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Gene expression profiling of prostate epithelial cells in response to tissue contextual changes

ABSTRACT: To conduct comparative transcriptomic analyses on normal or malignant prostate epithelial cells in response to tissue contextual changes, we cultured immortalized prostate epithelial cells or prostate cancer cells as cell monolayers or three-dimensional organoids and profiled their transcriptomes in respective culture contexts.

ORGANISM(S): Homo sapiens

PROVIDER: GSE30304 | GEO | 2011/07/03

SECONDARY ACCESSION(S): PRJNA143579

REPOSITORIES: GEO

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Gene expression profiling of prostate epithelial cells in response to tissue contextual changes

Project description:To conduct comparative transcriptomic analyses on normal or malignant prostate epithelial cells in response to tissue contextual changes, we cultured immortalized prostate epithelial cells or prostate cancer cells as cell monolayers or three-dimensional organoids and profiled their transcriptomes in respective culture contexts. RWPE-1 (immortalized prostate epithelial cells) and LNCaP cells (prostate cancer cells) were seeded on reconstituted basement membrane (rBM)-coated culture plastics or cultured within three-dimensional (3D) rBM gels. Total RNA samples were collected from cell monolayers or 3D cell clusters (formed at day 2) or acini or spheroids (formed at day 6) in the rBM culture, followed by global gene expression profiling.

2011-07-03 | E-GEOD-30304 | biostudies-arrayexpress

Gene expression profiling of pancreatic epithelial cells in response to tissue contextual changes

Project description:To understand the molecular process associated with tissue morphogenesis of pancreatic epithelial cells, we profiled the transcriptomes of normal or malignant pancreatic organoids formed in three-dimenstional reconsitututed basement membrance (rBM). Cell monolayers cultured on rBM-coated culture plastics were used as controls. HPDE (immortalized pancreatic epithelial cells) and PANC-1 cells (pancreatic cancer cells) were seeded on reconstituted basement membrane (rBM)-coated culture plastics or cultured on top of three-dimensional (3D) rBM gels. Total RNA samples were collected from cell monolayers or 3D cell clusters (formed at day 2), pancreatic tubules or tumor spheroids (formed at day 6) in the rBM culture, followed by global gene expression profiling.

2012-11-15 | E-GEOD-42270 | biostudies-arrayexpress

Gene expression in rat hippocampal CA1 during the extinction of contextual fear memory

Project description:Adult rats (male Lister hooded) were pre-exposed for 3 d for 10 min /d (24 hr interval) to two different novel contexts. On day 4 rats received a single unsignaled scrambled footshock (0.5 mA for 2 s) 2 min into a 3min exposure to one of the two contexts. Rats were either returned to the CS conditioned context (CS+, EXT group) or to the other (CS-, NOR group) context for 10 min, 48h after contextual fear conditioning. Rats were housed in the home cages at all times outside the conditioning and re-exposure components. The novel context chosen to be the conditioned context was counterbalanced across the experimental groups. Rats were killed by CO2 inhalation 2 hours after CS- or CS+ exposure. CA1-enriched dorsal hippocampus was immediately dissected on ice before rapid freezing and storage at -80oC. The CS+ group represents rats that underwent extinction of contextual fear memory.

2015-09-25 | GSE66151 | GEO

Gene expression profiling of pancreatic epithelial cells in response to tissue contextual changes

2012-11-15 | GSE42270 | GEO

Gene expression analysis of MCF7 breast cancer cells cultured as xenografts, in two dimensional cultures, in polyHEMA anchorage independent three dimansional cell culture models and in Matrigel three dimensional cultures.

Project description:The traditional method for studying cancer in vitro is to grow immortalized cancer cells in two-dimensional (2D) monolayers on plastic. However, many cellular features are impaired in these unnatural conditions and big alterations in gene expression in comparison to tumors have been reported. Three-dimensional (3D) cell culture models have become increasingly popular and are suggested to be better models than 2D monolayers due to improved cell-to-cell contacts and structures that resemble in vivo architecture. The aim of this study was to compare gene expression patterns of MCF7 breast cancer cells when grown as xenografts, in 2D, in polyHEMA coated anchorage independent 3D models and in Matrigel on-top 3D cell culture models. Surprisingly small variations in gene expression patterns were observed between the models indicating that 3D and xenograft are not always that different from 2D cell cultures. Gene expression analysis of MCF7 breast cancer cells cultured as xenografts for 43 days, in two dimensional cultures for seven days (2D7d), in polyHEMA three dimensional cell culture models for four and seven days (PH7d and PH7d), and in Matrigel three dimensional cultures for four and seven days (MG4d and MG7d). Two biological replicates was included for each sample.

2013-10-30 | E-GEOD-47583 | biostudies-arrayexpress

Sono-Seq analysis of contextual fear conditioning

Project description:This dataset constitutes the first Sono-Seq study of chromatin accessibility following contextual fear conditioning in the mouse hippocampus.

2017-11-20 | GSE98317 | GEO

RNA-seq analysis of contextual fear conditioning

Project description:This dataset constitutes the first RNA-seq study of gene expression following contextual fear conditioning in the mouse hippocampus.

2015-07-22 | GSE63412 | GEO

Comparing 2-dimensional vs. 3-dimensional human prostate cancer transcriptomes uncovers growth-specific gene signatures

Project description:Prostate cancer research has relied heavily on patient-derived cell lines, which may be used for in vitro (2-dimensional) studies or cultivated as 3-dimensional xenografts in mice. These approaches are likely to have differential impacts on cell differentiation, with implications for research outcomes. Therefore, defining and comparing the transcriptional signatures associated with 2-dimensional and 3-dimensional approaches is essential to adequately plan experiments and interpret research data. In this study, LNCaP, VCaP, and 22Rv1 human prostate cancer cells were either cultivated in monolayers or as xenografts in NOD Scid mice, and their gene transcription profiles were studied and compared using microarray and RT-PCR techniques. This comparison identified gene sets featuring similar expression patterns in all three cancer cell lines and unique transcriptional signatures associated with 3-dimensional versus 2-dimensional growth. Pathway over-representation analysis revealed an enrichment of pathways related to cell-cell interactions, differentiation and the extracellular matrix. Immunohistochemical analyses confirmed that gene up-regulation in xenografts occurred in implanted cancer cells and not mouse stromal cells. Cultivating cells in vitro in the presence of mouse - rather than bovine - serum failed to elicit the gene transcription profile observed in xenografts, further supporting the hypothesis that this profile reflects 3-dimensional growth and enhanced microenvironmental interactions, rather than exposure to mouse-related factors. Overall, these findings define the expression profiles observed in prostate cancer cells cultivated in monolayers and in xenografts, highlighting differentially regulated pathways in each setting and providing essential information for performing and interpreting research in this field.

2020-03-17 | GSE141545 | GEO

2013-10-30 | GSE47583 | GEO

Encoding of Contextual Fear Memory Requires De Novo Proteins in the Prelimbic Cortex

Project description:Time dependent coordinated hippocampal-prefrontal cortical interactions are required for the long-term storage of memories. However, the role of prefrontal cortex (PFC) in encoding of long-term memories remains elusive. Here, we discover a critical role of PFC in the encoding of contextual memories in mice. We demonstrate that specific pools of mRNAs are translated in the PFC following one and six hours of behavioral training. Moreover, disruption of protein synthesis in the prelimbic region of PFC immediately after training inhibits encoding contextual fear memories, whereas disruption at six hours after training is ineffective. Thus, early protein synthesis in the PFC is necessary and critical for the encoding of contextual fear memories. These findings establish key role for the prelimbic cortex in encoding of contextual memories.

2017-01-06 | GSE61529 | GEO

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