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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

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Next Generation Sequencing Facilitates Quantitative Analysis of in 14-day-old wt, brm-1, brm-3, brip1, brip2, brip1 brip2, brip1 brip2 brm-3 and brip1 brip2 brm-1 seedlings.

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: RNA from 14-day-old seedlings of wild-type, brip1, brip2, brm-3, brm-1, brip1 brip2, brip1 brip2 brm-3 and brip1 brip2 brm-1 was isolated using the RNAprep Pure Plant Kit as described above. RNAs from three biological replicates was sequenced separately at Novogene, using Illumina Hiseq X-Ten (Sequencing method: Hiseq-PE150). Results: Reads were mapped to the TAIR10 Arabidopsis genome using TopHat (Galaxy V2.1.1 in usegalaxy.org) with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 4,000 bp were required (Paired-end). Then, mapped reads were assembled according to TAIR10 version of genome annotation using cufflinks (version 2.1.1) with default settings. To analyze differential expression, the assembled transcripts from three independent biological replicates in Col and other mutants were included and compared using Cuffdiff (version 2.1.1) with default settings. Conclusions: Our study represents the first detailed analysis of brip1, brip2, brip1 brip2 transcriptomes, with biologic replicates, generated by RNA-seq technology.

2020-06-21 | GSE142622 | 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

Genome-wide profiling of SWI/SNF chromatin remodeler BRAHMA (BRM) and BRM Interacting Protein 1/2 (BRIP1/2) in Arabidopsis

Project description:SWI/SNF chromatin remodeling complexes control gene expression by regulating chromatin structure. However, the full subunit composition of SWI/SNF complexes in plants remains unclear. Here we show that BRAHMA Interacting Protein 1 (BRIP1) and BRIP2 in Arabidopsis thaliana are core subunits of plant SWI/SNF complexes. BRIP1 and 2 are two homolog proteins. brip1 brip2 double mutants exhibit developmental phenotypes and a transcriptome strikingly similar to those of BRAHMA (BRM) mutants. Genetic interaction tests indicated that BRIP1 and 2 act together with BRM to regulate gene expression. Furthermore, BRIP1 and 2 physically interact with BRM-containing SWI/SNF complexes, and extensively co-localize with BRM at endogenous genes. Loss-of-brip1brip2 results in decreased BRM occupancy at almost all BRM target genes and substantially reduced subunits incorporation into the BRM-containing SWI/SNF complexes. Together, our work identifies new core subunits of BRM-containing SWI/SNF complexes in plants, and uncovers the essential role of these subunits in regulating the integrity (assembly) of SWI/SNF complexes in plants.

2020-06-21 | GSE142621 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of in 14-day-old wt, brm-1, brm-3, brip1, brip2, brip1 brip2, brip1 brip2 brm-3 and brip1 brip2 brm-1 seedlings.

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of in 14-day-old wt, brm-1, brm-3, brip1, brip2, brip1 brip2, brip1 brip2 brm-3 and brip1 brip2 brm-1 seedlings.

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Integrated Profiling and Immunohistochemistry Analyses Link circ-BRIP1, circ-EPHB4 and Their Host Genes with Imatinib Resistance in Gastrointestinal Stromal Tumors

Project description:Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal neoplasms of the digestive tract. The majority of GIST patients eventually develop resistance to imatinib therapy. To identify the responsible mechanisms, we investigated the differentially expressed mRNAs and circRNAs in imatinib-resistant GISTs using SBC ceRNA microarrays. We found that 107 mRNAs and 521 circRNAs were significantly differentially expressed between imatinib-naïve and imatinib-resistant GIST tissue samples. qRT-PCR analyses validated that circ-BRIP1, circ-EPHB4 and circ-RECQL4 and their host genes were upregulated in imatinib-resistant GISTs, and circ-BRIP1, circ-EPHB4, and RECQL4 were associated with imatinib resistance, tumor relapse and progression, and metastasis in GIST patients. The expression levels of circ-BRIP1, circ-EPHB4 and their host genes were also evaluated using TMAs with 150 human GISTs. The expression level of EPHB4 was significantly increased in high-grade GISTs in comparison to low-grade GISTs and correlated with imatinib resistance. Specifically, we first developed a method for high-throughput analysis of the expression of differentially expressed circRNAs by ISH-IHC in a set of FFPE-tissue microarrays in GIST. Our results also suggested a possible role for circ-BRIP1, circ-EPHB4, and their host genes in the progression of GISTs.

2024-11-01 | GSE188700 | GEO