GEO DataSets

(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) To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. In this comparison, adult male Long-Evans rats (175-200g; N=45) were housed under a standard 12h light:12h dark photoperiod (LD 12:12; lights-on at 0600 hr). more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL85

18 Samples

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(Submitter supplied) To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour interval across 2 circadian cycles, cells from single 6-well plates were harvested and pooled for total RNA extraction. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL85

27 Samples

Download data: CEL, EXP, RPT

(Submitter supplied) In mammalian tissues circadian gene expression can be driven by local oscillators or systemic signals controlled by the master pacemaker in the suprachiasmatic nucleus. Here we show that simulated body temperature cycles, but not peripheral oscillators, can control the rhythmic expression of Cold-Inducible RNA binding Protein (CIRP) in cultured fibroblasts. In turn, loss-of-function experiments indicate that CIRP is required for high amplitude circadian gene expression. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

4 Samples

Download data: BEDGRAPH

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

30 Samples

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(Submitter supplied) This study was performed to characterize the rhythmic transcirptome of the murine adrenal gland with a focus on the corticosterone synthesis pathway. Keywords: time course

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS2232

Platform:

GPL1261

24 Samples

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Analysis of adrenal glands of wild type animals at various time points after transferring the animals from a light-day cycle to constant darkness. Results provide insight into the function of the adrenal cortical clock.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 12 time sets

Platform:

GPL1261

Series:

GSE4238

24 Samples

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(Submitter supplied) Male KO (Syt10-Cre/Cre x Bmal1-flox/-) and CON (Syt10-Cre/Cre x Bmal1-+/-) mice were entrained to 12h:12h light:dark conditions for two weeks and sacrificed at 4 different time points (CT1, 7, 13, 19) on the second day after release into constant darkness conditions. Total RNA was isolated from epididymal white adipose tissue biopsies and subjected to microarray hybridization.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

24 Samples

Download data: CEL

(Submitter supplied) One µg of total RNA from either an individual rat or from a pooled sample was amplified and labeled with a fluorescent dye (either Cy3 or Cy5) using the Low RNA Input Linear Amplification Labeling kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol. The amount and quality of the resulting fluorescently labeled cRNA was assessed using a Nanodrop ND-100 spectrophometer and an Agilent Bioanalyzer. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL890

20 Samples

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(Submitter supplied) Genome-wide expression analysis of two circadian oscillatory mechanisms in the mouse liver To identify the genes of which the circadian expression is regulated by endogenous glucocorticoids, we performed DNA microarray analysis using hepatic RNA from adrenalectomized (ADX) and sham-operated mice. Mice were housed in a 12:12 h light-dark cycle (LD12:12; lights on at zeitgeber time (ZT) 0) for at least two weeks before the day of the experiment. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS1870

Platform:

GPL81

4 Samples

Download data: CEL, EXP, RPT, TXT

Expression profiling of livers of adrenalectomized C57BL/6 males 2 hours into the light or dark periods of a 12:12 hour light cycle. Results identify genes regulated by endogenous glucocorticoids in a circadian manner.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 agent, 2 protocol, 2 time sets

Platform:

GPL81

Series:

GSE2162

4 Samples

Download data: CEL, EXP, RPT, 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) Background: Identifying the gene regulatory networks governing physiological signal integration remains an important challenge in circadian biology. Epidermal growth factor receptor (EGFR) has been implicated in circadian function and EGFR is expressed in the suprachiasmatic nucleus (SCN), the core circadian pacemaker. The transcription networks downstream of EGFR in the SCN are unknown, but by analogy to other SCN inputs we expect the response to EGFR activation to depend on circadian timing and thus be “circadian context–dependent”. more...

Organism:

Rattus norvegicus; synthetic construct

Type:

Expression profiling by array

Platform:

GPL3446

8 Samples

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(Submitter supplied) Described in Zak et al 2006 (Pubmed ID 16784547)

Organism:

Rattus norvegicus

1 Series

8 Samples

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(Submitter supplied) The circadian clock is an evolutionarily conserved mechanism that drives rhythmic expression of downstream genes. The core circadian clock drives the expression of clock-controlled genes either directly or indirectly, which in turn play critical roles in carrying out many rhythmic physiological processes. Nevertheless, the molecular mechanisms by which clock output genes orchestrate rhythmic signals from the brain to peripheral tissues are largely unknown. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21306

96 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; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

72 Samples

Download data: BED, BIGWIG

(Submitter supplied) To investigate the rhythmic gene expression in the SCN during day.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

24 Samples

Download data: TXT

(Submitter supplied) Histone ChIP-seq was performed at varied time of the day to map the gene promoter and active enhancer sites in the central clock; SCN (suprachiasmatic nuclei). Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K4me3 and H3K27ac in adult mouse SCN and cortex at distinct time of the day .

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

48 Samples

Download data: BED, BIGWIG

(Submitter supplied) We report circadian (time series, circadian time 0, 3, 6, 9, 12, 18, 21h) transcriptomic analysis of mouse fetal (embryonic day 17) suprachiasmatic nuclei (SCN) from either sham operarated ad libitum fed mothers (group A) or from SCN-lesioned mothers on resctricted feeding regime. The analysis revealed low amplitude rhythms in the fetal SCN driven by maternal SCN and/or maternal feeding behavior.

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20084

16 Samples

Download data: CSV

(Submitter supplied) One hundred ninety wildtype male C57BL/6J mice age 7-10 weeks were purchased from Jackson Laboratory and entrained to a 12:12 light:dark cycle for 2 weeks. Mice were placed in light-tight boxes on a 12:12 LD cycle for 4 weeks, then released into constant darkness. Starting 30 hours after entry into DD (CT18), tissues from 5 (skeletal muscle) or 10 (liver or SCN) wildtype mice were collected every 4 hours for 48 hours, for a total of 12 timepoints. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1073

76 Samples

Download data: CEL