GEO DataSets

(Submitter supplied) With aging, significant changes in circadian rhythms occur, including a shift in phase toward a “morning” chronotype and a loss of rhythmicity in circulating hormones. However, the effects of aging on molecular rhythms in the human brain have remained elusive. Here we employed a previously-described time-of-death analyses to identify transcripts throughout the genome that have a significant circadian rhythm in expression in the human prefrontal cortex (Brodmann’s areas (BA) 11 and 47). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL11532

420 Samples

Download data: CEL, TXT

(Submitter supplied) A cardinal symptom of Major Depressive Disorder (MDD) is the disruption of circadian patterns. Yet, to date, there is no direct evidence of circadian clock dysregulation in the brains of MDD patients. Circadian rhythmicity of gene expression has been observed in animals and peripheral human tissues, but its presence and variability in the human brain was difficult to characterize. Here we applied time-of-death analysis to gene expression data from high-quality postmortem brains, examining 24-hour cyclic patterns in six cortical and limbic regions of 55 subjects with no history of psychiatric or neurological illnesses ('Controls') and 34 MDD patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17027

670 Samples

Download data: CEL

(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) Mammalian gene expression displays widespread circadian oscillations. Rhythmic transcription underlies the core clock mechanism, but it cannot explain numerous observations made at the level of protein rhythmicity. We have used ribosome profiling in mouse liver to measure the translation of mRNAs into protein around-the-clock and at high temporal and nucleotide resolution. Transcriptome-wide, we discovered extensive rhythms in ribosome occupancy, and identified a core set of ≈150 mRNAs subject to particularly robust daily changes in translation efficiency. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

48 Samples

Download data: TXT

(Submitter supplied) To screen for specific circadian outputs that may distinguish the pacemaker in the mammalian suprachiasmatic nucleus (SCN) from peripheral-type oscillators in which the canonical clockworks are similarly regulated in a circadian manner, the rhythmic behavior of the transcriptome in forskolin-stimulated NIH/3T3 fibroblasts was analyzed and compared to that found in the rat SCN in vivo and SCN2.2 cells in vitro. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL81

27 Samples

Download data: CEL

(Submitter supplied) We use a conventional (pre-natal) Bmal1 KO (cKO) mouse strain to investigate the effect of circadian disruption on gene expression in the liver by comparing cKO mice with wild type (WT) mice using RNA-Seq. All mice were housed under 12h:12h LD conditions with free access to food and water. Three mice per genotype were sacrificed every 4 h for 20 h (6 time points). Illumina TruSeq Stranded mRNA Sample Prep Kit Set A was used for library construction and samples were sequenced on an Illumina HiSeq 2500. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

36 Samples

Download data: TXT

(Submitter supplied) Gene expression in the liver has been studied extensively in normal mice, but not in mice with circadian disruption. We use a tamoxifen-inducible Lox/Cre KO mouse strain with the most important clock gene knocked out, BMAL-1. The aim of this experiment was to study the effect of circadian disruption on gene expression in the liver by comparing conditional Bmal1 KO mice with WT mice using RNA-seq. All mice were housed under 12h:12h LD conditions with free access to food and water. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

48 Samples

Download data: TXT

(Submitter supplied) Background: Psychosis is a defining feature of schizophrenia and highly prevalent in bipolar disorder. Notably, individuals suffering with these illnesses also have major disruptions in sleep and circadian rhythms, and disturbances to sleep and circadian rhythms can precipitate or exacerbate psychotic symptoms. Psychosis is associated with the striatum, though no study to date has directly measured molecular rhythms and determined how they are altered in the striatum of subjects with psychosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

215 Samples

Download data: CSV

(Submitter supplied) The molecular basis of complex neuropsychiatric disorders most likely involves many genes. In recent years, specific genetic variations influencing risk for schizophrenia and other neuropsychiatric disorders have been reported. We have used custom DNA microarrays and qPCR to investigate the expression of putative schizophrenia susceptibility genes and related genes of interest in the normal human brain. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6893

72 Samples

Download data: TXT

(Submitter supplied) Background: The prefrontal cortex is important in regulating sleep and mood. Diurnally regulated genes in the prefrontal cortex may be controlled by the circadian system, by the sleep-wake states, or by cellular metabolism or environmental responses. Bioinformatics analysis of these genes will provide insights into a wide-range of pathways that are involved in the pathophysiology of sleep disorders and psychiatric disorders with sleep disturbances. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS3080

Platform:

GPL1261

12 Samples

Download data: CEL

Analysis of prefrontal cortices from C57BL/6J animals at 4 Zeitgeber time (ZT) points, 3 and 9 hrs after lights on (ZT3 and ZT9) and 3 and 9 hs after lights off (ZT15 and ZT21). The prefrontal cortex is important in regulating sleep and mood. Results provide insight into genes with diurnal rhythms.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 4 time sets

Platform:

GPL1261

Series:

GSE9471

12 Samples

Download data: CEL

(Submitter supplied) The aim of this analysis was the identification of candidate genes that might be regulated in a circadian manner in the filamentous ascomycete Pyronema confluens. The fungus was grown in submerged culture to promote vegetative growth, and after a period in constant light, the samples were shifted to darkness (DD). Cultures were sampled after 24 and 36 hours in DD. The samples were used for RNA-seq analysis, and candidate genes with significantly higher expression after 24 vs. more...

Organism:

Pyronema omphalodes CBS 100304

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19175

6 Samples

Download data: TXT

(Submitter supplied) Circadian regulation of gene expression in central and peripheral tissue has been studied in mice. The biomedical implications of this findings led us to the development of a model in which to study the circadian mechanisms underlying primate physiology. The objective of this experiment has been to identify genes that are circadianly regulated in the monkey (macaca mulatta) adrenal gland. We analyzed the data using three filters: the first one for presence in at least three out of six time points (presence call=P, P value<0.05). more...

Organism:

Macaca mulatta; Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS2110

Platform:

GPL96

6 Samples

Download data: CEL

Analysis of whole adrenal glands collected at 4-hour intervals across a 24-hour period from adult females acclimated to a 12hr light, 12hr dark photoperiod. Results provide insight into the nature of oscillatory patterns of gene expression in the adrenal gland.

Organism:

Macaca mulatta; Homo sapiens

Type:

Expression profiling by array, count, 6 time sets

Platform:

GPL96

Series:

GSE2703

6 Samples

Download data: CEL

(Submitter supplied) Background: Aging is accompanied by altered thinking (cognition) and feeling (mood) functions that depend to some extent on information processing by brain cortical cell microcircuits. We hypothesized that age-associated long-term functional and biological changes are mediated by gene transcriptomic changes within neuronal cell-types forming cortical microcircuits, namely excitatory pyramidal cells (PYC) and inhibitory GABAergic neurons expressing vasoactive intestinal peptide (Vip), somatostatin (Sst) and parvalbumin (Pvalb). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

83 Samples

Download data: TXT

(Submitter supplied) Circadian rhythmicity governs a remarkable array of fundamental biological functions and is mediated by cyclical transcriptomic and proteomic activities. Epigenetic factors are also involved in this circadian machinery; however, despite extensive efforts, detection and characterization of circadian cytosine modifications at the nucleotide level have remained elusive. In this study, we report that a large proportion of epigenetically variable cytosines show a circadian pattern in their modification status in mice. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

1244 Samples

Download data: TXT

(Submitter supplied) Why we sleep is still one of the most perplexing mysteries in biology. Strong evidence, however, indicates that sleep is necessary for normal brain function and that the need to sleep is a tightly regulated process. Surprisingly molecular mechanisms that determine the need to sleep are incompletely described. Moreover, very little is known about transcriptional changes that specifically accompany the accumulation and discharge of sleep need. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL17400

65 Samples

Download data: CEL

(Submitter supplied) See "Akula et al., Molecular Psychiatry in Press". RNA-sequencing (RNA-seq) is a powerful technique to investigate the complexity of gene expression in the human brain. We used RNA-seq to survey the brain transcriptome in high-quality post-mortem dorsolateral prefrontal cortex from 11 individuals diagnosed with bipolar disorder (BD) and from 11 age- and gender-matched controls. Deep sequencing was performed, with over 350 million reads per specimen. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15433 GPL9115

22 Samples

Download data: TXT

(Submitter supplied) Transcriptional alterations in dorsolateral prefrontal cortex and nucleus accumbens implicate neuroinflammation and synaptic remodeling in opioid use disorder. Transcriptomic profile of 20 control subjects and 20 OUD subjects in brain region DLPFC and NAC

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

80 Samples

Download data: CSV

(Submitter supplied) Skin is the largest organ in the body and serves important barrier, regulatory, and sensory functions. Like other tissues, skin is subject to temporal fluctuations in physiological responses under both homeostatic and stressed states. To gain insight into these fluctuations, we investigated the role of the circadian clock in the transcriptional regulation of human epidermal samples collected in a time-ordered fashion. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13667

298 Samples

Download data: CEL