Genes differentially expressed between Bmi1-overexpressing and empty vector control neural stem/progenitor cells
ABSTRACT: Neural stem/progenitor cells were isolated from the lateral ventricle wall of 4-6 week-old CD1 mice and grown as neurospheres under low density culture conditions. Test cells were transduced with bicistronic retroviral constructs for the over-expression of Bmi1 together with eGFP, and control cells were transduced with an empty vector construct expressing eGFP only. To identify genes, which are regulated by BMI1 in neural stem/progenitor cells, the gene expression profiles of neurosphere cells over-expressing Bmi1 were compared empty vector control cells using Affymetrix Gene mouse ST1.0 arrays 3 independent Bmi1-overexpressing neurosphere cultures (test samples) were compared to 3 independent empty vector neurosphere cultures (control samples).
Project description:Primary brain tumors are classified and treated based on their histological features, however the factors which specify these tumor types remain largely unknown. We demonstrate that the over-expression of HRAS (V12) and MYC alone or in combination directs the development of glioma, CNS PNET, and atypical teratoid/rhabdoid (AT/RT)-like tumors from postnatal murine p53-deficient neural stem/progenitor cells. Microarray analyses were performed to investigate the gene expression profile of the tumor cells generated by the different genetic perturbations. Murine brain tumors were generated by overexpressing different oncogenes in cultured neurosphere cells from the postnatal lateral ventricle wall region (LVW) of Trp53-deficient mice. Neurosphere cultures were established from isolated cells of the generated tumors, which still expressed the transgene/fluorescent marker gene cassette. Total RNA was isolated and used for gene expression analyses using the Affymetrix Gene 1.0 ST array platform.
Project description:Neural stem/progenitor cells were isolated from the lateral ventricle wall of 4-6 week-old CD1 mice and grown as neurospheres under low density culture conditions. Test cells were transduced with bicistronic retroviral constructs for the over-expression of Bmi1 together with eGFP, and control cells were transduced with an empty vector construct expressing eGFP only. To identify genes, which are regulated by BMI1 in neural stem/progenitor cells, the gene expression profiles of neurosphere cells over-expressing Bmi1 were compared empty vector control cells using Affymetrix Gene mouse ST1.0 arrays Overall design: 3 independent Bmi1-overexpressing neurosphere cultures (test samples) were compared to 3 independent empty vector neurosphere cultures (control samples).
Project description:We analyzed a role of Brd2 protein in transcription and alternative splicing. 289 genes change alternative splicing after Brd2 knockdown and 1459 genes alter gene expression compared to cells treated with negative control siRNA. 6 samples (3 independent samples of cells treated with Brd2 siRNA, 3 samples of cells treated with negative control siRNA)
Project description:We analyzed a role of histone deacetylases in alternative splicing regulation. Using human exon arrays we identified a list of 683 genes whose splicing changes after HDAC inhibition with sodium butyrate. 6 samples (3 nontreated controls and 3 sodium butyrate treated cells)
Project description:Tert-immortalized microvascular endothelial (TIME) cells are infected with human herpesvirus (HHV-8) or mocked infected to determine expression changes upon infection. Three samples to TIME cells are infected with HHV-8 and three samples are mock-infected.
Project description:MSCs are a heterogeneous population of cells with different capacities for lineage differentiation. MSC clones were prepared from a single adult human bone marrow sample and screened for their chondrogenic capacity using cartilage tissue engineering (measured by type II collagen content). The aim was to compare genes expressed by highly and poorly chondrogenic clones to identify genes associated with those MSCs with an enhanced capacity for cartilage formation. The 4 most highly chondrogenic and the 4 least chondrogenic MSC clones identified following screening by cartilage tissue engineering were selected for gene array comparison using Affymetrix microarrays.
Project description:Angiogenesis in cultures of rat aorta begins with neovessels sprouting from the aortic explant within the first three days of culture. We used microarrys to examine the effects of TNF-alpha on gene expression in both fibrin and collagen gels during the first 48 hours or culture. Rat aortic rings were cultured in either collagen or fibrin maticies. Half of the cultures from each matrix group were treated with 10ng/ml recombinant rat TNF-alpha, and half were left untreated. These cultures were used to prepare total RNA
Project description:We have previously shown that conditional overexpression of Bmi1 in NSC increases their proliferation both in the developing neocortexand in the postnatal brain (Yadirgi et al. 2011). However, during embryonic development, increased and ectopic proliferation induced by overexpression of Bmi1 in progenitors committed toward a neuronal lineage triggered apoptosis, leading eventually to a reduced overall brain size (Yadirgi et al. 2011). These findings –increased proliferation of neural stem/progenitor cells (NSPC) and apoptosis of neuronal committed progenitors - could be faithfully reproduced in an in vitro assay where NSPC isolated from Nestin-Cre; STOP FloxBmi1 embryos are cultured in floating conditions in the presence of EGF and FGF2 (neurosphere assay). We isolated NSPC from Nestin-Cre;STOP FloxBmi1 E16.5 neocortices and cultured them briefly under neurosphere inducing conditions. We then analysed their transcriptome by whole-genome Illumina platform mouse v2 and compared it to the transcriptome of NSPC isolated from non-transgenic or single transgenic littermates. The objective of this analysis was to identify genes differentially expressed upon overexpression of the PcG gene Bmi1 in neural stem/progenitor cells. 4 samples, 2 condition with 2 biological replicates per condition
Project description:Previous studies in our laboratory have shown that low folate diet (control diet with 2mg folate/kg, low folate diet with 0.3mg folate/kg) can induce intestinal tumors in BALB/c mice. We used microarrays to compare MTHFR+/+ BALB/c mice fed control diet and MTHFR+/- BALB/c mice fed low folate diet. After weaning, 4 BALB/c Mthfr +/+ mice were fed with a control diet (CD, 2mg folate/kg) and 4 BALB/c Mthfr +/- mice were fed a low folate diet (FD, 0.3mg folate/kg) for 1 year. Both diets contain succinylsulfanthiozole (1%) to prevent folate synthesis by intestine microbial biota.