Project description:Transcriptome data using microarray to identify difference across long-living, high-density cell type and short-living, low-density and Rho0 cell types
Project description:In yeast cells, preferential accessibility of the HIS3-PET56 promoter region is determined by a general property of the DNA sequence, not by defined sequence elements. In vivo, this region is largely devoid of nucleosomes, and accessibility is directly related to reduced histone density. The HIS3-PET56 and DED1 promoter regions associate poorly with histones in vitro, indicating that intrinsic nucleosome positioning and stability is a major determinant of preferential accessibility. Specific and genome-wide analyses indicate that low nucleosome density is a very common feature of yeast promoter regions that correlates poorly with transcriptional activation. Thus, the yeast genome is organized into structurally distinct promoter and non-promoter regions, whose DNA sequences inherently differ with respect to nucleosome formation. This organization ensures that transcription factors bind preferentially to appropriate sites in promoters, rather than to the excess of irrelevant sites in non-promoter regions. Keywords: other
Project description:ATAC sequencing of primary human monocytes cultured at low and high density. Monocytes isolated from PBMCs of 3 healthy donors were cultured at low density (1 x 10^6 cells/mL) or at high density (1 x10^7 cells/mL) for 24hrs and harvested for ATAC sequencing. Protein expression of FcgR2b is higher on monocytes in high density conditions compared to low density conditions, where expression is negligble. This study provides information on genome-wide chromatin accessibility changes that occur in high density culture in order to study associations with FcgR2b expression.
Project description:The extracellular matrix has been shown to control breast epithelial cell morphogenesis, proliferation and signalling. Here we compared changes in gene expression between 4T1 murine mammary carcinoma cells grown in a low or high density collagen matrix
Project description:Research in human immunobiology is mainly based on working with peripheral blood mononuclear cells (PBMC). However, recent investigations have shown that circulating CD4+ T cells are less sensitive to several T-cell activating monoclonal antibodies (mAb) and to recall antigens as compared to tissue-resident cells or cells that were in-vitro cultured at a high cell density of 10^7 cells/mL for 2 days at 37°C and 5% CO2 (RESTORE protocol, Römer et al., Blood 2011, PMID: 21931118). To explain the increase in sensitivity of CD4+ T-cells to mAbs and recall antigens on a molecular level, we performed microarray hybridizations of total RNA from T-cells isolated from PBMC that were cultured at a low or high cell density. To avoid the detection of genes that are up- or down-regulated by the culture process itself, we used low cell density cultured PBMC, instead of freshly prepared PBMC. We used microarrays to detail the global programme of gene expression underlying differences in the cell density of human PBMC and identified genes that are significantly up- or downregulated dependent on the cell density of PBMC.
Project description:Although high mammographic density (MD) is considered one of the strongest risk factors for invasive breast cancer, the genes involved in modulating this clinical feature are unknown. Histologically, areas of high MD are associated with low adipocyte content and high matrix content, both stromal phenotypes. We hypothesized that fibroblasts purified from low and high MD tissues would show gene expression differences responsible for these histologic differences.
Project description:Research in human immunobiology is mainly based on working with peripheral blood mononuclear cells (PBMC). However, recent investigations have shown that circulating CD4+ T cells are less sensitive to several T-cell activating monoclonal antibodies (mAb) and to recall antigens as compared to tissue-resident cells or cells that were in-vitro cultured at a high cell density of 10^7 cells/mL for 2 days at 37°C and 5% CO2 (RESTORE protocol, Römer et al., Blood 2011, PMID: 21931118). To explain the increase in sensitivity of CD4+ T-cells to mAbs and recall antigens on a molecular level, we performed microarray hybridizations of total RNA from T-cells isolated from PBMC that were cultured at a low or high cell density. To avoid the detection of genes that are up- or down-regulated by the culture process itself, we used low cell density cultured PBMC, instead of freshly prepared PBMC. We used microarrays to detail the global programme of gene expression underlying differences in the cell density of human PBMC and identified genes that are significantly up- or downregulated dependent on the cell density of PBMC. Human PBMC of one healthy blood donor were cultured at a low cell density (10^6 cells/mL) or at a high cell density (10^7 cells/mL) for 2 days at 37°C and 5% CO2 and CD4 or CD8 T-cells of both cultures were isolated by MACSbeads. Expression profiles from total RNA extracts were generated by hybridization to Affymetrix microarrays.