GEO DataSets

(Submitter supplied) CWO binding sites were genome-widely searched with Drosophila genome tiling array. Abstract: The Drosophila circadian clock consists of integrated autoregulatory feedback loops, making the clock difficult to elucidate without comprehensively identifying the network components in vivo. Previous studies have adopted genome-wide screening for clock-controlled genes using high-density oligonucleotide arrays that identified hundreds of clock-controlled genes. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3923

4 Samples

Download data: BED, CEL, ZIP

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

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platforms:

GPL1322 GPL72

45 Samples

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(Submitter supplied) S2 cells transfected with pAc-Clk or empty vector Keywords: S2 cells Clk

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

6 Samples

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(Submitter supplied) 6 Timepoint microarray from control strain Keywords: Timepoints yw

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

10 Samples

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(Submitter supplied) 6 Timepoints from 5073 strain Keywords: Timepoints 5073 cwo

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

9 Samples

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(Submitter supplied) CLK targets from fly heads using the TIM-GAL4; UAS-CLKGR line Keywords: CLK TARGETS

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platforms:

GPL1322 GPL72

12 Samples

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(Submitter supplied) Experiments performed in S2 cells to identify direct CLK targets Keywords: CLK targets

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platforms:

GPL1322 GPL72

8 Samples

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(Submitter supplied) Background: Broadly expressed transcriptions factors (TFs) control tissue-specific programs of gene expression through interactions with local TF networks. A prime example is the circadian clock: although the conserved TFs CLOCK (CLK) and CYCLE (CYC) control a transcriptional circuit throughout animal bodies, rhythms in behavior and physiology are generated tissue specifically. Yet, how CLK and CYC determine tissue-specific clock programs has remained unclear. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11203

24 Samples

Download data: TXT

(Submitter supplied) Chromatin organization plays a crucial role in gene regulation by controlling the accessibility of DNA to transcription machinery. While significant progress has been made in understanding the regulatory role of clock proteins in circadian rhythms, how chromatin organization affects circadian rhythms remains poorly understood. Here, we employed ATAC-seq (Assay for Transposase-Accessible Chromatin with Sequencing) on FAC-sorted Drosophila clock neurons to assess genome-wide chromatin accessibility at dawn and dusk over the circadian cycle. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25244

33 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) CLOCK (CLK) is a master transcriptional regulator of the circadian clock in Drosophila. To identify CLK direct target genes and address circadian transcriptional regulation in Drosophila, we performed chromatin immunoprecipitation-tiling array assays (ChIP-chip) with a number of circadian proteins. CLK binding cycles on at least 800 sites with maximal binding in the early night. The CLK partner protein CYCLE (CYC) is on most of these sites. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6629

21 Samples

Download data: BED, CEL

(Submitter supplied) RNAseq transcriptional profiling of Drosophila heads from Achilles RNAi or control animals

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16479

14 Samples

Download data: TXT, XLSX

(Submitter supplied) Circadian rhythms are cell-autonomous biological oscillations with a period of about 24 hours. Current models propose that transcriptional feedback loops are the primary mechanism for the generation of circadian oscillations1. In these models, Drosophila S2 cells are generally regarded as ‘non-rhythmic’ cells, as they do not express several canonical circadian components2,3. Using an unbiased multi-omics approach, we made the surprising discovery that Drosophila S2 cells do in fact display widespread daily rhythms. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21306

40 Samples

Download data: TXT

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

Organism:

Drosophila melanogaster

Type:

Expression profiling by array; Expression profiling by genome tiling array

Platforms:

GPL1322 GPL5919

28 Samples

Download data: BAR, CEL, TXT

(Submitter supplied) Little is known about the contribution of translational control to circadian rhythms. To address this issue and in particular translational control by microRNAs (miRNAs), we knocked down the miRNA biogenesis pathway in Drosophila circadian tissues. In combination with an increase in circadian-mediated transcription, this severely affected Drosophila behavioral rhythms, indicating that miRNAs function in circadian timekeeping. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

27 Samples

Download data: CEL

(Submitter supplied) Gene expression profiling of distinct members of a neuronal circuit has the potential to identify candidate molecules and mechanisms that underlie the formation, organization and function of the circuit. To this end, we report here the application of a novel method to characterize RNAs from small numbers of specific Drosophila brain neurons, which belong to the circadian circuit. We identified three different sets of mRNAs enriched in different subclasses of clock neurons: one is enriched in all clock neurons, a second is enriched in PDF-positive clock neurons and a third is enriched in PDF-negative clock neurons. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

23 Samples

Download data: CEL

(Submitter supplied) The transcription factor Mef2 regulates activity-dependent neuronal plasticity and morphology in mammals, and clock neurons are reported to experience activity-dependent circadian remodeling in Drosophila. We show here that Mef2 is required for this daily fasciculation-defasciculation cycle. Moreover, the master circadian transcription complex CLK/CYC directly regulates Mef2 transcription. ChIP-Chip analysis identified numerous Mef2 target genes implicated in neuronal plasticity, including the cell-adhesion gene Fas2. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6629

6 Samples

Download data: BED, CEL

(Submitter supplied) To address the contribution of transcriptional regulation to Drosophila clock gene expression and to behavior, we generated a series of CRISPR-mediated deletions within two regions of the circadian gene timeless (tim), an intronic E box region and an upstream E box region that are both recognized by the key transcription factor Clock (Clk) and its heterodimeric partner Cycle. The upstream deletions but not an intronic deletion dramatically impact tim expression in fly heads; the biggest upstream deletion reduces peak RNA levels and tim RNA cycling amplitude to about 15% of normal, and there are similar effects on tim protein (TIM). more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22106

42 Samples

Download data: BW

(Submitter supplied) The contribution of cis-regulatory elements to Drosophila circadian gene expression is poorly understood. We generated a series of CRISPR-mediated deletions within the regulatory regions of the circadian gene timeless (tim) and characterized them through multiple high-throughput sequencing experiments. We isolated heads from wild-type and mutant flies around the clock and performed RNA-Seq on them to determine the effects of regulatory element deletions on circadian gene expression.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22106

47 Samples

Download data: CSV, TXT

(Submitter supplied) To address the contribution of transcriptional regulation to Drosophila clock gene expression and to behavior, we generated a series of CRISPR-mediated deletions within two regions of the circadian gene timeless (tim), an intronic E box region and an upstream E box region that are both recognized by the key transcription factor Clock (Clk) and its heterodimeric partner Cycle. The upstream deletions but not an intronic deletion dramatically impact tim expression in fly heads; the biggest upstream deletion reduces peak RNA levels and tim RNA cycling amplitude to about 15% of normal, and there are similar effects on tim protein (TIM). more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22106

15 Samples

Download data: BW

(Submitter supplied) Many different functions are regulated by circadian rhythms, including those orchestrated by discrete clock neurons within animal brains. To comprehensively characterize and assign cell identity to the 75 pairs of Drosophila circadian neurons, we optimized a single cell RNA sequencing method and assayed clock neuron gene expression at different times of day. The data identify at least 17 clock neuron categories with striking spatial regulation of gene expression. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

84 Samples

Download data: CSV