Dataset Information

Gene expression analysis during heat shock in Drosophila melanogaster KC167 cells and 3rd instar dp cn bw larvae

ABSTRACT: Gene expression analysis of Drosophila melanogaster Kc167 cells and 3rd instar dp cn bw larvae, under heat shock and non-heat shock conditions (room temperature) using Nimblegen arrrays (GPL8443) Overall design: A 12 chip study using total RNA recovered from heat shocked or non-heat shocked (room temperature) samples in either cells or larvae, 3 biological replicates for each treatment

INSTRUMENT(S): NimbleGen Drosophila melanogaster 385K Array

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Zak Razak

PROVIDER: GSE19745 | GEO | 2011-01-05

SECONDARY ACCESSION(S): PRJNA123997

REPOSITORIES: GEO

ACCESS DATA

Similar Datasets

Project description:Circadian clocks are temporally aligned to the environment via signals, or Zeitgebers, such as daily light and temperature cycles, food availability, and social behavior. In this study, we show that genome-wide expression profiles from temperature-entrained flies show a dramatic difference in the presence or absence of a thermocycle. Whereas transcription appears to be modified globally by changes in temperature, there is a specific set of transcripts that continue to oscillate in constant conditions following temperature entrainment. These transcripts show a significant overlap with a previously defined set of transcripts oscillating in response to a photocycle. Further, these overlapping transcripts maintain the same mutual phase relationships after entrainment by temperature or light. Comparison of the collective temperature- and light-entrained circadian phases indicates that natural environmental light and temperature cycles cooperatively entrain the circadian clock. These findings suggest that a single transcriptional clock in the adult fly head is able to integrate information from both light and temperature. Keywords: circadian time course Overall design: cn bw flies that had been reared in constant darkness initially at 25 C and later in a 12-hr 18 C/ 12-hr 25 C thermocycle for more than 4 days were harvested every four hours during an additional two days at constant 25 C (also indicated as ambient/ambient or AA days 1 and 2) . Relative to time AA0 as the time of the onset of the subjective cryophase during constant 25 C, samples were collected in a AA2-AA6-AA10-AA14-AA18-AA22-AA26-AA30-AA34-AA38-AA42-AA46 schedule. Heads were isolated by breaking up frozen flies and passing them through a set of sieves. RNA was prepared using guanidine-thiocyanate extraction followed by purification over a CsCl gradient. Additional purification of the RNA samples was achieved by applying them to Rneasy columns (Qiagen). Biotin-labeled cRNA probe was generated from 25 μg of purified RNA and hybridized as described previously (Wijnen H, Naef F, and Young MW, Methods Enzymol. 2005; 393: 341-365). For more information see also http://biorhythm.rockefeller.edu

Project description:Growth and transcriptional profiles of the barophilic methanarchaeon Methanocaldococcus jannaschii were studied at temperatures up to 98C and pressures up to 500 atm. Application of 500 atm of hyperbaric pressure shifted the optimal growth temperature upwards, and heat shock from 88C to 98C at 500 atm resulted in termination of growth. Pressure shock of M. jannaschii from 7.8 to 500 atm over 15-min, the first pressure upshift reported for a barophile, did not accelerate growth. Transcriptional profiles indicated a similar pressure response under growth and heat shock at 500 atm and pressure shock to 500 atm suggesting that the commonly affected genes are important for high-pressure adaptation. Factorial microarray design allowed de-convolution of the interacting effect of elevated pressure and heat shock on expression profiles, thus suggesting genes that may contribute to the organism’s survival in the turbulent in situ conditions of deep-sea hydrothermal vents. Keywords: stress response, time course, high pressure, heat shock, pressure shock Overall design: The cDNA arrays that were used contained three technical replicate spots for each ORF in the genome of M. jannaschii. Twenty-four sub-arrays were hybridized with the following pairs of samples: four biological-replicate pairs of samples extracted from 7.8 atm and 500 atm, both without heat shock, four biological-replicate pairs of samples extracted from 7.8 atm without heat shock and 7.8 atm with heat shock (0.5 h and 1.5h), four biological-replicate pairs of samples extracted from 500 atm without heat shock and 500 atm with heat shock (0.5 h and 1.5h), and four biological-replicate pairs of samples extracted from 7 atm and 500 atm, both heat shocked (0.5 h). Each of the four pairs of biological replicates included two pairs of dye-swapped samples. Six sub-arrays were hybridized with the following pairs of samples: three biological-replicate pairs of samples extracted from cells pressure shocked to 500 atm (0.5 h and 1.5 h) and from cells grown at 7 atm without heat shock.