Circadian regulation of a limited set of microRNAs in Drosophila
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans Rattus norvegicus Mus musculus Homo sapiens Drosophila melanogaster
PROVIDER: GSE10005 | GEO | 2007/12/29
SECONDARY ACCESSION(S): PRJNA108187
REPOSITORIES: GEO
Similar Datasets
Project description:We used a microarray platform to survey the daily levels of 78 D. melanogaster miRNAs in adult heads of wildtype control flies and the arrhythmic clock mutant cyc01. At least 2 miRNAs were identified that showed robust daily abundance changes in control flies but not the cyc01 mutant. Keywords: microRNA, Circadian regulation yw and yw;cyc01 flies were maintained in standard media. For collections, approximately 50-100 young (2-5 day old) flies were placed in vials that were incubated at 25oC for four days in standard 12hr light-12hr dark cycles [LD; where zeitgeber time 0 (ZT0) is defined as lights-on]. Flies were collected by freezing in dry ice during the fourth LD cycle at the following times; ZT1, 7, 13 and 19. Subsequently low molecular RNAs were extracted for microarray analysis using a mirMAX microarray.
2010-05-27 | E-GEOD-10005 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are a class of small, endogenous RNAs that regulate mRNA expressions post-transcriptionally. To study their expression, we collected and sequenced small RNA libraries in Drosophila species. To survey their regulation divergence, we dissected testes from miR-983 mutant and control flies in two sibling species and performed an RNA-seq analysis.
2018-06-14 | GSE110086 | 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 investigated sleep deficits in Cyfip mutant Drosophila flies, a model for intellectual disabilities/neurodevelopmental disorders. RNA-seq was performed on heads at the circadian time point ZT16, i.e., during the night when wild-type flies are asleep.
2022-12-11 | GSE220524 | GEO
Project description:Investigation of sex-biased expression across species have relied on measurements from whole flies which sample the extensive expression differences found in the germline and gonads of females and males. We wanted to examine genes with sex-biased expression in a somatic tissue to analyze patterns of genes with sex-biased expression in the context of a tissue more phenotypically similar between females and males. We used a Nimblegen microarray designed for Drosophila melanogaster and two custom micoarrays designed for D. pseudoobscura and D. mojavensis to survey gene expression differences in heads of females and males. PolyA+ mRNA was isolated in quadruplicate from dissected heads of 8 day old adult females and males. Female and male mRNA were labeled with Cy3 or Cy5 dyes separately and co-hybridized to species-specific microarrays. We analyzed a total of 24 channels of data.
2010-07-30 | E-GEOD-23309 | biostudies-arrayexpress
Project description:Purpose: Validation of Drosophila A-to-I editing sites Methods: We collected heads of 5 day old male dAdar-/- mutant (y, Adar5G1, w)26 and wild type (w1118) flies. Poly(A)+ RNA was used to prepare RNA-seq libraries which were subsequently sequenced single-end by an Illumina GAII Results:We builded a framework to identify RNA editing events using RNA-seq data alone in Drosophila. To validate whether the identified A-to-G sites were bona fide A-to-I editing events, we performed RNA-seq for the D.melanogaster wild-type strain (w1118) and for the Adar5G1 null mutant that eliminates RNA editing. We found that our method achieved high accuracy; 98.2% of all A-to-G sites showed only adenosine in the Adar5G1 sample Conclusions: We anticipate that our method will be very effective in the future to identify RNA editing events in different species. mRNA profiles of heads of 5 day old male dAdar-/- mutant (y, Adar5G1, w)26 and wild type (w1118) flies
2012-12-20 | E-GEOD-42815 | 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. Keywords: Time course
2006-02-03 | GSE3832 | 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. Keywords: Time course
2006-02-03 | GSE3831 | GEO