Project description:Density-dependent regulation of cell growth is presumed to be caused by cell-cell contact, but the underlying molecular mechanism is not yet clearly defined. Our goal is to identify receptor-type protein tyrosine phosphatase-kappa (PTPRK) is an important regulator of cell contact-dependent growth inhibition and to elucidate the related mechanism regulated by PTPRK with analyzing transcriptome-based datasets generated from different condition of cell density combined with manipulation of R-PTP-kappa expression using siRNA.
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: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:20% of patients affected with diffuse low-grade brain tumors have high cell density foci harboring higher KI67 index and DNA alterations. These foci may represent tumor progression towards high-grade gliomas. Here we performed transcriptome analysis of those foci vs adjacent tumoral tissues dissected from formalin fixed and paraffin embedded blocks.
Project description:HeLa cells grown to subconfluent density and CaCo-2 cells grown to high density were either treated with an iron source (hemin) or an iron chelator (desferal). Cells were harvested and RNA was prepared by RNA-Clean (Hybaid-AGS) and the RNA was subjected to a subsequent clean up using the RNeasy (Qiagen) clean up procedure.