a novel 3D culture system (termed TUM622) derived from a patient-derived xenograft (PDX) of a lung squamous carcinoma (LUSC) that was grown in extracellular matrix (Damelin et al, Cancer Research; 71(12) June 15, 2011). Single TUM622 cells established acinar-like structures with proper apical-basal polarity, remained non-motile and demonstrated heterogeneous expression of stem-like and differentiation markers similar to the original PDX model and patient tumor, but nonetheless exhibited hyperplasia. Transcriptional profiling and gene set enrichment analysis (GSEA) revealed many similarities to the established acinar models, as well as modulation of the Wnt signaling pathway and stem cell signatures. These results demonstrate that the tumor microenvironment significantly influences the plasticity of NSCLC tumor cells. In order to gain a better understanding of the cell intrinsic mechanisms regulating TUM622 acinar morphogenesis in 3D, we performed transcriptional profiling of TUM622 cells collected from 2D and 3D cultures.We identified genes that vary more than 1.5-fold with reproducible changes among the biological replicates (p < 0.05) and found a total of 9227 genes differentially expressed, indicating that changing culture conditions from 2D to 3D exerts a major influence on gene expression in TUM622 cells.

2018-12-19 | GSE122538 | GEO

Expression data from PDE1C knockdown glioblastoma short-term cultures

2013-05-02 | GSE46538 | GEO

Expression data from PDE1C knockdown glioblastoma short-term cultures

Project description:In our lab we detected focal genomic amplification of PDE1C in 90% of short term GBM cultures. Knocking down of PDE1C was associated with compromised capacity opf these cultures to proliferate, migrate and invade. Therefore we carried out affymetric whole genome expression analysis to identify the down stream gene effectors of this function effects. IN1472 and IN1760 - 2 GBM short term cultures were transfected with siRNA either for PDE1C (siPD) or non-targeting (siNT) and its down gene effectors were studied.

2013-05-02 | E-GEOD-46538 | biostudies-arrayexpress

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