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Analysis of heat-shock treated Drosophila melanogaster embryos by SWATH-MS

ABSTRACT: Protein expression levels of Drosophila melanogaster embryos were monitored by SWATH-MS after heat-shock treatments.

INSTRUMENT(S):

ORGANISM(S): Drosophila Melanogaster (fruit Fly)

TISSUE(S): Embryo

SUBMITTER: Bertrand Fabre

LAB HEAD: Kathryn Susan Lilley

PROVIDER: PXD004753 | Pride | 2016-12-23

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	24072015_HS_1h_R0.wiff	Wiff
	24072015_HS_1h_R0.wiff.1.idx2	Wiff
	24072015_HS_1h_R0.wiff.scan	Wiff
	24072015_HS_1h_R1.wiff	Wiff
	24072015_HS_1h_R1.wiff.1.idx2	Wiff

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Publications

SWATH-MS data of Drosophila melanogaster proteome dynamics during embryogenesis.

Fabre Bertrand B Korona Dagmara D Nightingale Daniel J H DJ Russell Steven S Lilley Kathryn S KS

Data in brief 20161024

Embryogenesis is one of the most important processes in the life of an animal. During this dynamic process, progressive cell division and cellular differentiation are accompanied by significant changes in protein expression at the level of the proteome. However, very few studies to date have described the dynamics of the proteome during the early development of an embryo in any organism. In this dataset, we monitor changes in protein expression across a timecourse of more than 20 h of Drosoph ...[more]

PMID: 27844044

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SWATH-MS dataset of heat-shock treated Drosophila melanogaster embryos.

Project description:Data independent acquisition (DIA) has emerged as a promising mass spectrometry based approach, combining the advantages of shotgun and targeted proteomics. Here we applied a DIA approach (termed SWATH) to monitor the dynamics of the Drosophila melanogaster embryonic proteome upon heat-shock treatment. Embryos were incubated for 0.5, 1 or 3 h at 37 °C to induce heat-shock or maintained at 25 °C. The present dataset contains SWATH files acquired on a Sciex Triple-TOF 6600. A spectral library built in-house was used to analyse these data and led to the quantification of more than 2500 proteins at every timepoint. The files presented here are permanent digital maps and can be reanalysed to search for new questions. The data have been deposited with the ProteomeXchange Consortium with the dataset identifier PRIDE: PXD004753.

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Whole-genome analysis of heat shock factor binding sites in Drosophila melanogaster during heat shock

Project description:Whole-genome analysis of heat shock factor binding sites in Drosophila melanogaster. Heat shock factor IP DNA or Mock IP DNA from heat shocked Kc 167 cells compared to whole cell extract on Agilent 2x244k tiling arrays.

2011-01-05 | GSE19744 | GEO

Whole-genome analysis of heat shock factor binding sites in Drosophila melanogaster

Project description:Whole-genome analysis of heat shock factor binding sites in Drosophila melanogaster using Heat Shock factor IP or Mock IP vs Whole cell Extract on Agilent 2x244k tiling arrays Heat Shock Factor IP or MOCK IP vs Whole Cell Extract

2011-01-05 | E-GEOD-19744 | biostudies-arrayexpress

Heat shock protein expression enhances heat tolerance of reptile embryos.

Project description:The role of heat shock proteins (HSPs) in heat tolerance has been demonstrated in cultured cells and animal tissues, but rarely in whole organisms because of methodological difficulties associated with gene manipulation. By comparing HSP70 expression patterns among representative species of reptiles and birds, and by determining the effect of HSP70 overexpression on embryonic development and hatchling traits, we have identified the role of HSP70 in the heat tolerance of amniote embryos. Consistent with their thermal environment, and high incubation temperatures and heat tolerance, the embryos of birds have higher onset and maximum temperatures for induced HSP70 than do reptiles, and turtles have higher onset and maximum temperatures than do lizards. Interestingly, the trade-off between benefits and costs of HSP70 overexpression occurred between life-history stages: when turtle embryos developed at extreme high temperatures, HSP70 overexpression generated benefits by enhancing embryo heat tolerance and hatching success, but subsequently imposed costs by decreasing heat tolerance of surviving hatchlings. Taken together, the correlative and causal links between HSP70 and heat tolerance provide, to our knowledge, the first unequivocal evidence that HSP70 promotes thermal tolerance of embryos in oviparous amniotes.

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Gene expression analysis during heat shock in Drosophila melanogaster 3rd instar hsf4 cn bw larvae

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

Whole-genome analysis of heat shock factor binding sites in Drosophila melanogaster at room temperature

Project description:Whole-genome analysis of heat shock factor binding sites in Drosophila melanogaster. Heat shock factor IP DNA from non-shock (room temperature) Kc 167 cells compared to whole cell extract on Agilent 2x244k tiling arrays.

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Change in gene expression in Chlamydomonas reinhardtii upon heat shock

Project description:This was an accompanying experiment. Previously, the expression of genes hsp70A and hsp70B had been established as being tetrapyrrole-dependent (Kropat et al., 1997, 2000). Since both are well-known heat-shock proteins, we performed a one-step heat shock treatment by shifting the temperatures from 23M-BM-0C to 42M-BM-0C for 45 min. Moreover, this experiment served as an additional global control to further test the reliability of the microarray and our general conditions since the heat shock response in general is quite well investigated. 3988 responding genes were identified. Among them are 22 genes known to be regulated by HS, selected examples are: the heat shock proteins 22A, 22B and 22C, here leading the list of top-regulated genes on place 1 with a FC of 91297 (22A), place 3 with a FC of 45023 (22B) and place 5 with a FC of 6570 (22C). Other examples are several DnaJ-like proteins or the ClpB chaperone, from the Hsp100 family. In total the analysis comprises 8 samples. For heat shock, a 20 ml culture with ~4 M-CM-^W 106 cells per ml in a 100 ml Erlenmeyer flask was incubated at 42M-BM-0C for 45 min in the light with shaking. Control cultures were incubated in the light at 23M-BM-0C (von Gromoff et al., 1989; Kropat et al., 2000). For harvest, cultures were chilled immediately by pouring them onto crushed ice, centrifuged (5 min, 3000 g, 4M-BM-0C) and resuspended in 1 ml TAP. This procedure was repeated three times, resulting in 3 biological replicates.

2011-03-02 | E-GEOD-20859 | biostudies-arrayexpress

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

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2011-01-05 | GSE19745 | GEO

Interplay between RNA interference and heat shock response systems in Drosophila melanogaster

Project description:The genome expression pattern is strongly modified during the heat shock response (HSR) to form an adaptive state. This may be partly achieved by modulating microRNA levels that control the expression of a great number of genes that are embedded within the gene circuitry. Here, we investigated the cross-talk between two highly conserved and universal house-keeping systems, the HSR and microRNA machinery, in Drosophila melanogaster. We demonstrated that pronounced interstrain differences in the microRNA levels are alleviated after heat shock (HS) to form a uniform microRNA pattern. However, individual strains exhibit different patterns of microRNA expression during the course of recovery. Importantly, HS-regulated microRNAs may target functionally similar HS-responsive genes involved in the HSR. Despite the observed general downregulation of primary microRNA precursor expression as well as core microRNA pathway genes after HS, the levels of many mature microRNAs are upregulated. This indicates that the regulation of miRNA expression after HS occurs at transcriptional and post-transcriptional levels. It was also shown that deletion of all hsp70 genes had no significant effect on microRNA biogenesis but might influence the dynamics of microRNA expression during the HSR.

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Spectral library of Drosophila melanogaster for SWATH-MS

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