Project description:Gene expression profile of two reporgrammed cell lines iPSC CRL1831 (induced pluripotent stem cells) and CSC DLD1 (cancer stem-like cells) derived from normal colon CRL1831 and colorectal cancer DLD-1 cells, after transfer to 3D cell culture conditions and cell lines treated with single or fractionated ionizing radiation doses under 3D cell culture conditions. There are no data that cancer metastases arise due to specific mutations of cancer cells. Therefore ongoing investigation of reprogrammed cancer cells grown in three-dimensional (3D) cell culture models might provide researchers with essential data studying tumor oncogenesis and metastases formation. 3D culture models were shown to mimic in vivo cell microenvironment more accurately than the standard two-dimensional cell monolayer (2D) cultures. Also, growing evidence suggests that 2D and 3D cultured cells gene expression pattern variance following irradiation is highly dependent on cancer cell state and their interaction with microenvironment.
Project description:Comparison of gene expression of different colon carcinoma cell lines under 2D and 3D culturing conditions Cells were seeded under 2D and 3D culturing condition. After seven days total RNA was isolated and used for cDNA synthesis.
Project description:Recent studies have demonstrated extensive proliferative capacity of adult hepatocytes and biliary epithelial cells (BECs) in vitro, thereby allowing derivation of clonal cell lines named hepCLiPs and bilCLiPs, respectively. Both cell lines undergo hepatobiliary plastiticity in that they exhibit a BEC-like phenotype under a 2D culture condition, while they exhibit a hepatocyte-like phenotype under a 3D culture condition. This data set was obtained to comprehensively characterize the gene expression profiles of hepCLiPs and bilCLiPs which were cultured under 2D and 3D culture conditions.
Project description:Analysis of 2D (transwell) and 3D (collagen type I) cultured MDCK cells and HGF (a MAPK activator). Traditional 2D cultures are fast and inexpensive but do no mimic natural niche/cell environment as well as the more laborious and costly 3D-cultures. 3D cultures, arguably, are better models for the study of developmental processes, such as tubulogenesis. Epithelial organs (such as kidney) develop via tubulogenesis, a process, at least in part, regulated by MAPK signaling. Therefore, 2D and 3D cells also treated with HGF plus MAPK inhibitors. Results provide insights into differential response to HGF-induced tubulogenesis depending on cell culture conditions (2D vs. 3D). 29 samples total: 2D and 3D control (untreated) in quadruplicate, respectively; 2D and 3D + HGF in quadruplicate, respectively; 2D + HGF + PD-98059 in quadruplicate; 3D + HGF + PD-98059 in triplicate; 2D + HGF + U0126 in triplicate; and 3D + HGF + U0126 in triplicate.
Project description:Tumor cell response to irradiation also depends on their microenvironment. Therefore ongoing investigation of three-dimensional (3D) cell culture models provide researchers with essential data studying and remodeling radiotherapeutic implications in cancer treatment. 3D culture models were shown to mimic in vivo cell microenvironment more accurately than the standard two-dimensional cell monolayer (2D) cultures. Growing evidence suggests that 2D and 3D cultured cell gene expression pattern discrepancies following irradiation is highly dependent on cell-ECM interactions. It has been shown that laminin-rich-extracellular matrix (lr-ECM) used in 3D cultures not only alters cancer cell phenotype and response to external stimuli but also affects their differentiation, migration and survivability. Thus, a change in these fundamental cell properties demands us to reconsider data previously collected using 2D in vitro models. RNA was harvested from two colorectal cancer cell lines cultivated under 3D cell culture conditions, 4h after treatment of single (2 Gy or 10 Gy) or fractionated (5x2 Gy) ionizing radiation dose.
Project description:Purpose: the goal of this study is to detect and compare the transcriptome expression of mouse macrophages cultured in 3D and 2D environments, and find the effect of 3D culture on macrophages compared with traditional 2D culture. Methods: Total RNA was extracted from purified and untreated RAW264.7 cells from 3D and 2D culture systems using TRIzol. The RNA samples were analyzed using Whole Genome Oligo Microarrays. After RNA had been hybridized to the microarray, it was washed and scanned, and data were extracted using Agilent Feature Extraction Software. Gene expression data were generated using Affymetrix GeneChip Human Genome U133 Plus 2.0 on an Affymetrix 3000 instrument running Gene‑Chip operating software. Result: RNA-sequencing (RNA-seq) revealed that after 24 h of culture under the same conditions, 3D-cultured macrophages showed significant differences in gene expression. RNA-seq detected 18580 genes in the 2D group and 15777 genes in the 3D group, among which 6762 were differentially expressed (|log2(fold change)| >= 1, padj < 0.05) in both 3D and 2D groups. A total of 5949 genes were downregulated and 813 were upregulated. Conclusion: Our study represents the first detailed analysis of the effect of 3D culture on mouse macrophages, and the results showed that compared with traditional 2D culture, the gene expression of macrophages under 3D culture was significantly changed.These findings are therefore worthy of further investigation and verification, and provide novel avenues for future research in cytology and macrophages.
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
Project description:MDA-MB-231 cells were cultured in 2D and Matrigel based 3D culture for 4 days. Total DNA was extracted. Bisulfite treatment and BS-SEQ were carried out to profile global cytosine methylation in both culture conditions.
Project description:A549 and MDA-MB-231 cells were cultured in 2D and Matrigel based 3D culture for 4 days. Total RNA was extracted using Trizol. RNA-SEQ was carried out to profile the gene expression in both culture conditions.
Project description:Human bone marrow mesenchymal stromal cells (MSCs) are conventionally cultured as adherent monolayers on tissue culture plastic. MSCs can also be cultured as 3D cell aggregates (spheroids). Optimised 3D conditions (60,000 MSCs cultured as a spheroid for 5 days) inhibited MSC proliferation and induced cell shrinkage in the absence of cell death. Primary human MSCs isolated from 2 donors were cultured under both monolayer (2D MSCs) and optimised 3D (3D MSCs) conditions. High quality RNA was isolated from all samples, and global gene expression analysis was performed in duplicate (using Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays) to identify gene expression changes in 3D compared to 2D MSC cultures.
