E-MTAB-7529
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-7529 | ExpressionAtlas | 2019-03-20
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-MTAB-7529-analysis-methods.tsv | Tabular | |||
| E-MTAB-7529-atlasExperimentSummary.Rdata | Rdata | |||
| E-MTAB-7529-configuration.xml | Xml | |||
| E-MTAB-7529-percentile-ranks.tsv | Tabular | |||
| E-MTAB-7529.condensed-sdrf.tsv | Tabular |
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Project description:Further to a previous transcription profiling experiment using a GFP reporter gene construct expressing the Drosophila proneural gene atonal (Cachero et al. 2011), a later expressing transcription factor and downstream target of ato, cato (cousin of ato) was explored as the GFP reporter in this experiment. cato-GFP expressing cells were isolated from 10h45min and 11h45min old embryos. GFP+ and GFP- cells were compared on Affymetrix Drosophila version 2.0 chips.
2019-02-19 | E-MTAB-7529 | biostudies-arrayexpress
Project description:Wild-type Drosophila melanogaster expressing nuclear GFP-KASH fusion protein in photoreceptors for cell type-specific gene expression profiling (Rh1-Gal4>UAS-GFPKASH ; Genotype = w1118;; P{w+mC=[UAS-GFP-Msp300KASH}attP2, P{ry+t7.2=rh1-GAL4}3, ry506) were raised in 12:12h light:dark cycle at 25°C. Flies were aged for 10 or 40 days post-eclosion, and eyes were harvested from male flies for global quantitative proteomic analysis. Significantly changed proteins were identified that may contribute to age-associated retinal degeneration and loss of visual function in the aging Drosophila eye.
2021-07-23 | PXD027090 | Pride
Project description:Background: Differential gene expression specifies the highly diverse cell types that constitute the nervous system. With its sequenced genome and simple, well-defined neuroanatomy, the nematode C. elegans is a useful model system in which to correlate gene expression with neuron identity. The UNC-4 transcription factor is expressed in thirteen embryonic motor neurons where it specifies axonal morphology and synaptic function. These cells can be marked with an unc-4::GFP reporter transgene. Here we describe a powerful strategy, Micro-Array Profiling of C. elegans cells (MAPCeL), and confirm that this approach provides a comprehensive gene expression profile of unc-4::GFP motor neurons in vivo. Results: Fluorescence Activated Cell Sorting (FACS) was used to isolate unc-4::GFP neurons from primary cultures of C. elegans embryonic cells. Microarray experiments detected 6,217 unique transcripts of which ~1,000 are enriched in unc-4::GFP neurons relative to the average nematode embryonic cell. The reliability of these data was validated by the detection of known cell-specific transcripts and by expression in UNC-4 motor neurons of GFP reporters derived from the enriched data set. In addition to genes involved in neurotransmitter packaging and release, the microarray data include transcripts for receptors to a remarkably wide variety of signaling molecules. The added presence of a robust array of G-protein pathway components is indicative of complex and highly integrated mechanisms for modulating motor neuron activity. Over half of the enriched genes (537) have human homologs, a finding that could reflect substantial overlap with the gene expression repertoire of mammalian motor neurons. Conclusion: We have described a microarray-based method, MAPCeL, for profiling gene expression in specific C. elegans motor neurons and provide evidence that this approach can reveal candidate genes for key roles in the differentiation and function of these cells. These methods can now be applied to generate a gene expression map of the C. elegans nervous system. Keywords: expression profile
2007-06-18 | GSE8159 | GEO
Project description:Background: Differential gene expression specifies the highly diverse cell types that constitute the nervous system. With its sequenced genome and simple, well-defined neuroanatomy, the nematode C. elegans is a useful model system in which to correlate gene expression with neuron identity. The UNC-4 transcription factor is expressed in thirteen embryonic motor neurons where it specifies axonal morphology and synaptic function. These cells can be marked with an unc-4::GFP reporter transgene. Here we describe a powerful strategy, Micro-Array Profiling of C. elegans cells (MAPCeL), and confirm that this approach provides a comprehensive gene expression profile of unc-4::GFP motor neurons in vivo. Results: Fluorescence Activated Cell Sorting (FACS) was used to isolate unc-4::GFP neurons from primary cultures of C. elegans embryonic cells. Microarray experiments detected 6,217 unique transcripts of which ~1,000 are enriched in unc-4::GFP neurons relative to the average nematode embryonic cell. The reliability of these data was validated by the detection of known cell-specific transcripts and by expression in UNC-4 motor neurons of GFP reporters derived from the enriched data set. In addition to genes involved in neurotransmitter packaging and release, the microarray data include transcripts for receptors to a remarkably wide variety of signaling molecules. The added presence of a robust array of G-protein pathway components is indicative of complex and highly integrated mechanisms for modulating motor neuron activity. Over half of the enriched genes (537) have human homologs, a finding that could reflect substantial overlap with the gene expression repertoire of mammalian motor neurons. Conclusion: We have described a microarray-based method, MAPCeL, for profiling gene expression in specific C. elegans motor neurons and provide evidence that this approach can reveal candidate genes for key roles in the differentiation and function of these cells. These methods can now be applied to generate a gene expression map of the C. elegans nervous system. Experiment Overall Design: Our goal is to profile gene expression throughout the nervous system of the model organism Caenorhabditis elegans. As a first goal, we profiled a single class of embryonic motor neurons. To isolate transcripts from thesec neurons we developed the MAPCeL (Microarray Profiling C. elegans Cells) technique in which unc-4::GFP+ cells are captured by FACS for RNA isolation. We verified these data by bioinformatic means and by in vivo validation by creating GFP reporters for a random set of genes in our enriched gene list.
2008-06-16 | E-GEOD-8159 | biostudies-arrayexpress
Project description:Paper abstract: The transcription factors Abrupt (Ab) and Knot (Kn) act as selectors of distinct dendritic arbor morphologies in two classes of Drosophila sensory neurons, termed class I and class IV, respectively. We performed binding-site mapping and transcriptional profiling of isolated these neurons. Their profiles were similarly enriched in cell-type-specific enhancers of genes implicated in neural development. We identified a total of 429 target genes, of which 56 were common to Ab and Kn; these targets included genes necessary to shape dendritic arbors in either or both of the two sensory subtypes. Furthermore, a common target gene, encoding the cell adhesion molecule Ten-m, was expressed more strongly in class I than IV, and this differential was critical to the class-selective directional control of dendritic branch sprouting or extension. Our analyses illustrate how differentiating neurons employ distinct and shared repertoires of gene expression to produce class-selective morphological traits. da neurons were isolated by magnetic bead sorting from larvae of the following three genotypes and obtained genome-wide expression profiles: larvae expressing a cell-surface marker mCD8:GFP alone (Control), and larvae ectopically expressing Abrupt (Ab ME) or Knot (Kn ME) together with mCD8:GFP in all classes of da neurons. 3 biological replicates were collected.
2013-11-27 | E-GEOD-38660 | biostudies-arrayexpress
Project description:The purpose of this array was to investigate age-dependent changes the transcriptome of a highly homogenous cell population (Drosophila motor neurons) in order to help understand the contribution of changes in gene expression to age-dependent motor deficiencies. Drosophila motor neurons expressing GFP (via the UAS-Gal4 binary expression system) were isolated using flow cytometry from flies that were 7, 35 or 45 days old. The microarray design was highly redundant for calcium-binding and ion channel genes as we had apriori reasons to believe changes in these genes would be important. The ages were chosen because previous work had identified a major shift in neurotransmitter release between the ages of 35 and 45 days in Drosophila motor neurons. Although no significant changes were identified in that window, several genes showed elevated expression in old (35 day and 45 day) motor neurons compared to young (7 day) including matrix metalloproteinase 1 (dMMP1).
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Project description:RNA sequencing analysis of Hb9::GFP mouse embryonic fibroblasts, Hb9::GFP+ primary mouse embryonic motor neurons at day E13.5, Hb9::GFP+ mouse embryonic stem cell-derived motor neurons, Hb9::GFP+ mouse induced pluripotent stem cell derived motor neurons, and Hb9::GFP+ mouse induced motor neurons generated using transcription factor overexpression. The goal of this project is to evaluate the ability of directed differentiation and lineage conversion techniques to generate a bona fide neuronal subtype.
2016-11-08 | GSE89619 | GEO
Project description:A challenge in systems biology is to understand the gene regulatory networks that connect early cellular specification to terminal differentiation of specific cell types. In neurogenesis, neural specification has been well studied, but the link between the proneural transcriptional regulators of specification and the genes that must be activated to construct differentiated neurons is obscure. High resolution temporal profiling of gene expression reveals the events downstream of Atonal (Ato) proneural gene function in Drosophila sensory neurons. Unexpectedly, many differentiation genes are activated soon after specification, even before cell cycle exit and overt neuronal differentiation. Prominent among them are genes required for construction of the ciliary dendrite. Ato activates differentiation both directly and indirectly via several intermediate transcriptional regulators, including Rfx and a new Forkhead family factor. Our analysis of these factors and their regulation provides insight into how proneural factors regulate neuronal subtype differentiation. Investigating the molecular mechanisms of peripheral nervous sytem development in Drosophila melanogaster. Affymetrix Drosophila version 2.0 chips used to measure gene expression from GFP+ and GFP- cells from embryos expressing GFP under the control of the atonal gene enhancer in both wild type and mutant embryos. Data generated for three developmental time-points in quadruplicate.
2011-02-18 | E-GEOD-21520 | biostudies-arrayexpress
Project description:Drosophila Embryo Cell Culture samples allowed to differentiate 3-5 days in culture. Samples express a GFP reporter in cholinergic neurons (7.4 kb ChaGal4:UAS-GFP) or an RFP reporter (2.1 kb Gad1-RFP) in glutamic acid decarboxylase 1 expressing Neurons. This group of samples contains the negatively sorted FACS fractions (2 Cha and 2 Gad negative samples). Keywords: other
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Project description:Primary cultured hippocampal neurons were infected with lentiviral particles bearing constitutively active versions of the transcription factors CREB, SRF, EGR1 and FOS to define the downstream genetic program associated with each of these paradigmatic transcription factors in neurons. For CREB, we also extracted samples at a shorter infection time to try to dissect the different components of the wider genetic response observed upon expression of a constitutively active version of this transcription factor. In order to further explore the contribution of these transcriptional regulators to activity-driven gene expression, we also treated cultured hippocampal neurons infected with GFP-only expressing lentiviral particles with different drugs (bicuculline, forskokine, and BDNF) and profiled the associated transcriptional response. Finally, in order to further explore the role of CREB in forskolin-mediated gene expression, we also used A-CREB, a dominant negative form of this transcription factor. Specifically, we stimulated neurons with forskolin in the presence or absence of lentiviral particles expressing A-CREB and carried out genome-wide transcriptional profiling.
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