MRNA profiling of JHDM2 knockdown Drosophila midguts post-infection with Ecc15
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ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE53788 | GEO | 2014/12/31
SECONDARY ACCESSION(S): PRJNA232941
REPOSITORIES: GEO
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Project description:We performed an mRNA-sequencing experiment using Drosophila midgut to find uracil-induced signaling pathways and biological processes in response to uracil. The sequenced reads from Illumina Hiseq2000 that passed quality filters were mapped to Drosophila genome (NCBI build 5.3) using Tophat and then quantitatively analyzed by HTseq at the gene level. By comparing uracil-treated and non-treated samplesl, we profiled uracil-dependent gene expression changes.
2014-12-31 | GSE57941 | GEO
Project description:Bowman-Birk Inhibitor (BBI) has both insecticidal and anti-cancerous properties. It has been hypothesized that dietary BBI slows insect growth by inhibiting the catalytic activity of digestive enzymes trypsins and chyomotrypsins, resulting in the midgut having reduced access to amino acids needed for growth. In mammals, BBI was hypothesized to influence cellular energy metabolism. Thus, we tested the hypothesis that dietary BBI also impacts energy-associated pathways in the midgut of Drosophila melanogaster. We investigated the impact of dietary BBI on the following parameters in the midguts of third-instar Drosophila larvae: (i) cellular metabolites, (ii) global transcriptome response, (iii) putative transcription factor binding sites (TFBSs) associated with the differentially expressed transcripts, and (iv) epithelial cellular structure. Dietary BBI caused: (i) a reduction of cellular DHAP, glucose, and succinate; and, (ii) increased Fructuse-6-phosphate; (ii) differential expression of genes associated with the glucose and fatty acid utilization; and, (iii) a shortening of midgut epithelial microvilli, a phenomenon previously associated with glucose starvation. Additionally, fifty seven percent of the putative TFBSs associated with the differentially expressed transcripts have previously been associated with glucose and insulin activities in mammalian studies. Collectively these results support the hypothesis that dietary BBI influences energy utilization in the Drosophila midgut. Keywords: stress response
2008-10-03 | GSE11046 | GEO
Project description:Bowman-Birk Inhibitor (BBI) has both insecticidal and anti-cancerous properties. It has been hypothesized that dietary BBI slows insect growth by inhibiting the catalytic activity of digestive enzymes trypsins and chyomotrypsins, resulting in the midgut having reduced access to amino acids needed for growth. In mammals, BBI was hypothesized to influence cellular energy metabolism. Thus, we tested the hypothesis that dietary BBI also impacts energy-associated pathways in the midgut of Drosophila melanogaster. We investigated the impact of dietary BBI on the following parameters in the midguts of third-instar Drosophila larvae: (i) cellular metabolites, (ii) global transcriptome response, (iii) putative transcription factor binding sites (TFBSs) associated with the differentially expressed transcripts, and (iv) epithelial cellular structure. Dietary BBI caused: (i) a reduction of cellular DHAP, glucose, and succinate; and, (ii) increased Fructuse-6-phosphate; (ii) differential expression of genes associated with the glucose and fatty acid utilization; and, (iii) a shortening of midgut epithelial microvilli, a phenomenon previously associated with glucose starvation. Additionally, fifty seven percent of the putative TFBSs associated with the differentially expressed transcripts have previously been associated with glucose and insulin activities in mammalian studies. Collectively these results support the hypothesis that dietary BBI influences energy utilization in the Drosophila midgut. Experiment Overall Design: Two treatments (control vs BBI-fed), and three replicates were conducted. There were total six samples. There was no dye-swap.
2008-10-26 | E-GEOD-11046 | biostudies-arrayexpress
Project description:The goal of these experiments is to identify RNAs bound by individual RNA-binding proteins. Drosophila S2R+ cells were transiently transfected with vectors encoding the indicated HA-tagged RNA-binding proteins, or without an insert as a control. Expression was induced with CuSO4, whole cell lysates were prepared and protein-RNA complexes were isolated by immunoprecipitation with HA immunoaffinity resin. RNA was then isolated from the immunoprecipitated material, and RNA-Seq libraries were prepared and sequenced. Sequence reads were aligned to the D. melanogaster reference genome Dm3 using TopHat and expression levels were quantitated using cufflinks. This work was funded as part of the modENCODE project by NHGRI. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf At least two biological replicates were performed for each protein studied. In addition, control experiments were performed in which cells were transfected with the same vector lacking an open reading frame.
2012-05-05 | E-GEOD-37756 | biostudies-arrayexpress
Project description:Differential Gene and Transcript Expression Analysis with TopHat and Cufflinks
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Project description:Purpose: We isolated Drosophila midgut cells : Delta+ intestinal stem cells (ISCs), Su(H)+enteroblasts (EBs), Esg+ cells (ISC+EB), Myo1A+Enterocytes (ECs), Pros+Enteroendocrine cells (EEs) and How+Visceral muscle cells (VM) from whole midguts to identify stem cell specific genes and study cell type specificities of midgut cells. We also isolated all the cell types from the 5 major regions (R1-R5) of the Drosophila midgut to study differences in cells in different regions. Methods: 3-7 day old female flies were dissected. Flies with GFP/YFP marking different cell types (using the GAL4-UAS system) were used to separate cells of the midgut.The midguts were dissociated with Elastase and FACS sorted using FACS AriaIII. RNA was extracted, amplified and sequenced. Whole midgut samples were sequenced on Illumina GAIIX and regional cell populations were sequenced on HiSeq2000. Methods:Raw fastqc reads were mapped to the Drosophila genome (Drosophila_melanogaster.BDGP5.70.dna.toplevel.fa) using Tophat 2.0.9 at default (using boost_1_54_0, bowtie2-2.1.0, samtools-0.1.19). Methods: For differential expression analysis, DESeq (p-value adjustment 0.05 by method Benjamini-Hochberg) was used. The reads were normalized also to Reads per kilobase of transcript per million mapped reads (RPKM). Results: More than 50% of the genome is expressed in the adult midgut (FlyAtlas- Chintapalli et al., 2007), of these genes about 50% (2457) were differentially expressed (DE) between all 4 cell types (ISCs, EBs, ECs and EEs) atleast 2 folds with 95% confidence Results: 159 genes that were specifically enriched in ISCs, 509 genes were specifically repressed in ISCs Conclusions: Our study represents the first detailed analysis of Drosophila intestinal cell transcriptomes, with biologic replicates, generated by RNA-seq technology.Our data facilitates comparative investigations of expression profiles of cells and reveals novel stem cell genes. Further region specific profiling adds precision to the analysis of variances in the midgut regions. We identify transcriptional regulators and regional transcription factors which modulate the midgut physiology. The dataset will be a great resource for hypothesis generation, tool building and fine tuned studies on the Drosophila midgut.
2015-05-23 | GSE61361 | GEO
Project description:Purpose: We isolated Drosophila midgut cells : Delta+ intestinal stem cells (ISCs), Su(H)+enteroblasts (EBs), Esg+ cells (ISC+EB), Myo1A+Enterocytes (ECs), Pros+Enteroendocrine cells (EEs) and How+Visceral muscle cells (VM) from whole midguts to identify stem cell specific genes and study cell type specificities of midgut cells. We also isolated all the cell types from the 5 major regions (R1-R5) of the Drosophila midgut to study differences in cells in different regions. Methods: 3-7 day old female flies were dissected. Flies with GFP/YFP marking different cell types (using the GAL4-UAS system) were used to separate cells of the midgut.The midguts were dissociated with Elastase and FACS sorted using FACS AriaIII. RNA was extracted, amplified and sequenced. Whole midgut samples were sequenced on Illumina GAIIX and regional cell populations were sequenced on HiSeq2000. Methods:Raw fastqc reads were mapped to the Drosophila genome (Drosophila_melanogaster.BDGP5.70.dna.toplevel.fa) using Tophat 2.0.9 at default (using boost_1_54_0, bowtie2-2.1.0, samtools-0.1.19). Methods: For differential expression analysis, DESeq (p-value adjustment 0.05 by method Benjamini-Hochberg) was used. The reads were normalized also to Reads per kilobase of transcript per million mapped reads (RPKM). Results: More than 50% of the genome is expressed in the adult midgut (FlyAtlas- Chintapalli et al., 2007), of these genes about 50% (2457) were differentially expressed (DE) between all 4 cell types (ISCs, EBs, ECs and EEs) atleast 2 folds with 95% confidence Results: 159 genes that were specifically enriched in ISCs, 509 genes were specifically repressed in ISCs Conclusions: Our study represents the first detailed analysis of Drosophila intestinal cell transcriptomes, with biologic replicates, generated by RNA-seq technology.Our data facilitates comparative investigations of expression profiles of cells and reveals novel stem cell genes. Further region specific profiling adds precision to the analysis of variances in the midgut regions. We identify transcriptional regulators and regional transcription factors which modulate the midgut physiology. The dataset will be a great resource for hypothesis generation, tool building and fine tuned studies on the Drosophila midgut. mRNA profiles of Drosophila intestinal cells from whole midguts and midgut regions were generated by Deep Sequencing. Whole midgut profiles were generated in triplicates (Illumina GAIIx, 72 bp read length) and regional cell type profiles were genrated in duplicates (HiSeq 2000, 50bp read length).
2015-05-23 | E-GEOD-61361 | biostudies-arrayexpress
Project description:The goal of these experiments is to identify RNAs bound by individual RNA-binding proteins. Drosophila S2R+ cells were transiently transfected with vectors encoding the indicated HA-tagged RNA-binding proteins, or without an insert as a control. Expression was induced with CuSO4, whole cell lysates were prepared and protein-RNA complexes were isolated by immunoprecipitation with HA immunoaffinity resin. RNA was then isolated from the immunoprecipitated material, and RNA-Seq libraries were prepared and sequenced. Sequence reads were aligned to the D. melanogaster reference genome Dm3 using TopHat and expression levels were quantitated using cufflinks. This work was funded as part of the modENCODE project by NHGRI. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2012-05-05 | GSE37756 | GEO
Project description:A general understanding of redox homeostasis in An. gambiae midgut epithelial cells under different oxidative conditions during P. falciparum ookinete invasion is missing. We used an ex vivo midgut culture model to understand AgTrx-1 protein expression pattern in An. gambiae midguts under oxidative stress of the ROS inducer, tert-butyl hydroperoxide (tBHP). We then quantified the midgut proteomic expression profile to understand organ-level regulation of the response to oxidative stress. An. gambiae midguts under low (50M) and high (200M) tBHP concentrations were enriched in ribosomal proteins (RPs), consistent with cells undergoing ribosomal/nucleolar stress. Nevertheless, these midguts were also enriched in peptidases, integral membrane proteins, and cytochrome P450s indicating cells that are undergoing protein processing and folding through post-translational modification (PTMs), and detoxification of toxic compounds through active efflux. This response to oxidative stress was strikingly dissimilar to that observed from previous studies with another dipteran, Drosophila following oxidative stress induction. Our data indicates that the response to tBHP induced oxidative stress is mild and suggests that the associated antioxidant response is similar to what is observed during midgut invasion of P. falciparum okinete. Furthermore, our data shows that ribosomal/nucleolar stress is crucial in the regulation of oxidative stress in An. gambiae midguts. Given this importance, its possible to develop mechanisms to perturb this ribosomal/nucleolar stress response in An. gambiae resulting into unmanageable levels of oxidative stress exposure to Plasmodium parasite in the midgut, yet still allowing the mosquito to survive the perturbation. Unmanageable levels of oxidative stress could result to harmful effect to the Plasmodium and eventually its death resulting into halting of its transmission.
2018-11-21 | PXD008251 | Pride
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) of intestinal progenitor cells in Drosophila wild type and Sox21a mutant midgut. Methods: mRNA profiles of intestinal progenitor cells isolated from 7-day-old wild-type (WT) and Sox21a knockout (Sox21a−/−) Drosophila midgut were generated by deep sequencing using Illumina HiSeq 4000. Results: Each sequencing experiment generated an average 11.18 million raw reads, and 86% was successfully mapped for each experiment. 7608 transcripts were identified in the progenitor cells of WT and Sox21a−/− Drosophila midgut with TopHat workflow. 389 genes of the transcripts showed differential expression between the WT and Sox21a−/− progenitor cells, with a fold change ≥2.0 and p value <0.05. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to intestinal function.
2017-02-14 | GSE76621 | GEO