ATAC-seq and RNA-seq for MDCKII 3D and 2D epithelial morphogenesis
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ABSTRACT:
PROVIDER: PRJNA532904 | ENA |
REPOSITORIES: ENA
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Project description:We performed ATAC-seq experiments for MDCKII 3D cells, confluent 2D cells as well as seeding day0 cells to study if transcriptome changes during epithelial morphogenesis is associated with chromatin changes.
2020-09-25 | GSE129822 | GEO
Project description:ATAC-seq for MDCKII 3D and 2D epithelial morphogenesis
| PRJNA532907 | ENA
Project description:RNA-seq for MDCKII 3D and 2D epithelial morphogenesis.
| PRJNA532909 | ENA
Project description:Formation of epithelial tissues requires the generation of apical-basal polarity and the co-ordination of this polarity between neighboring cells to form a central lumen. MDCK cell line has proven to be a powerful model to study mammalian polarized epithelia in vitro. MDCK cells plated in extracellular matrix (ECM) form cysts, a spherical structure of polarized cells enclosing a central lumen which resembles epithelial tubular structures. The morphogenetic process requires drastic changes in cell architecture, which are regulated by change in gene expression. We used microarrays to identify genes up-regulated in lumen formation. The identification of up-regulated genes could lead us to characterize novel pathways needed for this process. MDCKII cells were plated in two different conditions: Cells cultured in confluence in plastic dishes, forming polarized monolayers (2D); or cells cultured in plastic dishes covered with Matrigel (ECM) forming three dimensional cysts (3D). Comparison of both transcriptomic profiles would lead us to identify up-regulated genes in the 3D condition, which would be good candidates to be key regulators of novel processes involved in lumen morphogenesis.
2011-09-30 | E-GEOD-32495 | biostudies-arrayexpress
Project description:We performed time-course RNA-seq experiments for MDCKII 3D cell culture, and included seeding day0 cells and over-confluent 2D cells. To study how intracellular trafficking affects transcriptome changes, we also profiled trancriptome of DENND5A and AVL9 KD MDCKII cells by RNA-seq.
2020-09-25 | GSE129823 | GEO
Project description:* To compare surgical and oncological outcomes in patients underwent to colorectal resection with 3D vs 2D laparoscopic technique.
* To evaluate the visual overload in surgeons using 3D laparoscopic technique.
| 2220465 | ecrin-mdr-crc
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
Project description:Interventions: 2D group:2D laparoscopic surgery;3D group:3D laparoscopic surgery
Primary outcome(s): operation time;The amount of bleeding;Number of lymph nodes;Postoperative gastrointestinal function recovery time;Postoperative complications
Study Design: Randomized parallel controlled trial
| 2663755 | ecrin-mdr-crc
Project description:Background. Fallopian tube secretory epithelial cells (FTSECs) have been implicated as a cell-of-origin for high-grade serous epithelial ovarian cancer. However, there are relatively few in vitro models of this tissue type available for use in studies of FTSEC biology and malignant transformation. In vitro three-dimensional (3D) cell culture models aim to recreate the architecture and geometry of tissues in vivo and restore the complex network of cell-cell/cell-matrix interactions that occur throughout the surface of the cell membrane. Results. We have established and characterized 3D spheroid culture models of primary FTSECs. FTSEC spheroids contain central cores of hyaline matrix surrounded by mono- or multi-layer epithelial sheets. We found that 3D culturing alters the molecular characteristics of FTSECs compared to 2D cultures of the same cells. Gene expression profiling identified more than a thousand differentially expressed genes between 3D and 2D cultures of the same FTSEC lines. Pathways significantly under-represented in 3D FTSEC cultures were associated with cell cycle progression and DNA replication. This was also reflected in the reduced proliferative indices observed in 3D spheroids stained for the proliferation marker MIB1. Comparisons with gene expression profiles of fresh fallopian tube tissues revealed that 2D FTSEC cultures clustered with follicular phase tubal epithelium, whereas 3D FTSEC cultures clustered with luteal phase samples. Conclusions. This 3D model of fallopian tube secretory epithelial cells will advance our ability to study the underlying biology and etiology of fallopian tube tissues and the pathogenesis of high-grade serous epithelial ovarian cancer. 3 primary FTSEC lines were plated in 2D, or in 3D on polyHEMA coated plates
2013-09-27 | E-GEOD-51220 | biostudies-arrayexpress
Project description:Recent studies have characterized the genomic structures of many eukaryotic cells, often with a focus on their relation to gene expression. So far, these studies have largely only investigated cells grown in 2D culture, although the transcriptomes of 3D cultured cells are generally closer to their in vivo phenotype. To examine the effects of spatial constraints on chromosome conformation, we investigated the genomic architecture of mouse hepatocytes grown in 2D and 3D cultures using in situ Hi-C. Our results reveal significant differences in long-range genomic interactions, notably in compartment identity and strength as well as in TAD-TAD interactions, but only minor differences at the TAD level. RNA-seq analysis reveals an up-regulation in the 3D cultured cells of those genes involved in physiological hepatocyte functions. We find that these genes are associated with only a subset of the structural changes, suggesting that the differences in genomic structure are indeed critically important for transcriptional regulation but also that there are major structural differences owing to other functions than gene expression. Overall, our results indicate that growth in 3D significantly alters longer-range genomic interactions, which may be consequential for a subset of genes that are important for the physiological functioning of the cell.
2020-09-30 | E-MTAB-8303 | biostudies-arrayexpress