GEO DataSets

(Submitter supplied) KDM5 family proteins are best known for their demethylation of the promoter proximal chromatin mark H3K4me3. KDM5-regulated transcription is critical in the brain, with variants in the X-linked paralog KDM5C causing the intellectual disability (ID) disorder, Claes-Jensen syndrome. Although the demethylase activity of KDM5C is known to be important for neuronal function, the contribution of non-enzymatic activities remains less characterized. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16479

12 Samples

Download data: BW

(Submitter supplied) In Drosophila ovarian somatic cells, Piwi and piRNA assemble Piwi-piRISC and protect the genome against transposons. The Piwi-piRISC precursor is produced in Yb bodies and translocates with Armi to mitochondria for Zuc-dependent maturation. Daed features in this maturation phase, but the details remain unclear. Here, we show that Daed stabilizes its partner Gasz through protein?protein interaction, and tethers Armi to mitochondria to allow Zuc to process substrates. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL16479

12 Samples

Download data: TXT

(Submitter supplied) Cancer-driving mutations synergize with inflammatory stress signaling pathways during carcinogenesis. Drosophila melanogaster tumour models are increasingly recognized as models to inform conserved molecular mechanisms of tumorigenesis with both local and systemic effects of cancer. Although initial discoveries of the Toll-NFkB signaling pathway in development and immunity was pioneered in Drosophila, limited information is available for its role in cancer progression. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16479

3 Samples

Download data: XLSX

(Submitter supplied) Fragile X syndrome (FXS) is a neuro-developmental disorder caused by silencing Fmr1, which encodes the RNA-binding protein FMRP. Although Fmr1 is expressed in adult neurons, it has been challenging to separate acute from chronic effects of loss of Fmr1 in models of FXS. We have used the precision of Drosophila genetics to test if Fmr1 acutely affects adult neuronal plasticity in vivo, focusing on the s-LNv circadian pacemaker neurons that show 24-hour rhythms in structural plasticity. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19132 GPL16479

6 Samples

Download data: CSV

(Submitter supplied) Piwi-interacting RNAs (piRNAs) are the main repressors of transposable elements (TEs) in animal germlines. In Drosophila, Piwi-piRNA complexes associate with nascent TE transcripts to drive heterochromatin formation and TE repression. However, previous studies have shown that Piwi also associates with large amounts of mRNAs, raising the question of how Piwi discriminates between mRNAs and TEs. To answer this question, we performed a comprehensive analysis of Piwi-associated RNAs, compositionally and functionally, to decipher the targeting rules of Piwi-piRNA complexes. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

33 Samples

Download data: BED, BEDGRAPH, BW, CSV, FA, FASTA, GTF, TSV, TXT

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

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL19806 GPL16479 GPL19132

16 Samples

Download data: BW, TXT

(Submitter supplied) Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases enzymes catalyzing the transition of 5mC to 5hmC in DNA and have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16479

2 Samples

Download data: BW, TXT

(Submitter supplied) Color vision in Drosophila is mediated by photoreceptors R7 and R8, which express various combinations of opsins Rh3, Rh4, Rh5 and Rh6 depending on their cellular identity. Most ommatidia are classified as either “pale” or “yellow” subtypes with pale ommatidia coordinately expressing Rh3 and Rh5—in R7 and R8 cells respectively—while yellow express Rh4 and Rh6. Subtype identity is established initially in R7 photoreceptors via a stochastic mechanism then transmitted to the R8 via an inductive signal to ensure paired opsin expression. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16479

8 Samples

Download data: CSV

(Submitter supplied) Drosophila GCN5 activity profoundly impacts gene expression.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19132 GPL16479

36 Samples

Download data: CSV, TXT

(Submitter supplied) System-wide metabolic homeostasis is crucial for maintaining physiological functions of living organisms. Stable-isotope tracing metabolomics allows to unravel metabolic activity quantitatively by measuring the isotopically labeled metabolites, but has been largely restricted by coverage. Yet, delineating system-wide metabolic homeostasis at the whole-organism level remains non-trivial. Here, we develop a global isotope tracing metabolomics technology to measure labeled metabolites with a metabolome-wide coverage. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16479

6 Samples

Download data: CSV

(Submitter supplied) A single H4 variant gene (H4r) that is located outside of the histone cluster and gives rise to a polyA tailed messager RNA via replication-independent expression is preserved in Drosophila strains despite that its protein product is identical with canonical H4. In order to reveal information on the possible role of this alternative H4 we epitope tagged endogenous H4r and revealed its genome-wide localization to chromatin at the nucleosomal level. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16479

24 Samples

Download data: BW

(Submitter supplied) It has been proposed that nucleome organization and genome function involve interplays between protein, RNA and chromatin architectures. However, how chromatin interactions are cooperatively mediated by nuclear proteins and RNAs have not been fully explored. Here, we report the multivalent interplays in Drosophila cells involving RNA Polymerase II (RNAPII), nuclear RNAs and chromatin interactions. Using a novel genomic approach (pRChIA-PET) for protein-RNA-chromatin interactions, we discovered that extensive combination of nuclear RNAs cooperatively act in trans and co-localize with RNAPII and associated protein cofactors at chromatin interaction loci of active promoters and enhancers. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL16479 GPL19132

22 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) We report the 4C-seq data and ChIP-seq to study Shep regulation of chromatin looping. We also reported ATAC-seq and CUT&Tag data on sorted neurons that reveal chromatin accessibility and states during the neuronal remodeling of Drosophila melanogaster

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL19132 GPL17275 GPL16479

23 Samples

Download data: BW

(Submitter supplied) Noncoding RNAs (ncRNAs) are an emerging class of regulatory molecules with a broad range of regulatory functions believed to be mediated by ncRNA-chromatin interactions. Genome-wide understanding of ncRNA functions requires precise mapping of all ncRNAs and their target loci. Current methods for studying chromatin-associated ncRNA lack specificity or are limited to singly assessing RNAs. We devised an unbiased strategy to identify all RNA Interactions with Chromatin by Paired-End-Taging (RICh-PET) and applied this approach to characterize the Drosophila RNA-chromatin interactome. more...

Organism:

Homo sapiens; Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL22339 GPL16479

19 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) PIWI-interacting RNAs (piRNAs) are germline-specific small RNAs that form effector complexes with PIWI proteins (Piwi–piRNA complexes), and plays a critical role for preserving genomic integrity by repressing transposable elements (TEs). Drosophila Piwi transcriptionally silences specific targets through heterochromatin formation, and increases H3K9me3 and histone H1. Additionally, Nxf2, a nuclear RNA export factor variant, has been identified as a co-factor. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL21306 GPL23702 GPL16479

36 Samples

Download data: BEDGRAPH, TSV, WIG

(Submitter supplied) CRTC modulates one-carbon metabolism and insulin signaling during fasting

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16479

21 Samples

Download data: DIFF, TXT

(Submitter supplied) The ability of neural stem cells (NSCs) to switch between quiescence and proliferation is crucial for brain development and homeostasis. Increasing evidence suggest that variants of histone lysine methyltransferases including KMT5A are associated with neurodevelopmental disorders. However, the function of KMT5A/Pr-set7/SETD8 in the central nervous system is not well established. Here, we show that Drosophila Pr-Set7 is a novel regulator of NSC reactivation. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16479

4 Samples

Download data: BED

(Submitter supplied) Drosophila Piwi associates with PIWI-interacting RNAs (piRNAs) and represses transposons transcriptionally through heterochromatinization; however, this process is poorly understood. Here, we identify Brahma (Brm), the core adenosine triphosphatase of the SWI/SNF chromatin remodeling complex, as a new Piwi interactor, and show Brm involvement in activating transcription of Piwi-targeted transposons before silencing. more...

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL16479 GPL13304

18 Samples

Download data: BEDGRAPH, CSV, TXT

(Submitter supplied) The circadian system produces ~24-hr oscillations in behavioral and physiological processes to ensure that they occur at optimal times of day and in the correct temporal order. At its core, the circadian system is composed of dedicated central clock neurons that keep time through a cell-autonomous molecular clock. To produce rhythmic behaviors, time-of-day information generated by clock neurons must be transmitted across output pathways to regulate the downstream neuronal populations that control the relevant behaviors. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16479

5 Samples

Download data: TXT

(Submitter supplied) We identified NAP-1 as regulator of histone H1 acetyation.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16479

6 Samples

Download data: TXT