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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome expressed in the mouse suprachiasmatic nucleus

ABSTRACT: This array set was used to identify the genes that are highly expressed in the mouse suprachiasmatic nucleus (SCN). Because pharmacological inhibition of Gai/o activity with pertussis toxin hampers intercellular synchronization and causes dampened rhythms of the entire SCN, we hypothesized that member(s) of the Regulator of G protein Signaling (RGS) family might contribute to synchronized cellular oscillations in the SCN. To test this hypothesis, we surveyed all known mouse Rgs genes for their expression by using GeneChip and selected the genes that are highly expressed in the SCN for further analysis. 12h light:12h dark cycle entrained animals were released into constant darkess. SCN punches were taken from 10 animals at CT2 and 10 animals at CT14, pooled together, and subjected to DNA microarray analysis. CT2 and CT14 correspond, respectively, to 2 and 14 hours after presumptive onset of daytime under constant darkness.

ORGANISM(S): Mus musculus

SUBMITTER: Hitoshi Okamura

PROVIDER: E-GEOD-28574 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome expressed in the mouse suprachiasmatic nucleus

Project description:This array set was used to identify the genes that are highly expressed in the mouse suprachiasmatic nucleus (SCN). Because pharmacological inhibition of Gai/o activity with pertussis toxin hampers intercellular synchronization and causes dampened rhythms of the entire SCN, we hypothesized that member(s) of the Regulator of G protein Signaling (RGS) family might contribute to synchronized cellular oscillations in the SCN. To test this hypothesis, we surveyed all known mouse Rgs genes for their expression by using GeneChip and selected the genes that are highly expressed in the SCN for further analysis.

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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: 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 â??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 â??80Â°C before routine processing for GeneChip analysis.

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RNA sequencing of suprachiasmatic nuclues, retina, liver and lung collected at day and night from African Four Striped Mice (Rhabdomys pumilio) housed under dim vs bright daytime light

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2023-07-31 | E-MTAB-12024 | biostudies-arrayexpress

Circadian rhythms in mouse choroid plexus identified by time-resolved RNAseq require clock in the suprachiasmatic nucleus

Project description:The aim of our study was to investigate the circadian regulation of cellular processes in mouse choroid plexus (ChP) and to determine their dependence on signals from the clock in the suprachiasmatic nuclei (SCN). We performed time-resolved transcriptomics of ChP samples from C57Bl6J mice with intact (Ctrl) or surgically removed SCN (SCNx) collected every 4 h over 2 days in constant darkness and from FoxJ1-ERT2-Cre+/-; Bmal1fl/fl mice with ChP-specific clock disruption (Bmal1-KO) collected at 2 time points. We found widespread circadian gene expression in Ctrl mice that was not present in SCNx mice, and the SCNx day/night ratios were reduced similarly to Bmal1-KO.

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