LD/DD time course of y w; tim01, cn bw, and y w Drosophila
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ABSTRACT:
PROVIDER: PRJNA94061 | ENA |
REPOSITORIES: ENA
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Project description:This SuperSeries is composed of the following subset Series:; GSE3826: LD/DD time course of y w Drosophila #1; GSE3828: LD/DD time course of y w Drosophila #2; GSE3829: LD/DD time course of cn bw Drosophila; GSE3830: LD/DD time course of y w Drosophila #3; GSE3831: LD/DD time course of y w; tim01 Drosophila #1; GSE3832: LD/DD time course of y w; tim01 Drosophila #2 Experiment Overall Design: Refer to individual Series
2008-06-12 | E-GEOD-3842 | biostudies-arrayexpress
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 Keywords: Time course
2006-02-03 | GSE3829 | 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: cn bw 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 ZT4- Experiment Overall Design: ZT8-ZT12-ZT16-ZT20-ZT24-CT4-CT8-CT12-CT16-CT20-CT24 Experiment Overall Design: 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-3829 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2006-02-03 | GSE3842 | GEO
Project description:modENCODE_submission_720 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Most terminally differentiated Drosophila tissues are either polyploid or polytene. Unlike normal chromosomes, where the entire chromosome must be replicated exactly once, polytene chromosomes are often differentially replicated with many regions underreplicated and some overreplicated. We will characterize five different polytene tissues using comparative genomic hybridization (CGH) to identify differentially replicated regions of each chromosome. These studies will also identify tissue specific amplicons, where the replication mediated amplification of specific loci is essential for up-regulation of mRNA levels encoding proteins critical for development. The differential replication of polytene chromosomes in Drosophila will provide a unique opportunity to understand how developmental cues and chromosomal domains influence replication initiation. Keywords: CGH For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CGH. BIOLOGICAL SOURCE 1: Strain: Y cn bw sp; Tissue: larval salivary gland; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; Sex: Unknown; BIOLOGICAL SOURCE 2: Strain: Y cn bw sp; Developmental Stage: Embryo 0-4h; Sex: Unknown; NUMBER OF REPLICATES: 1; EXPERIMENTAL FACTORS: Tissue larval salivary gland
2010-05-15 | E-GEOD-17288 | biostudies-arrayexpress
Project description:Gene expression analysis of Drosophila melanogaster 3rd instar hsf4 cn bw larvae, under heat shock and non-heat shock conditions (room temperature) using Nimblegen arrrays (GPL8443)
2011-01-05 | GSE22332 | GEO
Project description:modENCODE_submission_763 This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 6-8h; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS: Strain Y cn bw sp; Developmental Stage Embryo 6-8h
2010-08-04 | E-GEOD-23230 | biostudies-arrayexpress
Project description:modENCODE_submission_541 This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Pupae, WPP + 2 days; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Strain Y cn bw sp; Developmental Stage Pupae, WPP + 2 days
2010-08-04 | E-GEOD-23223 | biostudies-arrayexpress
Project description:modENCODE_submission_3248 This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: Transcript tiling array analysis. BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 4-6h; Genotype: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]; NUMBER OF REPLICATES: 3; EXPERIMENTAL FACTORS: Strain Y cn bw sp; Developmental Stage Embryo 4-6h
2010-11-18 | E-GEOD-25347 | biostudies-arrayexpress