Cortical diurnal rhythms remain intact with microglial depletion
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE188989 | GEO | 2021/11/18
REPOSITORIES: GEO
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Project description:Cyclic regulatory systems are ubiquitous in cells and tissues. In the liver rhythms in mRNA expression are determined by the homeostatic regulation that operates on daily circumstances. In particular the specific response to nutrients, as well as systemic and peripheral circadian oscillators, contribute to the set up of the hepatic homeostasis at different phases of the day. In this series we used microarrays to detail the global program of gene expression in the mouse liver under physiological daily variations, determined by both the feeding and the circadian cycles. We examined 7 samples, each consisting in a pool of RNAs extracted from the whole liver of 5 mice. Samples were collected at times ZT2, ZT6, ZT10 ,ZT14, ZT18, ZT22, ZT26 (ZT0/24 and ZT12 are the times when the lights are switched on and off, respectively)
2012-12-06 | E-GEOD-35789 | biostudies-arrayexpress
Project description:In order to identify the RNAs bound by NONO complexes in different nutritional conditions, we carried out RNA immunoprecipitation followed by sequencing (RIP-seq) of NONO from mouse liver nuclei collected at three different times of the day. Samples were collected after fasting (ZT10), 2h after re-feeding (ZT14) and towards the end of the feeding period (ZT22). The co-immunoprecipitated RNA (along with input RNA and unspecific IgG bound RNA) was sequenced.
2018-01-18 | GSE98040 | GEO
Project description:Mechanisms composing Drosophila's clock are conserved within the animal kingdom. To learn how such clocks influence behavioral and physiological rhythms, we determined the complement of circadian transcripts in adult Drosophila heads. High-density oligonucleotide arrays were used to collect data in the form of three 12-point time course experiments spanning a total of 6 days. Analyses of 24 hr Fourier components of the expression patterns revealed significant oscillations for 400 transcripts. Based on secondary filters and experimental verifications, a subset of 158 genes showed particularly robust cycling and many oscillatory phases. Circadian expression was associated with genes involved in diverse biological processes, including learning and memory/synapse function, vision, olfaction, locomotion, detoxification, and areas of metabolism. Data collected from three different clock mutants (per0, tim01, and ClkJrk), are consistent with both known and novel regulatory mechanisms controlling circadian transcription (Claridge-Chang et al., Neuron. 2001 Nov 20;32(4):657-71). For more information see also http://biorhythm.rockefeller.edu Experiment Overall Design: y w flies that had been kept in a 12-hr light/ 12-hr dark cycle for three days were harvested every four hours during an additional light/dark day (ZT) and a subsequent day in constant darkness (CT). Relative to Zeitgeber time 0 (ZT0) as the time of lightson Experiment Overall Design: during the LD cycle and Circadian time 0 (CT0) as the time corresponding to Experiment Overall Design: subjective lights-on during freerun in DD, time courses were collected in a ZT2- Experiment Overall Design: ZT6-ZT10-ZT14-ZT18-ZT22-CT2-CT6-CT10-CT14-CT18-CT22 schedule. Heads Experiment Overall Design: were isolated by breaking up frozen flies and passing them through a set of Experiment Overall Design: sieves. RNA was prepared using Rnazol (Tel-test) or Trizol (Life Technologies) extraction. Additional purification of the RNA samples was Experiment Overall Design: achieved by applying them to Rneasy columns (Qiagen). Biotin-labeled cRNA Experiment Overall Design: probe was generated from 25 μg of purified RNA and hybridized as described Experiment Overall Design: previously (Claridge-Chang et al., Neuron. 2001 Nov 20;32(4):657-71). Experiment Overall Design: For more information see also http://biorhythm.rockefeller.edu
2008-06-12 | E-GEOD-3826 | biostudies-arrayexpress
Project description:We prepared adrenalectomized (ADX) and sham-operated (sham) mice kept under a light-controlled room (ZT, zeitgeber time; ZT0, light on; ZT12, light off), and thereafter their sciatic nerve was partially ligated; mice undergone partial sciatic nerve ligation (PSL) was used as an animal model of neuropathic pain. To screen pain-related genes whose spinal expression exhibits circadian oscillation in a glucocorticoid-dependent manner, we performed oligonucleotide microarray analyses using RNA isolated from the spinal cords of sham-PSL mice or ADX-PSL mice at ZT10 and ZT22 when circulating glucocorticoid levels in sham-PSL mice peaked and declined, respectively
2017-01-01 | GSE65756 | GEO
Project description:Background. The transcriptional circuits of circadian clocks control physiological; and behavioral rhythms. Light may affect such overt rhythms in two ways: (1) by; entraining the clock circuits and (2) via clock-independent molecular pathways. In; this study we examine the relationship between autonomous transcript; oscillations and light-driven transcript responses; Methodology/Principal Findings. Transcript profiles of wild-type and arrhythmic; mutant Drosophila were recorded both in the presence of an environmental; photocycle and in constant darkness. Systematic autonomous oscillations in the; 12-48 hr period range were detectable only in wild-type flies and occurred; preferentially at the circadian period length. However, an extensive program of; light-driven expression was confirmed in arrhythmic mutant flies. Many lightresponsive; transcripts are preferentially expressed in the adult compound eye; and the phospholipase C component of phototransduction, NO RECEPTOR; POTENTIAL (NORPA), is required for their light-dependent regulation. Conclusions/Significance. Although there is growing evidence for the existence; of multiple molecular clock circuits in plants and fungi, Drosophila appears to; possess only one such system. The sustained photic expression responses; identified here are partially coupled to the circadian clock and may reflect a; mechanism for flies to modulate functions such as visual sensitivity and synaptic; transmission in response to seasonal changes in photoperiod. Experiment Overall Design: y w; tim01 flies that had been kept in a 12-hr light/ 12-hr dark cycle for three days were harvested every four hours during an additional light/dark day (ZT) and a subsequent day in constant darkness (CT). Relative to Zeitgeber time 0 (ZT0) as the time of lights on Experiment Overall Design: during the LD cycle and Circadian time 0 (CT0) as the time corresponding to Experiment Overall Design: subjective lights-on during freerun in DD, time courses were collected in a ZT2- Experiment Overall Design: ZT6-ZT10-ZT14-ZT18-ZT22-CT2-CT6-CT10-CT14-CT18-CT22 schedule. Heads Experiment Overall Design: were isolated by breaking up frozen flies and passing them through a set of Experiment Overall Design: sieves. RNA was prepared using guanidine-thiocyanate extraction followed by Experiment Overall Design: purification over a CsCl gradient. Additional purification of the RNA samples was Experiment Overall Design: achieved by applying them to Rneasy columns (Qiagen). Biotin-labeled cRNA Experiment Overall Design: probe was generated from 25 μg of purified RNA and hybridized as described Experiment Overall Design: previously (Wijnen H, Naef F, and Young MW, Methods Enzymol. 2005; 393: 341-365). Experiment Overall Design: For more information see also http://biorhythm.rockefeller.edu
2008-06-12 | E-GEOD-3831 | biostudies-arrayexpress
Project description:Background. The transcriptional circuits of circadian clocks control physiological; and behavioral rhythms. Light may affect such overt rhythms in two ways: (1) by; entraining the clock circuits and (2) via clock-independent molecular pathways. In; this study we examine the relationship between autonomous transcript; oscillations and light-driven transcript responses; Methodology/Principal Findings. Transcript profiles of wild-type and arrhythmic; mutant Drosophila were recorded both in the presence of an environmental; photocycle and in constant darkness. Systematic autonomous oscillations in the; 12-48 hr period range were detectable only in wild-type flies and occurred; preferentially at the circadian period length. However, an extensive program of; light-driven expression was confirmed in arrhythmic mutant flies. Many lightresponsive; transcripts are preferentially expressed in the adult compound eye; and the phospholipase C component of phototransduction, NO RECEPTOR; POTENTIAL (NORPA), is required for their light-dependent regulation. Conclusions/Significance. Although there is growing evidence for the existence; of multiple molecular clock circuits in plants and fungi, Drosophila appears to; possess only one such system. The sustained photic expression responses; identified here are partially coupled to the circadian clock and may reflect a; mechanism for flies to modulate functions such as visual sensitivity and synaptic; transmission in response to seasonal changes in photoperiod. For more information see also http://biorhythm.rockefeller.edu. Experiment Overall Design: y w flies that had been kept in a 12-hr light/ 12-hr dark cycle for three days were harvested every four hours during an additional light/dark day (ZT) and a subsequent day in constant darkness (CT). Relative to Zeitgeber time 0 (ZT0) as the time of lights on Experiment Overall Design: during the LD cycle and Circadian time 0 (CT0) as the time corresponding to Experiment Overall Design: subjective lights-on during freerun in DD, time courses were collected in a ZT2- Experiment Overall Design: ZT6-ZT10-ZT14-ZT18-ZT22-CT2-CT6-CT10-CT14-CT18-CT22 schedule. Heads Experiment Overall Design: were isolated by breaking up frozen flies and passing them through a set of Experiment Overall Design: sieves. RNA was prepared using guanidine-thiocyanate extraction followed by Experiment Overall Design: purification over a CsCl gradient. Additional purification of the RNA samples was Experiment Overall Design: achieved by applying them to Rneasy columns (Qiagen). Biotin-labeled cRNA Experiment Overall Design: probe was generated from 25 μg of purified RNA and hybridized as described Experiment Overall Design: previously (Wijnen H, Naef F, and Young MW, Methods Enzymol. 2005; 393: 341-365). Experiment Overall Design: For more information see also http://biorhythm.rockefeller.edu
2008-06-12 | E-GEOD-3830 | biostudies-arrayexpress
Project description:Background. The transcriptional circuits of circadian clocks control physiological; and behavioral rhythms. Light may affect such overt rhythms in two ways: (1) by; entraining the clock circuits and (2) via clock-independent molecular pathways. In; this study we examine the relationship between autonomous transcript; oscillations and light-driven transcript responses; Methodology/Principal Findings. Transcript profiles of wild-type and arrhythmic; mutant Drosophila were recorded both in the presence of an environmental; photocycle and in constant darkness. Systematic autonomous oscillations in the; 12-48 hr period range were detectable only in wild-type flies and occurred; preferentially at the circadian period length. However, an extensive program of; light-driven expression was confirmed in arrhythmic mutant flies. Many lightresponsive; transcripts are preferentially expressed in the adult compound eye; and the phospholipase C component of phototransduction, NO RECEPTOR; POTENTIAL (NORPA), is required for their light-dependent regulation. Conclusions/Significance. Although there is growing evidence for the existence; of multiple molecular clock circuits in plants and fungi, Drosophila appears to; possess only one such system. The sustained photic expression responses; identified here are partially coupled to the circadian clock and may reflect a; mechanism for flies to modulate functions such as visual sensitivity and synaptic; transmission in response to seasonal changes in photoperiod. Experiment Overall Design: y w; tim01 flies that had been kept in a 12-hr light/ 12-hr dark cycle for three days were harvested every four hours during an additional light/dark day (ZT) and a subsequent day in constant darkness (CT). Relative to Zeitgeber time 0 (ZT0) as the time of lights on Experiment Overall Design: during the LD cycle and Circadian time 0 (CT0) as the time corresponding to Experiment Overall Design: subjective lights-on during freerun in DD, time courses were collected in a ZT2- Experiment Overall Design: ZT6-ZT10-ZT14-ZT18-ZT22-CT2-CT6-CT10-CT14-CT18-CT22 schedule. Heads Experiment Overall Design: were isolated by breaking up frozen flies and passing them through a set of Experiment Overall Design: sieves. RNA was prepared using guanidine-thiocyanate extraction followed by Experiment Overall Design: purification over a CsCl gradient. Additional purification of the RNA samples was Experiment Overall Design: achieved by applying them to Rneasy columns (Qiagen). Biotin-labeled cRNA Experiment Overall Design: probe was generated from 25 μg of purified RNA and hybridized as described Experiment Overall Design: previously (Wijnen H, Naef F, and Young MW, Methods Enzymol. 2005; 393: 341-365). Experiment Overall Design: For more information see also http://biorhythm.rockefeller.edu
2008-06-12 | E-GEOD-3832 | biostudies-arrayexpress
Project description:We reported a diurnal changes in the recruitment of HDAC3, Rev-erbα, NCoR and Pol II to the mouse liver genome as well as H3K9 acetylation in vivo at ZT10 and ZT22. ChIP-Seq profiling of HDAC3, Rev-erbα, NCoR and Pol II binding and H3K9Ac in mouse liver harvested at 2 different times (ZT10 and ZT22) of the day
2011-03-11 | E-GEOD-26345 | biostudies-arrayexpress
Project description:We reported a diurnal changes in the recruitment of HDAC3, Rev-erbα, NCoR and Pol II to the mouse liver genome as well as H3K9 acetylation in vivo at ZT10 and ZT22.
2011-03-11 | GSE26345 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to evaluate the effects of liver-specific E4BP4 overexpression under mouse albumin promoter on the liver glucose and lipid metabolism. Methods: We generated transgenic mice (TG) with liver-specific E4BP4 overexpression. Livers were isolated at Zeitgeber Time (ZT) 2 or 14 from transgenic mice and WT littermates and total RNA was extracted. Liver RNA profiles were generated by deep sequencing for four groups with three mouse samples each. Results: Compared with the livers from the WT mice, those from Transgenic mice featured 290 differentially expressed genes (DEGs) (106 at ZT2, 134 at ZT14, and 14 at both times). Conclusions: Lipid metabolism might be altered in the transgenic liver.
2020-12-02 | GSE150835 | GEO