GEO DataSets

(Submitter supplied) The R-loop in the genome participates in modulating transcription, replication and DNA damage repair, yet its regulation and biologic impact on development in vivo remain to be explored. Here, we modified CUT&Tag strategy and established R-loop profiles of Drosophila across multiple developmental stages. While lack of GC preference, the broad class of R-loops in Drosophila all highly follow the RNAPII pausing, which is also a conserved R-loop regulatory mechanism in mammals. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL25244 GPL32518

40 Samples

Download data: BW, NARROWPEAK, TXT

(Submitter supplied) Intracellular ribonucleases (RNases) are essential in all aspects of RNA metabolism, including maintaining accurate RNA levels. Inherited mutations in genes encoding ubiquitous RNases are associated with human diseases, primarily affecting the nervous system. Recessive mutations in genes encoding an evolutionarily conserved RNase complex, the RNA exosome, lead to syndromic neurodevelopmental disorders characterized by progressive neurodegeneration, such as Pontocerebellar Hypoplasia Type 1b (PCH1b). more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

6 Samples

Download data: MTX, TSV

(Submitter supplied) Innate immunity in Drosophila acts as an organismal surveillance system that measures external stimuli or cellular fitness and triggers context-specific responses to fight infections and maintain tissue homeostasis. However, uncontrolled activation of innate immune pathways can be detrimental to the system. In mammals, innate immune signaling is often overactivated in malignant cells and contributes to tumor progression. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

12 Samples

Download data: TSV

(Submitter supplied) Adult stem cells are essential for maintaining tissue homeostasis. We employ Drosophila tracheal progenitors to understand the mechanism controlling the polarity of stem cell migration. Here, we show that polarity of tracheal progenitors depends on the function of fat body. Cytokine, Upd2, produced by fat body, signals to tracheal progenitors and activation JAK/STAT signal transduction. Perturbation of Upd2 production or loss-of-function of JAK/STAT signaling in the trachea cause aberrant bidirectional migration of tracheal progenitors. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

6 Samples

Download data: CSV

(Submitter supplied) After injury, severed axons separated from their somas activate programmed axon degeneration, a conserved pathway to initiate their degeneration within a day. Conversely, severed projections deficient in programmed axon degeneration remain morphologically preserved with functional synapses for weeks to months after injury. How this synaptic function is sustained remains currently unknown. Here, we demonstrate that dNmnat-mediated over-expression attenuates programmed axon degeneration in distinct neuronal populations. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

36 Samples

Download data: TXT

(Submitter supplied) Muscle development and diversity require a large number of spatially and temporally regulated events controlled by transcription factors (TFs). Drosophila has long stood as a model organism to study myogenesis due to the highly conserved key TFs involved at all stages of muscle development, from specification to differentiation. While many studies focused on the diversification of Drosophila larval musculature, how distinct adult muscle types are generated is much less characterised. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21306 GPL25244

10 Samples

Download data

(Submitter supplied) Muscle development and diversity require a large number of spatially and temporally regulated events controlled by transcription factors (TFs). Drosophila has long stood as a model organism to study myogenesis due to the highly conserved key TFs involved at all stages of muscle development, from specification to differentiation. While many studies focused on the diversification of Drosophila larval musculature, how distinct adult muscle types are generated is much less characterised. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

6 Samples

Download data: TXT

(Submitter supplied) Arthropod genitalia and walking legs are serially homologous appendages derived from a ventral appendage ‘ground state’ shaped by different Hox inputs. However, there has been little comparison between the downstream gene regulatory networks and how they build and pattern serially homologous appendages differently. In the pre-tarsal region of the developing leg and antennae of Drosophila, a combination of the transcription factors C15, Lim1 homeobox 1 (Lim1), and Al (Aristaless) are required for the development of the terminal structures, the tarsal claws and aristae, respectively, but the role and interactions among these factors as well as other genes known to regulate leg development was not known in the developing genitalia. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25244

1 Sample

Download data: BW, NARROWPEAK

(Submitter supplied) Current models of MSL spreading in the context of Drosophila dosage compensation (DC) focus on interactions of MSL3 (male-specific lethal 3) with histone marks; especially Set2-dependent H3 lysine-36 trimethylation (H3K36me3). However, previous studies investigating the role of H3K36me3 in DC do not fully account for: other targets of Set2, redundancy between canonical H3.2 and replication-dependent H3.3, and X chromosome effects that are not sex-specific.To differentiate amongst these possibilities and to assess whether Set2 and/or H3K36 is essential for DC, we use RNA-Seq in WL3 brain (male and female) and L1 larvae (mixed sex) to compare Set2, H3.2K36R, H3.3K36R, and combined H3K36R mutant genotypes. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

23 Samples

Download data: TXT

(Submitter supplied) Current models of MSL spreading in the context of Drosophila dosage compensation (DC) focus on interactions of MSL3 (male-specific lethal 3) with histone marks; especially Set2-dependent H3 lysine-36 trimethylation (H3K36me3). However, previous studies investigating the role of H3K36me3 in DC do not fully account for: other targets of Set2, redundancy between canonical H3.2 and replication-dependent H3.3, and X chromosome effects that are not sex-specific.To differentiate amongst these possibilities and to assess whether Set2 and/or H3K36 is essential for DC, we use RNA-Seq in WL3 brain (male and female) and L1 larvae (mixed sex) to compare Set2, H3.2K36R, H3.3K36R, and combined H3K36R mutant genotypes. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

36 Samples

Download data: TXT

(Submitter supplied) Deficits in chemosensory processing are associated with healthy aging, as well as numerous neurodegenerative disorders, including Alzheimer’s Disease (AD). In many cases, chemosensory deficits are harbingers of neurodegenerative disease, and understanding the mechanistic basis for these changes may provide insight into the fundamental dysfunction associated with aging and neurodegeneration. The fruit fly, Drosophila melanogaster, is a powerful model for studying chemosensation, aging, and aging-related pathologies, yet the effects of aging and neurodegeneration on chemosensation remain largely unexplored in this model, particularly with respect to taste. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

6 Samples

Download data: MTX, TSV

(Submitter supplied) 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). more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

147 Samples

Download data

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis elegans; Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

5 related Platforms

171 Samples

Download data

(Submitter supplied) R-loops are involved in many biological processes in cells, yet the regulatory principles for R-loops in vivo and their impact on development remain to be explored. Here, we modified the CUT&Tag strategy to profile R-loops in Drosophila at multiple developmental stages. While high GC content promotes R-loop formation in mammalian cells, it is not required in Drosophila. In contrast, RNAPII abundance on chromatin appears to be a universal inducing factor for R-loop formation in the Drosophila genome, including active promoters and enhancers, and H3K27me3 decorated repressive regions and intergenic repeat sequences. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL32518 GPL25244

40 Samples

Download data: BW, NARROWPEAK, TXT

(Submitter supplied) The Drosophila melanogaster male accessory gland (AG) is crucial for reproductive success, producing seminal fluid proteins that impact female post-mating behavior and physiology. To understand the regulatory networks governing accessory gland function, we conducted a bulk RNA sequencing (RNA-Seq) study to analyze the effects of overexpressing three key regulatory genes: dMyc, Yorkie (Yki), and the E2F-Dp heterodimer, compared to wild-type (WT) controls. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

12 Samples

Download data: CSV

(Submitter supplied) Loss of proteostasis is an aging hallmark and the culprit of many age-related diseases. Different cell compartments experience distinctive challenges to maintain protein quality control but it remains underexplored how subcellular proteostasis is regulated by aging. Here, by targeting the misfolding_x0002_prone FlucDM luciferase to the cytoplasm, mitochondria, and nucleus, we have established transgenic sensors to examine subcellular proteostasis in Drosophila. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

54 Samples

Download data: TXT

(Submitter supplied) Histone modifications are critical for regulating chromatin structure and gene expression. Dysregulation of histone modifications likely contributes to disease states and cancer. Depletion of the chromatin-binding protein BRWD3, a known substrate-specificity factor of the Cul4-DDB1 E3 ubiquitin ligase complex, results in increased in H3K4me1 levels. The underlying mechanism linking BRWD3 and H3K4 methylation, however, has yet to be defined. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25244

4 Samples

Download data: BIGWIG

(Submitter supplied) To validate the applicability of pre-amplified low-input RNA sequencing method in Drosophila melanogaster cell types, we used Drosophila nephrocytes as an example case.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

3 Samples

Download data: RESULTS

(Submitter supplied) Long-range transcriptional activation of gene promoters by abundant enhancers in animal genomes raises the need for mechanisms to limit inappropriate gene regulation. DNA elements known as insulators provide one such mechanism by shielding promoters from an enhancer when placed in between these two elements. Whereas promoters and enhancers have been extensively characterized in animal genomes, insulators have not because of the lack of a high-throughput screening assay. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL25244 GPL34080

16 Samples

Download data: BEDGRAPH, MCOOL, TSV

(Submitter supplied) tRNA quantification of neuron-biased and neuroblast-biased Drosophila larval brains

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL25244

6 Samples

Download data: CSV