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EGF treated SCN versus intra-animal control at two circadian times

ABSTRACT: EGF treated SCN versus intra-animal control at two circadian times

OTHER RELATED OMICS DATASETS IN: GSE4245

PROVIDER: PRJNA94907 | ENA |

REPOSITORIES: ENA

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EGF treated SCN versus intra-animal control at two circadian times

Project description: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”. Results: We have undertaken a systems level analysis of EGFR circadian context–dependent signaling in the SCN. We collected gene expression profiles to study how the SCN response to EGFR activation depends on circadian timing. Mixed–model analysis of variance (ANOVA) was employed to identify genes with circadian context–dependent EGFR regulation. The expression data was integrated with transcription factor (TF) binding predictions through gene group enrichment analyses to generate robust hypotheses about TFs responsible for the circadian phase–dependent EGFR responses. Conclusions: The analysis results suggest that the transcriptional response to EGFR signaling in the SCN may be partly mediated by established EGFR signaling regulated TFs (AP1, Ets1), TFs involved in circadian clock entrainment (CREB), and by core clock TFs (Rorα). qRT-PCR measurements of several TF expression levels support a model in which circadian context-dependent EGFR responses are partly achieved by circadian regulation of upstream signaling components. Our study suggests an important role for EGFR signaling in SCN function and provides an example for gaining physiological insights through systems-level analysis. Keywords: dose response; repeat sample

2006-06-21 | GSE4245 | GEO

Circadian Profiling of the Transcriptome in Immortalized Rat SCN Cells: Comparison to Long-Evans Rat SCN

Project description: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). At 1800 hr (circadian time [CT] 12), animals were exposed to constant darkness (DD) and 12 hours later (0600 hr or CT 0), sacrificed under isoflurane anesthesia at 6-hr intervals (N=5) for 48 hours by decapitation using an infrared viewer. After the eyes were removed in the dark, SCN tissue was immediately dissected under dim light, frozen in liquid nitrogen, and stored at –800C. SCN tissue from individual animals was separately homogenized in TRIzol reagent by aspiration through a 25-gauge needle and then extracted cellular RNA for all animals at each timepoint was pooled into a single sample. RNA samples were subjected to on-column treatment with DNAse-1 to digest genomic DNA and then were stored at –80°C before routine processing for GeneChip analysis. Keywords: other

2004-10-09 | GSE1673 | GEO

Transcription profiling of rat immortalized SCN cells - circadian experiment

2008-06-11 | E-GEOD-1654 | biostudies-arrayexpress

Circadian Profiling of the Transcriptome in Immortalized Rat SCN Cells (3 biological replicates)

2004-10-08 | GSE1654 | GEO

Mouse SCN in LC-MSMS - The suprachiasmatic nucleus (SCN) acts as the central clock to coordinate circadian oscillations in mammalian behavior, physiology and gene expression. Despite our knowledge of the circadian transcriptome of the SCN, how it impacts genome-wide protein expression is not well understood. Here, we interrogated the murine SCN proteome across the circadian cycle using SILAC-based quantitative mass spectrometry.

Project description:The suprachiasmatic nucleus (SCN) acts as the central clock to coordinate circadian oscillations in mammalian behavior, physiology and gene expression. Despite our knowledge of the circadian transcriptome of the SCN, how it impacts genome-wide protein expression is not well understood. Here, we interrogated the murine SCN proteome across the circadian cycle using SILAC-based quantitative mass spectrometry.

2014-09-10 | PXD000778 | Pride

SCN Proteomic Study:electroacupuncture induced circadian control in Suprachiasmatic Nucleus

Project description:Recent reports highlight phosphorylation as a major role in the regulation of sleep-wake cycles, to a lesser extent, the phosphoproteome in Suprachiasmatic Nucleus (SCN) is not well understood. We use multiplex tandem mass tag (TMT) - labelling coupled with liquid chromatography-mass spectrometry (LC-MS) to study the rhythmic regulatory effects of electroacupuncture(EA) at different times in constant darkness and the mechanism of EA mediated SCN protein phosphorylation. We applied the mass spectrometry-based phosphoproteome to explore the molecular characteristics of EA-induced phosphorylation modification in the SCN.

2021-10-31 | PXD029450 |

Circadian regulation of gene expression in the SCN (gene expression)

Project description:We performed a circadian RNA expression profile of the mammalian biological clock, the suprachiasmatic nucleus (SCN) in C57/BL6 mice, at 2-hour resolution using microarrays, and at 6-hour resolution using RNA-seq. 24 samples total covering 24 time points, with no replicates. SCN samples from mouse brains collected every 2 hours for 2 days (24 samples total).

2015-12-31 | E-GEOD-70384 | biostudies-arrayexpress

Circadian regulation of gene expression in the SCN (RNA-seq)

Project description:We performed a circadian RNA expression profile of the mammalian biological clock, the suprachiasmatic nucleus (SCN) in C57/BL6 mice, at 2-hour resolution using microarrays, and at 6-hour resolution using RNA-seq.Â 8 samples total covering 8 time points, with no replicates. SCN samples from mouse brains collected every 6 hours for 2 days (8 samples total).

2015-12-31 | E-GEOD-70391 | biostudies-arrayexpress

Circadian regulation of gene expression in the SCN (RNA-seq)

2015-12-31 | GSE70391 | GEO

Circadian regulation of gene expression in the SCN (gene expression)

2015-12-31 | GSE70384 | GEO