GEO DataSets

(Submitter supplied) Organisms use endogenous clocks to adapt to the rhythmicity of the environment and to synchronize social activities. Although circadian rhythms have been implicated in multiple aspects of aging, it remains uncertain whether evolutionary selection of circadian cycle gene variants contributes to changes in longevity and aging traits within animal populations. We have sequenced the genomes of Drosophila melanogaster strains with exceptional longevity that were obtained via multiple rounds of selection for reduced senescence from a parental strain. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

72 Samples

Download data: TXT

(Submitter supplied) The spliceosome is a dynamic RNA-protein complex that executes pre-mRNA splicing and is composed of five core small nuclear ribonucleoprotein particles (U1, U2, U4/5/6 snRNP) and >150 additional proteins specific for each snRNP. We report a circadian role for Pre-mRNA Processing factor 4 (PRP4), a conserved component of the spliceosomal U4/U6.U5 triple small nuclear ribonucleoprotein (tri-snRNP) complex. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

15 Samples

Download data: TXT

(Submitter supplied) Study on differential gene expression and splicing between wildtype and clock mutants. This study is part of a comparative analysis of the role of Protein Methyltransferase 5 in the regulation of transcriptional and post-transcriptional processes simultaneously in Arabidopsis and Drosophila. Circadian rhythms allow organisms to time biological processes to the most appropriate phases of the day/night cycle1. more...

Organism:

Arabidopsis thaliana; Drosophila melanogaster

Type:

Expression profiling by array; Expression profiling by genome tiling array

Platforms:

GPL1979 GPL198 GPL6882

18 Samples

Download data: CEL

(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) We investigated the consequences of chronic circadian misalignment (CCM) in the powerful model system of the fruit fly, Drosophila melanogaster. We subjected flies to daily 4-hr phase delays in the light-dark schedule and used the Drosophila Activity Monitoring (DAM) system to continuously track locomotor activity and sleep while simultaneously monitoring fly lifespan. Consistent with previous results, we find that exposing flies to CCM leads to a ~15% reduction in median lifespan in both male and female flies. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

12 Samples

Download data: PDF, 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) Samples 1-8: Tissue-specific RNA sequencing (Illumina) using dissected ring glands isolated from TWO different time points of control (phm>w1118) third instar larvae. Time points are: light phase zt0-4 (which corresponde to 2-4 hours from second to third instar larvae molt); and dark phase zt18-22 (which corresponde to 16-20 hours from second to third instar larvae molt) Samples 9-32: Tissue-specific gene expression (RNA seq Illumina) using dissected ring glands isolated from TWO different time points of third instar larvae. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

16 Samples

Download data: XLSX

(Submitter supplied) This study aims to elucidate how the core circadian transcription factor, CLOCK (Clk), mediates diet-dependent transcriptional changes in fly heads. In particular, we sought to identify how CLK influences gene-level expression changes in fly heads from flies that had been reared on either a high nutrient or low nutrient (dietary restriction) diet.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

24 Samples

Download data: TXT

(Submitter supplied) This study aims to elucidate nutrient dependent changes to the circadian transcriptome of whole flies. In particular, we aim to identify how dietary restriction influence circadian transcriptional output. Circadian analyses were performed to invesitigate diet-dependent changes in the number of circadian transcripts as well as their phases and circadian amplitude.

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL15486

96 Samples

Download data: PAIR, TXT

(Submitter supplied) Single microRNAs are usually associated with hundreds of putative target genes that can influence multiple phenotypic traits in Drosophila, ranging from development to behaviour. We investigated the function of Drosophila miR-210 in circadian behaviour by misexpressing it within circadian clock cells. Manipulation of miR-210 expression levels in the PDF (pigment dispersing factor) positive neurons affected the phase of locomotor activity, under both light-dark conditions and constant darkness. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL18767

16 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are a novel class of small RNAs which act as modulators of gene expression either by inhibiting the translation or by inducing the degradation of their target mRNAs. Several studies suggest a role for miRNAs as regulators of the circadian clock in mammals and Drosophila. Based on computational predictions of target mRNAs of clock (or clock related) genes, we have selected the miR-210 as a putative regulator of the period clock gene. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL18767

8 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are a novel class of small RNAs which act as modulators of gene expression either by inhibiting the translation or by inducing the degradation of their target mRNAs. Several studies suggest a role for miRNAs as regulators of the circadian clock in mammals and Drosophila. Based on computational predictions of target mRNAs of clock (or clock related) genes, we have selected the miR-210 as a putative regulator of the period clock gene. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL18767

8 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL19057

120 Samples

Download data

(Submitter supplied) The circadian clock and rhythmic food intake are both important regulators of rhythmic gene expression in the liver. It remains, however, elusive to which extent the circadian clock network and natural feeding rhythms contribute to rhythmic gene expression. To systematically address this question, we developed an algorithm to investigate differential rhythmicity between a varying number of conditions. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

96 Samples

Download data: TXT

(Submitter supplied) The circadian clock and rhythmic food intake are both important regulators of rhythmic gene expression in the liver. It remains, however, elusive to which extent the circadian clock network and natural feeding rhythms contribute to rhythmic gene expression. To systematically address this question, we developed an algorithm to investigate differential rhythmicity between a varying number of conditions. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

24 Samples

Download data: TXT

(Submitter supplied) Disruption of the circadian clock, which directs rhythmic expression of numerous genes, accelerates aging. To inquire how the circadian system protects organisms during aging, we compared circadian transcriptomes in heads of young and old Drosophila melanogaster. These data revealed a class of genes that adopt de novo rhythmicity during aging, termed "late life cyclers" (LLCs). We show that application of exogenous oxidative stress in young flies mimics aging by inducing robust, rhythmic LLC upregulation in a light- and CLOCK-dependent fashion. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

24 Samples

Download data: DIFF, TXT

(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) We report a large-scale transcriptomic analysis of several tissues of a reference Drosophila melanogaster strain as well as 141 Drosophila Genetic Reference Panel (DGRP) lines at high temporal resolution. Comprehensive data analysis has identified thousands of genes under clock- and tissue-specific control. By using a molecular time table approach, we uncovered that >20% of probed DGRP lines exhibit aberrant circadian expression, and the genetic dissection of one line (DGRP-796) revelled disrupted circadian gene expression in all analysed tissues, revealing a novel deletion in the cry gene. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

778 Samples

Download data: CSV

(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) 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