Transcription profiling of Drosophila embryos with differenct ewg transcription factor isoforms identifies a subset of differentially regulated genes important for synaptic growth regulation
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Matthias Soller
PROVIDER: E-MEXP-2363 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Ewg differentially regulated genes in 16-18 h Drosophila embryos. The experiment contains expression measurements from wild type, ewg l1 protein null allele and ewg l1 elavEWG (elavEWG rescue construct expressing a ewg cDNA from the elav promoter) mutants.
2008-04-30 | E-MEXP-1312 | biostudies-arrayexpress
Project description:Comparisons of gnotobiotic Rag1-/- mice, with and without subcutaneous 260.8 hybridomas, disclosed that this IgA does not affect B. thetaiotaomicron population density or suppress 260.8 epitope production but does affect bacterial gene expression in ways that are emblematic of a diminished host innate immune response. C57BL/6 wildtype, C57BL/6J Rag1-/- , and C57BL/6J Rag1-/- mice harboring the 260.8 IgA producing hybridoma were colonized for 10 days with Bacteroides thetaiotaomicron VPI-5482.
2015-06-29 | E-GEOD-65455 | biostudies-arrayexpress
Project description:Osteoporosis is the consequence of altered bone metabolism resulting in the systemic reduction of bone strength and increased risk of fragility fractures. MicroRNAs (miRNAs) regulate gene expression on a post-transcriptional level are known to take part in the control of bone formation and bone resorption. Recently, targeted secretion of miRNAs from cells originating from various tissues has been described, which allows for their minimal-invasive detection in serum/plasma and use as biomarkers for presence and progression of pathological conditions. One pilot study has reported circulating miRNAs in serum and tissue of fracture patients. However, further studies are required to explore whether a dysbalance in bone homeostasis of fracture patients can reliably be reflected by specific circulating miRNAs, and whether these miRNAs might serve as drugable targets. Here, we report results from a comprehensive multiplex study of 175 miRNAs in serum samples obtained from 7 patients with osteoporotic fractures at the femoral neck, and 7 age-matched controls. Following elaborate quality control statistical analysis of this exploratory dataset identified 9 microRNAs with altered serum levels in response to fracture (adjusted p-value < 0.1). Of these, hsa-miR-10a/b gave excellent discrimination of both groups (AUC = 1.0), and clustering of samples based on the top10 miRNAs confirmed the high discriminatory power of circulating microRNAs for osteoporotic fractures. In the next step 3 miRNAs with unknown roles in osteogenic differentiation and 4 miRNA from a previous study were tested for their effects on osteogenic differentiation. Of these, 3 miRNAs showed robust effects on osteogenic differentiation. Overall, these data provide important insights into changes in serum miRNA in post-traumatic patients. Future studies will show, whether this knowledge can be used to improve current diagnostic methodologies to predict fracture risk and design novel treatment strategies for osteoporosis patients. Two groups with n=7 per group; one groups represents cases with osteoporotic fractures, the control group is age-matched without fractures
2015-06-26 | E-GEOD-60230 | biostudies-arrayexpress
Project description:modENCODE_submission_3172 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Tissue: reference (early embryo); Developmental Stage: Mixed stage of embryos 20dC; Genotype: wild type; Sex: Hermaphrodite; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Strain N2; temperature 20; Developmental Stage Mixed stage of embryos 20dC; Tissue reference (early embryo)
2010-11-18 | E-GEOD-25350 | biostudies-arrayexpress
Project description:modENCODE_submission_540 This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: L3 stage larvae, dark blue gut PS(1-2) stage; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Strain Y cn bw sp; Developmental Stage L3 stage larvae, dark blue gut PS(1-2) stage
2010-08-05 | E-GEOD-23222 | biostudies-arrayexpress
Project description:modENCODE_submission_538 This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: L3 stage larvae, 12 hr post-molt; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Strain Y cn bw sp; Developmental Stage L3 stage larvae, 12 hr post-molt
2010-08-05 | E-GEOD-23220 | biostudies-arrayexpress
Project description:To identify molecular effects of the antineoplastic agent PKC412 (Midostaurin), we applied gene expression profiling in zebrafish using whole genome microarrays. Zebrafish eleuthero-embryos were exposed for 6 dpf to nominal levels of 2 μg/L and 40 μg/L PKC412. Among the 259 and 511 altered transcripts at both concentrations, respectively, the expressions of genes involved in the circadian rhythm were of interest. Alteration of swimming behaviour was not noted. Pathways of interest affected by PKC412 were angiogenesis, apoptosis, DNA damage response and response to oxidative stress. Angiogenesis was not altered by PKC412 treatment at both concentrations. Apoptosis occurred in olfactory placodes of embryos exposed to 40 μg/L, and DNA damage was induced at both PKC412 concentrations. However, there were no significant effects on reactive oxygen species formation. This study leads to the conclusion that PKC412-induced alterations of gene transcripts are partly paralleled by physiological effects at high, but not at low PKC412 concentrations expected to be of environmental relevance. Gene expression in zebrafish eleuthero-embryos was measured after exposure for 6dpf to 2 ug/L and 40 ug/L PKC412 or to the respective controls. A total of 12 arrays (Agilent 4 × 44 K Zebrafish microarray) were used, including four for the water control group, four for the solvent control group, four for the 2 μg/L and four for the 40 μg/L PKC412 dose group.
2011-07-22 | E-GEOD-23156 | biostudies-arrayexpress
Project description:Tip60 is a key histone acetyltransferase (HAT) enzyme that plays a central role in diverse biological processes critical for general cell function, however the chromatin-mediated cell-type specific developmental pathways that are dependent exclusively upon the HAT activity of Tip60 remain to be explored. Here, we investigate the role of Tip60 HAT activity in transcriptional control during multicellular development, in vivo by examining genome-wide changes in gene expression in a Drosophila model system specifically depleted for endogenous dTip60 HAT function. We show that amino acid residue E431 in the catalytic HAT domain of dTip60 is critical for the acetylation of endogenous histone H4 in our fly model in vivo, and demonstrate that dTip60 HAT activity is essential for multicellular development. Moreover, our results uncover a novel role for Tip60 HAT activity in controlling neuronal specific gene expression profiles essential for nervous system function as well as a central regulatory role for Tip60 HAT function in general metabolism. Drosophila larvae ubiquitously expressing either our dTIP60 HAT specific mutant or an additional copy of wild type dTIP60 were selected along with age-matched wild type controls for RNA extraction. Two samples, each containing a pool of thirty-five staged whole larvae, were collected from each respective genotypic cross, and were used for hybridization on a separate Affymetrix microarray.
2010-11-29 | E-GEOD-25635 | biostudies-arrayexpress
Project description:modENCODE_submission_484 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: larva mid-L1 25dC 4.0 hrs post-L1; Genotype: wild type; Sex: Unknown; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Strain N2; Developmental Stage larva mid-L1 25dC 4.0 hrs post-L1
2010-08-04 | E-GEOD-23270 | biostudies-arrayexpress
Project description:modENCODE_submission_477 This submission comes from a modENCODE project of Robert Waterston. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Our experiments are designed to detect all C. elegans transcripts by hybridizing RNA to commerically available genome tiling arrays. To maximize the chances of detecting rare transcripts with limited expression in specific cells, we are extracting RNA from selected embryonic cells isolated by FACS and from postembryonic cells by use of the mRNA tagging method. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: larva mid-L2 25dC 17.75 hrs post-L1; Genotype: wild type; Sex: Hermaphrodite; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS: Strain N2; Developmental Stage larva mid-L2 25dC 17.75 hrs post-L1
2010-08-04 | E-GEOD-23266 | biostudies-arrayexpress