Project description:We examined whether SATB1 functions as a global gene regulator in order to maintain the aggressive phenotype of the MDA-MB-231 cell line. We compared the gene expression profiles between control_shRNA-MDA-MB-231 cells, which express SATB1 at high levels, and SATB1_shRNA1-MDA-MB-231 in which the level of SATB1 was greatly downregulated by RNAi technology. This comparative studies were performed using two different platforms (Codelink and Affymetrix genechip) with two culture conditions either on plastic dish (2D) or on matrigel (3D) which allows cells to form a breast-like morphology only for non-aggressive cells. Keywords: Comparative studies on Control_shRNA and SATB1_shRNA1 expressing MDA-MB-231 from 2D or 3D culture. We examined control_shRNA-MDA-MB-231 cells and SATB1_shRNA1-MDA-MB-231 cells under two culture condition;on plastic dish(2D culture) and on Matrigel coated dish(3D culture). When SATB1 was depleted by RNAi technology, these normally aggressive cells exhibited normal breast like morphology on 3D. We used two different microarray platforms (Codelink and Affymetrix) to make expression data. Initial analysis of data and cross-platform comparison were performed using Codelink expression analysis and GeneSpring software. We provide ratio for control_shRNA/SATB1_shRNA1-MDA-MB-231 cells for 2D and 3D on this series.
Project description:We examined whether SATB1 functions as a global gene regulator in order to maintain the aggressive phenotype of the MDA-MB-231 cell line. We compared the gene expression profiles between control_shRNA-MDA-MB-231 cells, which express SATB1 at high levels, and SATB1_shRNA1-MDA-MB-231 in which the level of SATB1 was greatly downregulated by RNAi technology. This comparative studies were performed using two different platforms (Codelink and Affymetrix genechip) with two culture conditions either on plastic dish (2D) or on matrigel (3D) which allows cells to form a breast-like morphology only for non-aggressive cells. Keywords: Comparative studies on Control_shRNA and SATB1_shRNA1 expressing MDA-MB-231 from 2D or 3D culture.
Project description:To investigate the differential transcriptomics upon DMT1 in 2D vs 3D cell culture in breast cancer cells Gene expression analysis from MDA-MB-231 RNA-seq data of WT and DMT1 KO cells both in 2D and 3D cell culture conditions
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:CD44, an adhesion molecule that binds to extracellular matrix, primarily to hyaluronan (HA), has been implicated in cancer cell migration, invasion, and metastasis. CD44 has also recently been recognized as a marker for stem cells of several types of cancer. However, the roles of CD44 in the development of bone metastasis still remain unclear. To explore this issue, we established the MDA-MB-231 human breast cancer cells stably expressing short hairpin RNA against CD44. The CD44-knockdown MDA-MB-231 cells (MDA-MB-231 shCD44-2 and shCD44-3) were analyzed. As control, MDA-MB-231 cells stably expressing shRNA against firefly luciferase (shLuc) were used. Total of three samples. No replicates.
Project description:Mesenchymal stromal cells were cultured in 3D PEG hydrogels for 7 days in the presence of serum-free media or conditioned media from a panel of breast cancer cells (MCF-7, MDA-MB-231, MDA-MB-231 lung-tropic, MDA-MB-231 brain-tropic, MDA-MB-231 bone-tropic). In all cases, the secretomes were collected after cancer cells were in serum-free media for 24h.
Project description:Analysis of the effect of shRNA-mediated knockdown of SOX4 on global gene expression levels in MDA-MB-231 human breast cancer cells. Results were used for the identification of overlapping up- and downregulated genes in TRPM7 + SOX4 shRNA MDA-MB-231 cells
Project description:Using mass spectrometry–based proteomics, we analysed the components of integrin adhesion complexes of MDA-MB-435S cells and two MDA-MB-435S-derived integrin αV-specific shRNA-expressing cell clones. Among integrins, we detected αV and β5 integrin subunits in the MDA-MB-435S adhesome, thus showing that in long term culture these cells use preferentially integrin αVβ5 for adhesion. Our data represents the first published adhesome of αVβ5 integrin heterodimer.
