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Gene expression profile of frazzled (fra) mutant Drosophila embryos

ABSTRACT: In order to analyze the global changes in gene expression resulting from loss of Fra signaling, we performed a microarray experiment comparing Drosophila embryos containing a loss of function fra[3] mutation to age matched wildtype embryos. RNA extracted from fra[3] mutant vs. wildtype embryos were hybridized to the Affymetrix GeneChip Drosophila Genome 2.0 . We selected Drosophila embryos at stage 13, which marks the onset of Fra expression in the embryonic CNS and the early stages of commissural axon guidance in the ventral nerve cord. RNA was extracted from both fra[3] and wildtype embryos. Hybridization experiments were performed on Affymetrix Drosophila Genome 2.0 microarrays.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Molly Scheel

PROVIDER: E-GEOD-47112 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profile of frazzled (fra) mutant Drosophila embryos

Project description:In order to analyze the global changes in gene expression resulting from loss of Fra signaling, we performed a microarray experiment comparing Drosophila embryos containing a loss of function fra[3] mutation to age matched wildtype embryos. RNA extracted from fra[3] mutant vs. wildtype embryos were hybridized to the Affymetrix GeneChip Drosophila Genome 2.0 .

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Gene expression profile of Drosophila third instar larval wing imaginal discs overexpressing netrinA (netA) and frazzled (fra).

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Comparative analysis of gene expression in Fra-1+/+ and Fra-1-/- mice lung

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Identification of Fra-1 and/or Fra-2 regulated genes in MDA-MB231 cells

Project description:In the paper "Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers" by Bejjani et al., we identified Fra-1 and/or Fra-2 target genes in MDA-MB-231 cells. si RNA against Fra-1 and against Fra-2 were transfected in MDA-MB-231 cells either independenlty or simultaneously to identify genes regulated specifically by Fra-1 or Fra-2 and genes regulated redundantly or complementarily by Fra-1 and Fra-2 total RNA were purified and biotinylated sense-strand cDNA were produced. cDNA targets were used to probe Affymetrix GeneChip Human Gene 2.0 ST arrays

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Comparative analysis of gene expression in Fra-1+/+ and Fra-1-/- mice lung

Project description:We hypothesized that gene expression in lungs of Fra-1+/+ and Fra-1-/- mice are divergent thus contributing fibrosis. More specifically, Fra-1-/- mice are increased susceptible to fibrosis. In order to test these hypotheses at the gene expression level, we utilized microarray analysis to examine transcriptional differences between Fra-1+/+ and Fra-1-/- mice at early time point. This study utilizes microarray analysis to test these hypotheses. 5 days PBS and bleomycin treated lung samples from both Fra-1+/+ and Fra-1-/- mice were used. RNA was isolated and used for global gene expression profiling (Affymetrix MoGene 1.0ST v1 Array). The raw probe signal intensities were quantile normalized over all samples, summarized with the robust multi-array average (RMA) algorithm and log2 transformed with a median polish, using the Affymetrix Power Tools. We considered a transcript cluster (gene-level) to be reliably expressed in a sample if the Affymetrix implemented DABG (detection above ground) p-value was less than 0.05. We used local-pooled-error (LPE) estimates and robust statistical tests for evaluating significance of each gene's differential expression in a comparison.

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