Transcription profiling of Drosophila SL2 cells treated with E. coli with RNAi knock-down of Dsor1 or Gap1
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Anan Ragab
PROVIDER: E-MEXP-2145 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Shared Molecules
Only show the datasets with similarity scores above: 0.5
Threshold
0.5
Similar Datasets
Project description:RNA-Seq on libraries made from External RNA Controls Consortium (ERCC) external RNA controls, and a mixture of mRNA from Drosophila melanogaster S2 cell and ERCC mRNAs. We evaluated performance of RNA-Seq on known synthetic PolyA+ mRNAs from the External RNA Controls Consortium (ERCC) alone and in mixtures with PolyA+ mRNA from Drosophila S2 cells. ERCC mRNAs were obtained under Phase V testing from the National Institutes of Standards and Technology (NIST). The ERCC pool contained 96 species of mRNA of various lengths and GC content covering a 2^20 concentration range. Libraries were constructed using 100ng S2 mRNA with 5ng, 2.5ng, or 1ng ERCC mRNAs, and using 50ng ERCC mRNA without S2 cell mRNA. Our data shows an outstanding linear fit between RNA-Seq read density and known input amounts. We made libraries with 100ng S2 mRNA with 5ng, 2.5ng or 1ng ERCC mRNAs and with 50ng ERCC mRNAs only. For each library, one lane was sequenced for a 36bp run and around 15 million reads were obtained for each lane.
2010-04-19 | E-GEOD-20579 | biostudies-arrayexpress
Project description:miRNAs silence gene expression by repressing translation and/or by promoting mRNA decay. AGO1 is a key protein required for miRNA-mediated gene silencing. In animal cells, mRNA degradation of partially complementary miRNA targets occurs via deadenylation by the CAF1-CCR4-NOT1 deadenylase complex, followed by decapping and subsequent exonucleolytic digestion. To determine how generally miRNAs trigger deadenylation, we compared mRNA expression profiles in D. melanogaster cells depleted of AGO1, CAF1 or NOT1. We show that approximately 45% of AGO1-targets are regulated by both CAF1 and NOT1, indicating deadenylation is a widespread effect of miRNA regulation.<br><br>We employed RNA interference using long double-stranded RNAs to deplete cultured S2 cells of AGO1 (CG6671, 2 independent samples), CAF1 (CG5684, 2 independent samples), or NOT1 (CG1884, 3 independent samples). Further, we used Affymetrix oligonucleotide microarrays to analyze expression profiles in these samples. We included the following controls: mock RNAi treatment and GFP dsRNA treatment (3 and 2 independent samples, respectively).<br>
2008-12-03 | E-MEXP-1713 | biostudies-arrayexpress
Project description:Drosophila larvae and adults possess a potent innate immune response, but the response of their eggs is particularly poor. Here we show that eggs of the beetle Tribolium castaneum, in contrast, possess a full range of immune defence mechanisms, based on complete transcriptome comparisons of naïve, sterilely injured, and bacterially challenged eggs. Upon infection, we find massive upregulation of AMPs and differential regulation of 375 other genes including both IMD and Toll signalling components. Importantly, we show that this extensive response depends on the serosa, an extraembryonic epithelium enveloping yolk and embryo. When we delete the serosa using Tc-zen1 RNAi, none of the AMPs and merely 57 other genes are differentially regulated upon infection. Furthermore, unchallenged eggs reveal serosa-biased expression of several bacterial recognition genes. Thus, the serosa is an immune competent frontier epithelium, and its loss in higher flies might account for the poor immune response of Drosophila eggs. Three different types of eggs were analysed. Wildtype eggs, eggs of which the mother was injected with a control dsRNA, and eggs without a serosa of which the mothers were injected with Tc-zen1 dsRNA. These three egg-types were subjected to three treatments, untreated (naïve), pricked with a sterile needle (sterile injury) and pricked with a mix of E.coli and M.luteus. This resulted in 9 samples which were all collected three times resulting in a total of 27 samples.
2014-12-09 | E-GEOD-54018 | biostudies-arrayexpress
Project description:THO2 and HPR1 proteins were co-depleted from Drosophila S2 cells and their role in mRNA export analysed by comparing total RNA and cytoplasmic RNA
2005-01-01 | E-MEXP-88 | biostudies-arrayexpress
Project description:Phenotypic plasticity, the ability of one genotype to express different phenotypes in response to changing environmental conditions, is one of the most common phenomena characterising the living world and is not only relevant for the ecology but also for the evolution of species. Daphnia, the waterflea, is a textbook example for predator induced phenotypic plastic defences including changes in life-history, behaviour and morphology. However, the analysis of molecular mechanisms underlying these inducible defences is still in its early stages.<br><br>We exposed Daphnia magna to chemical cues of the predator Triops cancriformis to identify key processes underlying plastic defensive trait formation. D. magna is known to develop an array of morphological changes in the presence of T. cancriformis including changes of carapace morphology and cuticle hardening. To get a more comprehensive idea of this phenomenon, we studied four different genotypes originating from habitats with different predation history, reaching from predator-free to temporary habitats containing T. cancriformis.<br><br>We analysed the morphologies as well as proteomes of predator-exposed and control animals. Three genotypes showed morphological changes when the predator was present. Using a high-throughput proteomics approach, we found 294 proteins which were significantly altered in their abundance after predator exposure in a general or genotype dependant manner. Proteins connected to genotype dependant responses were related to the cuticle, protein synthesis and calcium binding whereas the yolk protein vitellogenin increased in abundance in all genotypes, indicating their involvement in a more general response. Furthermore, genotype dependant responses at the proteome level correlated well with local adaptation to Triops predation.<br><br>Altogether, our study provides new insights concerning genotype dependant and general molecular processes involved in predator-induced phenotypic plasticity in D. magna.
2015-07-03 | PXD001787 | Pride
Project description:The aim of this study was to identify target genes of the SR protein kinase SPK-1. spk-1(RNAi) leads to defects in cell polarity. We were therefore primarily interested in genes who exhibit changes in splicing regulation upon depletion of SPK-1 and could underlie the polarity phenotype of spk-1(RNAi). Transcriptome profiling of control and spk-1(RNAi) worms by RNAseq
2014-07-24 | E-GEOD-59705 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE20555: RNA-Seq on libraries made from serial dilutions of Drosophila melanogaster S2 cell mRNA and ERCC external RNA controls GSE20579: RNA-Seq on libraries made from ERCC external RNA controls, and a mixture of D. melanogaster S2 cell mRNA and ERCC mRNAs Refer to individual Series
2010-04-18 | E-GEOD-20580 | biostudies-arrayexpress
Project description:MSL (Male-specific lethal) complex increases transcription on the single X chromosome of Drosophila males in order to equalize expression of X-linked genes between males (XY) and females (XX). The increase in transcript levels correlates with MSL- dependent acetylation of histone H4 at K16 within the bodies of active genes, but identification of the transcriptional step affected has not been possible. In this study, we use global run-on sequencing (GRO-seq) to examine the specific effect of MSL complex on RNA Polymerase II (RNAP II) on a genome-wide level. Results indicate that MSL complex enhances transcription by facilitating the progression of RNAP II across the bodies of active X-linked genes. Improving transcriptional output downstream of typical gene-specific control may explain how dosage compensation can be imposed on the diverse set of genes along an entire chromosome. Global Run-On Sequencing (GRO-Seq) reads, i.e., RNA-Seq of nascent RNA transcripts, from D. Melanogaster SL2 cells. Two biological replicates of cells treated with control GFP RNAi and cells treated with MSL2 RNAi were analyzed.
2011-03-03 | E-GEOD-25887 | biostudies-arrayexpress
Project description:Polycomb group (PcG) proteins are involved in chromatin modifications for maintaining gene repression that play important roles in the regulation of gene expression, tumorigenesis, chromosome X-inactivation, and genomic imprinting in Drosophila melanogaster, mammals, and even plants. PcG proteins act together in three multimeric complexes, Polycomb repressive complex 1 (PRC1), Polycomb repressive complex 2 (PRC2), and Pleiohomeotic repressive complex (PhoRC), to repress transcription of the target genes. Here, we identified Polycomb target genes in Bombyx mori using genome-wide expression screening based on the knockdown of the BmSCE, BmESC, BmPHO, or BmSCM gene, which represent the distinct complexes. As a result, most genes were up-regulated after knocking down these four PcG genes, which indicated a potential epigenetic mechanism on the regulation of these genes expression by the PcG system. The further analysis of our data will provide some important information for the regulation mediated by PcG proteins in Bombyx mori. Transcription profiling experiments, knockdowns of four Polycomb genes (four samples) in silkworm BmN4-SID1 cells, were analyzed. Dual-channel experiments, with test samples labeled by Cy5 and common reference samples labeled by Cy3. The common reference sample, knockdown of the EGFP gene in BmN4-SID1 cells, was used for data normalization. One biological replicate. No dye-swaps.
2012-04-17 | E-GEOD-34246 | biostudies-arrayexpress
Project description:We integrated metabolome and proteome profiles of the parental cell line 143B.TK- versus ρ0, including PTM analyses such as phosphorylation and ubiquitination to characterize the impact of the absence of mtDNA for the entire cell. For quantitative proteome profiling, we used a shotgun LC-MS/MS approach including the classical SILAC labeling. For comprehensive metabolome profiling, we applied a targeted LC-MS approach, based on multiple reaction monitoring (MRM).</br></br>Our study revealed that mtDNA depletion leads to a non-uniform down-regulation of the mitochondrial energy metabolism in ρ0 cells on the proteome level. Metabolites of the TCA cycle were highly dysregulated which in turn had an impact on the amino acid levels, which were up regulated. Perturbation of the mitochondrial energy metabolism could lead to an activation of the retrograde response, indicated by sets of up-regulated signaling pathways in ρ0 cells, further supported by altered phosphorylation in signaling pathways and the cytoskeleton as well as de-ubiquitination of SLC transporters.
2016-02-08 | PXD002425 | Pride