Project description:Genetic heterogeneity is an important feature of solid tumors, however it is often assumed that most cancer cell lines are genetically homogeneous. A disparity in genetic complexity between cell lines and the disease they model could result in problems such as in vitro preclinical experiments overstating the effectiveness of putative therapeutics. We therefore derived clonal sublines by single cell cloning of in house derived early passage melanoma cell lines (LM-MEL-series), and compared their genomes to each other and the parental cell line using Illumina 610-Quad SNP arrays.
Project description:Cells from patient melanoma samples were grown de novo in either a stem cell media (SCM) or in standard serum containing media, as well as xenografts derived from each culture type. The expression profile of these samples were compaired to the expression profile of the original patient tumour sample.
Project description:Cells from patient melanoma samples were grown de novo in either a stem cell media (SCM) or in standard serum containing media, as well as xenografts derived from each culture type. The expression profile of these samples were compared to the expression
Project description:In order to identify cells expressing RUNX1c during hematopoietic differentiation of human embryonic stem cells (hESCs), we targeted GFP downstream of the RUNX1 distal promoter. GFP was observed from 10-25 days of embryoid body differentiation and accurately mirrored expression of the endogenous RUNX1c isoform. GFP was restricted to CD45+ hematopoietic cells and GFP+CD34+ cells were highly enriched for progenitor cells. Appearance of the first wave of hematopoietic blast colony forming cells (Bl-CFC) in d3-4 embryoid bodies, antedated the expression of RUNX1c. These results confirm a role for RUNX1c in marking a second wave of hematopoietic progenitor cells in differentiating hESCs. The purpose of the cord blood samples was to perform comparison of them to the gene expression profiles of the Runx fractions - as the cord blood represents a heterogeneous mix of hematopoietic stem cells and multipotent progenitors cells.
Project description:Epigenetic regulation of tumor suppressor genes (TSGs) has been shown to play a central role in melanomagenesis. Integrating gene expression and methylation array analysis we identified novel candidate TSGs frequently methylated in melanoma. We validated the methylation status of the most promising TSGs using the highly sensitive, specific and comprehensive Sequenom Epityper assay in a large panel of melanoma cell lines and resected melanomas, and compared the findings with that from cultured melanocytes. We found transcript levels of UCHL1, COL1A2, THBS1 and TNFRSF10D were inversely correlated with promoter methylation. The effect of this methylation on expression was confirmed at the protein level. Identification of these candidate TSGs and how their silencing is related to melanoma development will increase our understanding of the etiology of this cancer and may provide tools for its early diagnosis. Analysed samples consisted of 11 melanoma cell lines and 1 neonatal foreskin melanocyte pool as a reference. Melanoma cell lines overlap with members of the DNA copy number analysis series GSE9003 and expression profiling series GSE7127 . The matching copy number data GEO samples IDs are noted in characteristics: Matching CN Sample ID and characteristics: Matching expn Sample ID columns respectively.
Project description:To test the impact of nonsense-mediated decay (NMD) on BCR/TCR RNA sequences, we treated peripheral blood mononuclear cells (PBMCs) with cycloheximide to block NMD and analyzed treated and untreated cells by scRNA-seq with scVDJ-seq.
Project description:In the present study, we investigated PAX5TEL function in transcription processes by transduction of PAX5TEL construct in wild type preBI cells, a primary culture of immature B cells expressing endogenous wild type PAX5 protein.