Project description:Ferroptosis is one of the regulated cell deaths, induced by the accumulation of lipid peroxidation. Induction of ferroptosis is often influenced by the cell environment; however, much remains unknown about cellular states altering ferroptosis susceptibility. We found that melanoma cell lines become resistant to ferroptosis along with an increase in cell density. To elcidate the mechanism, we have investigated the differences in gene expression between A375 cells at different densities/culture systems.
Project description:Whole-genome microarray gene expression profiling of primary human monocytes and B-cells cultured at high density. Monocytes and B-cells were isolated from PMBCs of 2 healthy donors and cultured at 1x10^7 cells/mL (high density). Samples were harvested for microarray gene expresssion profiling at 0, 2, 10 or 24hrs (monocytes) or 0 or 24hrs (B-cells). Protein expression of FcgR2b is higher on monocytes in high density conditions compared to low density (1x10^6 cells/mL) conditions where expression is negligble. This study provides information on genome-wide gene expression changes that occur in high density culture in order to study associations with FcgR2b expression. B-cells cultured at high density and low density show similar levels of moderate FcgR2b expression. B cells at 0hr and after 24hr of high density culture are included in this dataset as a comparators.
Project description:Human embryonic stem cells (hESC) show great promise for clinical and research applications, but genomic instability hampers the development of their full potential. Here we demonstrate that increased culture density causes medium acidification due to lactic acid accumulation. hESC are able to cope with this, but acquire increased DNA damage associated to DNA replication stress. Also, single-cell genomics analysis reveals a strong correlation of the occurrence of de novo CNVs and culture density after only five days of culture. However, by an improved control over the accumulation of metabolites through more frequent medium changes, we were able to counter the effect of culture density on DNA damage and CNVs. These data underline the importance of optimal culture conditions, even at short-term, in the light of bringing hESC to their full potential.
Project description:Analysis of gene expression and compare the significant changed genes with associated phenotypes Total RNA extracted from adherent and suspension culture of A375 cells
Project description:In vitro expansion of endothelial progenitor cells (EPCs) remains a challenge in stem cell research and its application. We hypothesize that high density culture is able to expansion EPCs from bone marrow by mimicking cell-cell interactions of the bone marrow niche. To test the hypothesis, rat bone marrow cells were either cultured in high density by seeding or cultured in regular density. Flow cytometric analyses of the cells cultured for 15 days showed that high density cells exhibited smaller cell size and higher levels of marker expression related to EPCs when compared to regular density cultured cells. Global gene expression pattern difference between the high density and the regular density cultured cells was analyzed by a microarray assay.
Project description:MAP4K5 is serine/threonine protein kinase similar to yeast SPS1/STE20 kinase. MAP4K5 activates JNK in mammalian cells, which suggests a role in stress response. MAP4K5 is involved in immune functions. We used microarray to investigate genome-wide transcriptional change from MAP4K5 knockdown in A375 cells. Total RNA's from the A375 cells where MAP4K5 was stably knocked down by shRNA were analyzed. As a control, RNA's from A375 cells were also analyzed.