Project description:RNA microarray was performed to evaluate the efficacy of silicon nano-particles on renal transcriptomes of rats against ischemia reperfusion injury. We compared the transcriptomes of ischemia reperfusion injury model rats with or without oral administration of silicon nano-particles. We also tried to check whether the oral silicon nano-particles intake downregulated the biological processes related to oxidative stress.
Project description:Single cell derived clones were extracted from four glioblastoma tumors using fluorescence activated cell sorting with CD15 and CD133 markers. Unsorted bulk tumors were also derived. Gene expression analysis of clones of tumor GBM-482 involved comparison between TMZ resistant (n=5) and sensitive (n=2) clones.
Project description:The prognosis of colorectal cancer (CRC) stage II and III patients is still a challenge due to the difficulties of finding robust biomarkers and assays. The majority of published gene signatures of CRC have been generated on frozen colorectal tissues. Because collection of fresh frozen tissues is not routine and the quantity and quality of RNA derived from formalin-fixed paraffin-embedded (FFPE) tissues is vastly inferior to that derived from fresh frozen tissue, a clinical test for improving staging of colon cancer will need to be designed for FFPE tissues in order to be widely applicable. We have designed a custom Nanostring nCounter assay for quantitative assessment of expression of 414 gene elements consisting of multiple published gene signatures for colon cancer prognosis, and systematically compared the gene expression quantification between nCounter data from FFPE and Affymetrix microarray array data from matched frozen tissues using 414 genes. For microarray studies, representative sections of fresh tissue specimens were flash frozen in liquid nitrogen and stored at −80°C until RNA isolation. RNA was purified from tissue sections containing >80% epithelial tumor tissue using RNeasy (QIAGEN, Valencia, CA) according to manufacturer’s instructions. Samples were hybridized to Affymetrix arrays Human Genome U133 Plus 2.0 GeneChip Expression Arrays, Santa Clara, CA). The samples included four healthy control patient tissues, 12 stage I, 17 stage II, 20 stage III and 15 stage IV CRC patient tissues. Please note that only the *matched.csv files containing matched 414 genes' microarray and nanostring data are provided without the nanostring experimental descriptions. The matching samples between GSE62932 and the Nanostring study are indicated in the matching_samples.txt.
Project description:Analysis of expression changes between colon tumors (Duke's stage II) and matching colon mucosa tissues using Affymetrix GeneChip® Human Gene 2.0 ST arrays. All experiments were performed simultaneously for matching tissue samples.
Project description:Dendritic cell (DC)-based immunotherapy against glioblastoma multiforme is a novel treatment hope. Glioblastoma stem-like cells are, however, potentially causing immunoresistance. Glioblastoma cells cultured as gliomaspheres show a stem-like phenotype as opposed to classical adherent culture. They are thus a promising antigen source to specifically target glioblastoma stem-like cells via DC therapy and so overcome immunoresistance. Here we study the importance of gliomasphere-specific. Methodologically, we used 7 gliomaspheres, 3 of them patient-derived, as model system. Gliomasphere-specific protein expression was explored via quantitative proteomics.
Project description:Yerba mate (YM) has been shown to have anti-inflammatory properties in several studies. However, this effect has been found mainly in obesity-related in inflammation. The aim of this work was to study the effect of YM in cultured peripheral blood mononuclear cells to see whether it has anti-inflammatory properties. We stimulated peripheral blood mononuclear cells in vitro with phitohemaglutinin in the presence of yerba mate and determined their activation measuring the the expression of CD25 by flow cytometry. We observed that YM treatment produced a dose-dependent reduction in PBMC activation (CD25 positive cells) when they were stimulated with PHA. This effect was also observed in T cells (CD3 positive) subpopulation. Microarray analysis revealed the differential expression of 128 genes in YM-treated cells. According to a protein-protein interaction database, these genes were highly connected and they are involved in inflammatory response. In summary, it was demonstrated that YM produces a reduction in the amount of activated cells under the stimulation of PHA. Therefore, it might be used in diseases with an inflammatory component. PBMC samples from a healthy individual were cultured and stimulated with phytohemagglutinin. Gene expression of yerba mate treated and non-treated cells was analyzed in duplicates, having in total four microarrays.
Project description:Human pluripotent stem cells (hPSCs) can differentiate into all cell types in the body that may replace current cell sources applied in regenerative medicine, cell therapy, drug discovery and development and general research. Human PSC-derived hepatocyte-like cells (HLCs) have the potential to replace primary hepatocytes and other cell models applied in liver disease treatment and drug discovery and development. These cells share many features with their in vivo counterparts however, the generation of fully functional hPSC-derive HLCs is still lacking, which prevent their application in the previously mentioned fields. This study followed the transcriptome dynamics during the differentiation of hPSC-derived HLCs at definitive endoderm, hepatoblast, early HLC and late HLC developmental stages and the controls hPSCs and human liver tissues which consists of at least 70% hepatocytes. The aim is to reveal expression deviations between hPSC-derived hepatocytes and their in vivo counterparts that may contribute to the modification of differentiation protocols to generate fully functional hepatocytes.
Project description:In order to identify biologically relevant tumor markers with prognostic significance, we set out to analyze gene expression profiling of tumor and adjacent non-tumor tissues from PDAC cases. We compared the microarray gene-expression profiles of 45 matching pairs of pancreatic tumor and adjacent non-tumor tissues. This data set were used to obtained genes that were differentially expressed and associated with survival. 51 genes were selected for further validation. 90 total samples were analyzed. We compared gene expression profile of 45 pairs of pancreatic tumor and adjacent non-tumor tissues using Affymetrix GeneChip Human Gene 1.0 ST arrays. Tumor gene expression profiles were distinctly different from non-tumor profiles. Using ANOVA in Partek®, 7352 independent genes were found to be differentially expressed in tumors (P<0.01). We next performed Cox-regression analysis and identified 928 of the differentially expressed genes that were associated with survival (P<0.1). The list of genes was then subjected to pathway and biomarker analyses using Ingenuity Pathways Analysis (IPA). Based on literatures supporting their roles in cancer, 51 genes were selected for further analyses
Project description:Glioblastoma (GBM) derived sphere lines and adherent cell lines are an important tool for research in basic and translational neuro-oncology. Documentation of their genetic identity has become a requirement for scientific journals and grant applications to exclude cross-contamination and misidentification that lead to misinterpretation of results. Here, we report expression data for 26 samples including 4 GBM derived sphere lines (4 x 3 replicates), 2 GBM derived sphere lines passaged through intracranial transplantation (2x 1), 2 adherent GBM derived cell lines (2 + 2 x 3 replicates), 4 corresponding glioblastoma tumors and 2 non-tumor brain tissues. Overall design: 26 samples including 4 GBM derived sphere lines (4 x 3 replicates), 2 GBM derived sphere lines passaged through intracranial transplantation (2x 1), 2 adherent GBM derived cell lines (2 + 2 x 3 replicates), 4 corresponding glioblastoma tumors and 2 non-tumor brain tissues