Project description:Comparison of gene expression data between cell lines grown on 2D tissue culture plastic or 3D matrigel A427, A549, H23, H358, H460, H661, H1437, and H1703 cells were compared
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.
Project description:Gene expression analysis was performed through RNA-Sequencing on samples prepared from a panel of four CRC cell lines (HT29, HCT116, LS174T, LS513) grown in either 2D or 3D cell culture conditions. Our gene expression data reveal that more than 2000 gene expression profiles are affected by the growth conditions for each cell lines even if samples prepared from each cell line still group together. Our data also demonstrate that hierarchical clustering mostly relies on the MSS/MSI phenotypes of the CRC cells.
Project description:This study used Illumina single-end RNA-sequencing to examine gene expression differences between 2 mouse-derived pancreatic stellate cell lines (PSC4, PSC5) grown either in 2D monolayers, as 3D quiescent cultures, or as 3D activated transwell cocultures with 2 mouse tumor-derived pancreatic ductal organoid lines (T4, T5). Mouse pancreatic stellate cell (PSC) lines were derived from the pancreata of wild-type C57Bl/6J mice. Mouse tumor organoid lines were derived from mouse pancreata containing pancreatic ductal adenocarcinoma (PDAC) from the KrasLSL-G12D; Trp53LSL-R162H; Pdx1-Cre mouse model. We measured genes differentially expressed among 2D, quiescent, and 3D activated PSCs that may reflect the expression changes of heterogeneous CAF population in pancreatic tumors.
Project description:We used a microarray to examine the global gene expression profile of MCF7 cells grown in 2D and 3D culture conditions. Our goal was to identify changes in the expression of genes that regulate iron metabolism when cellular spatial organization was altered.
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.
Project description:The objective of this study was to use RNAseq to determine which gene change in expression when LKR10 cells are grown in monolayers (2D) or methylcellulose on ultra low attachment plates (3D), which prevents attachment of cells to the plate and promotes formation of 3D sphere-like clusters. A secondary objective was to determine whether knockdown of Ankrd35 altered gene expression of specific genes in 2D or 3D.
