Drosophila melanogaster
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Project description:The mutation in the C9orf72 gene with a hexanucleotide repeat has been reported multiple times to be the most common genetic cause of FTD and ALS (Frontotemporal Dementia and Amyotrophic Lateral Sclerosis), both of which are devastating neurodegenerative diseases having no cures currently. Our lab previously created fruit fly models expressing 36(C4G2) repeats, these are highly toxic to adult neurons of fruit flies. This is one of the most commonly used fly models of disease. Like many neurodegenerative diseases, FTD and ALS display selective neuronal vulnerability: only some neuronal populations succumb to disease, even though the toxic species are ubiquitously expressed. Our lab proposes to identify which neuronal populations are selectively depleted in response to the expression of the repeats and analyse which pathways are activated in vulnerable and resistant neuronal populations using our fly model of disease. This is done by scRNA sequencing across multiple time points, tracking disease development. The workflow was first having the flies ready and their brains being dissected. The brains were then dissociated by collagenase and dispase, and the cell suspensions were passed through a 10um cell strainer. The single-cell suspensions were checked for viability and the single-cell libraries were prepared with 10X Chromium 3' platform.
2023-11-09 | E-MTAB-12440 | biostudies-arrayexpress
Project description:Transfer RNAs (tRNAs) are vital in determining the specificity of translation. Mutations in tRNAs can result in the mis-incorporation of amino acids into nascent polypeptides in a process known as mistranslation. Here, our goal was to test the impacts of different types of mistranslation in the model organism Drosophila melanogaster, as impact of mistranslation depends on the type of amino acid substitution. We created two fly lines - one expressing a serine tRNA variant with valine anticodon and the other with a serine tRNA variant with a threonine anticodon. Using mass spectrometry, we measure the amount of mistranslation at various points in fly development.
2024-06-15 | PXD052492 | Pride
Project description:Lead (Pb2+) is an environmental contaminant that is widely distributed around the world, mainly due to anthropogenic sources. Developmental exposure to Pb2+ has been linked to neurodevelopmental impairments in different animal species. Studies have shown that developmental exposure to Pb2+ could interfere with normal gene expression patterns in the immature brain leading to neurodevelopmental neuropathologies. However, the precise molecular mechanisms underlying the neurotoxicity of developmental Pb2+ exposure are still to be elucidated. We used the fruit fly to gain insights into the molecular mechanisms affected by exposure to this neurotoxicant. The fruit fly, has been used recently to understand the behavioral, synaptic and molecular changes after developmental exposure to Pb+2. Our overarching hypothesis is that developmental exposure of the fruit fly to Pb+2 results in global gene expression dysregulation in the larval brain resulting in central nervous system developmental impairments. We collected RNA samples from larval brain of control and Pb2+-exposed flies and performed cRNA hybridization on a 4x44K Agilent microarray. Overall, Pb+2 results in transcriptional disturbances of important developmental signaling pathways in the larval brain.
2016-12-31 | GSE77417 | GEO
Project description:A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here we present the culmination of the efforts of the modENCODE (Model Organism ENCyclopedia Of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms, Drosophila melanogaster (fly) and Caenorhabditis elegans (worm). These datasets comprise 605 TFs identifying 3.6M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks”, that larger metapeaks have characteristics of high occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single cell RNA-seq data in a machine learning model identifies particular TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent-daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing GFP-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface (http://epic.gs.washington.edu/modERN/) that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell type-specific TF-target relationships.
2024-10-06 | GSE278063 | GEO
Project description:Background: A prominent hallmark of aging is inflammaging—the increased expression of innate immune genes without identifiable infection. Model organisms with shorter lifespans, such as the fruit fly, provide an essential platform for probing the mechanisms of inflammaging. Multiple groups have reported that, like mammalian models, old flies have significantly higher levels of expression of anti-microbial peptide genes. However, whether some of these genes—or any others—can serve as reliable markers for assessing and comparing inflammaging in different strains remains unclear. Methods and Results: We compared RNA-Seq datasets generated by different groups. Although the fly strains used in these studies differ significantly, we found that they share a core group of genes with strong aging-associated expression. In addition to anti-microbial peptide genes, we identified other genes that have prominently increased expression in old flies, especially SPH93. We further showed that machine learning models can be used to predict the “inflammatory age” of the fruit fly.
2024-04-17 | GSE262759 | GEO
Project description:The fly is a powerful tool for studying complex biological processes, with more than 60% of genes associated with various diseases and genetic similarities to humans. Based on the genetic advantages of this model organism, our study aims to perform a toxicogenic assessment of human health impact induced by the CMIT/MIT (chloromethyl-Methylisothiazolone).
2024-05-13 | GSE263572 | GEO
Project description:A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here we present the culmination of the efforts of the modENCODE (Model Organism ENCyclopedia Of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms, Drosophila melanogaster (fly) and Caenorhabditis elegans (worm). These datasets comprise 605 TFs identifying 3.6M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks”, that larger metapeaks have characteristics of high occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single cell RNA-seq data in a machine learning model identifies particular TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent-daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing GFP-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface (http://epic.gs.washington.edu/modERN/) that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell type-specific TF-target relationships.
2024-11-16 | GSE280213 | GEO
Project description:A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here we present the culmination of the efforts of the modENCODE (Model Organism ENCyclopedia Of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms, Drosophila melanogaster (fly) and Caenorhabditis elegans (worm). These datasets comprise 605 TFs identifying 3.6M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks”, that larger metapeaks have characteristics of high occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single cell RNA-seq data in a machine learning model identifies particular TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent-daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing GFP-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface (http://epic.gs.washington.edu/modERN/) that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell type-specific TF-target relationships.
2024-10-06 | GSE278904 | GEO
Project description:In prospective human exploration of outer space, the need to maintain a species over several generations under changed gravity conditions may arise. This paper reports the analysis of the third generation of fruit fly Drosophila melanogaster obtained during the 44.5-day space flight (Foton-M4 satellite, 2014, Russia), followed by the fourth generation on Earth and the fifth generation under conditions of a 12-day space flight (2014, in the Russian Segment of the ISS). The obtained results show that it is possible to obtain the third-fifth generations of a complex multicellular Earth organism under changed gravity conditions (in the cycle “weightlessness – Earth – weightlessness”), which preserves fertility and normal development. However, there were a number of changes in the expression levels and content of cytoskeletal proteins that are the key components of the spindle apparatus and the contractile ring of cells.
2016-10-19 | GSE88866 | GEO
Project description:Drosophila melanogaster is a well-studied genetic model organism with several large-scale transcriptome resources. Here we investigate 7,952 proteins during the fly life cycle from embryo to adult and also provide a high-resolution temporal time course proteome of 5,458 proteins during embryogenesis. We use our large scale data set to compare transcript/protein expression, uncovering examples of extreme differences between mRNA and protein abundance. In the embryogenesis proteome, the time delay in protein synthesis after transcript expression was determined. For some proteins, including the transcription factor lola, we monitor isoform specific expression levels during early fly development. Furthermore, we obtained firm evidence of 268 small proteins, which are hard to predict by bioinformatics. We observe peptides originating from non-coding regions of the genome and identified Cyp9f3psi as a protein-coding gene. As a powerful resource to the community, we additionally created an interactive web interface (http://www.butterlab.org) advancing the access to our data.
2017-04-07 | PXD005713 | Pride