E. coli rnpb mutants: wild type proxy strain DW2/pFLP-Ec vs. DW2/pFLP-Bs strain
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ABSTRACT: Transcriptional profiling of DW2 E. coli cells in exponential growth phase that have a chromosomal deletion of the rnpb gene (which encodes the catalytic subunit of Ribonuclease P). We compared the test strain DW2/pFLP-Bs that expresses Bacillus subtilis rnpb from plasmid pFLP-Bs to reference strain DW2/pFLP-Ec, which expresses E. coli rnpb from plasmid pFLP-Ec. Two-strain experiment, wildtype proxy strain DW2/pFLP-Ec (reference) vs DW2/pFLP-Bs RT-10-2 (test) on each array. Biological replicates: 1 reference, 2 test. Four slides plus one dyeflip slide
Project description:IL-1B is an important cytokine that is often found to be up-regulated during osteoarthritic and rheumatoid joint diseases. It is viewed as a catabolic factor, inducing enzymes that allow for the degradation of the cartilage extracellular matrix and also has essential roles as an autocrine and paracrine factor in fibronectin fragment-mediated degradation. It can also reduce the synthesis of the major cartilage components, type II collagen and aggrecan. On the other hand, IL-1B also has the ability to induce the growth and morphogenic factor BMP-2. During joint diseases, IL-1B is synthesized by both synovial cells and chondrocytes. Addition of IL-1 biological antagonists such as IL-1 receptor antagonists can suppress cartilage degradation in vitro. Thus, the production of IL-1B could act as the first step in mediating a cascade of other mediators in cartilage which could be relevant to the fate of the cartilage. In order to obtain a global picture of the effect of IL-1B production on human adult articular chondrocytes, we analyzed changes in gene expression induced by IL-1B by microarray analysis. We found that IL-1B has a diverse effect on gene expression profile in chondrocytes. One of the predominant responses that we observed in adult human articular chondrocytes on exposure to IL-1B is a dramatic increase in a large set of chemokines and other genes related to the inflammatory cascade. Keywords: Gene response to IL-1B (10 ng/ml) Cartilage was obtained from adult human tissue donors with above the knee amputations due to chondrosarcoma or traumatic injury or from autopsy. Chondrocytes were isolated following established protocols, maintained in high density, and treated with IL-1B (10 ng/ml). Chondrocytes treated with buffer only served as the untreated control. The experiment was carried out in duplicate. Total RNA was extracted from these chondrocytes, labeled with fluorophores (Cy3 or Cy5) and analyzed for expression changes using the Human Operon/Qiagen v3.0 oligonucleotide array. The analysis was repeated with the fluorophore dyes exchanged between the untreated and experimental RNAs.
Project description:This SuperSeries is composed of the following subset Series: GSE12321: Brain_22A-Scrapie_End-point_PR04-39-to-46_using_GPL7118 GSE12322: Brain_22A-Scrapie_End-point_PR06-11-to-14_using_GPL7121 Refer to individual Series
Project description:Examining the transcriptional change in whole mouse (VM) brain miRNA expression during prion (22A) induced neurodegeneration in order to identify miRNAs that are differentially expressed. MicroRNAs (miRNAs) are small, non-coding RNA molecules which are emerging as key regulators of numerous cellular processes. Compelling evidence links miRNAs to the control of neuronal development and differentiation, however, little is known about their role in neurodegeneration. De-regulation of a unique subset of miRNAs may suggest a conserved, disease-specific pattern of differentially expressed miRNAs is associated with prionâinduced neurodegeneration. MiRNA extracted from the whole brains of 3 VM mice treated with mouse-adapted 22A scrapie strain were analyzed on GPL7118 (array was divided into top and bottom) for differential expression. Age-matched, PBS treated control mice were used for comparison (competitive hybridization). A technical replicate for each mouse was performed as well as a technical replicate for each of the dye-swaps.
Project description:Examining the transcriptional change in whole mouse (VM) brain miRNA expression during prion (22A) induced neurodegeneration in order to identify miRNAs that are differentially expressed. MicroRNAs (miRNAs) are small, non-coding RNA molecules which are emerging as key regulators of numerous cellular processes. Compelling evidence links miRNAs to the control of neuronal development and differentiation, however, little is known about their role in neurodegeneration. De-regulation of a unique subset of miRNAs may suggest a conserved, disease-specific pattern of differentially expressed miRNAs is associated with prionâ??induced neurodegeneration. MiRNA extracted from the whole brains of 4 VM mice treated with mouse-adapted 22A scrapie strain were analyzed on GPL7121 (array was divided into top and bottom) for differential expression. Age-matched, PBS treated control mice were used for comparison (competitive hybridization). A technical replicate for each mouse was performed as well as a technical replicate for each of the dye-swaps.
Project description:SAGE identification of differentiation responsive genes in P19 embryonic cells induced to form cardiomyocytes in vitro. P19 embryonic carcinoma (EC) cells, induced to form cardiomyocytes in vitro - undifferentiated cells, day 3+0.5 and day 3+3.0 of differentiation protocol. Keywords = EC cells, P19, differentiation, cardiomyocytes Keywords: time-course