Unknown,Transcriptomics,Genomics,Proteomics

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Whole-genome expression profiling of C. elegans larvae and adults

ABSTRACT: Temperature, as a universal enviromental factor, has prolonged effect on physiological and pathological functions of different species. In order to expolore the temperol effect of temperature on C.elegans longevity, we used microarray to check the whole-genome expression profiling of L4 larvae and Day3-old adults of C.elegans maintaining at different temperature Adult worms are collected after maintained at 25 degree and 15 degree for 3days from later L4 stage, while Larva worms are collected after growing at 25 degree and 15 degree from embryo to late L4 stege. Then total RNA are extracted with TRI reagent(Life Technologies) from~120 adults or ~300 larvae. The concentrations and quality of total RNA are checked with Thermo Nanodrop 2000c(Thermo Scientific,WilminGton,DE) and Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). Total RNA samples were hybrydized with Affymetrix C. elegans Gene 1.1 ST Array Strip. Preparation of cDNA, hybridization, quality controls and scanning of arrays were performed according to the manufacturer's protocol (Affymetrix, Santa Clara, CA) at the microarray core facility of University of Michigan .

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: X.Z Shawn Xu

PROVIDER: E-GEOD-62297 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Reports that low-intensity microwave radiation can induce heat-shock reporter gene expression in the nematode, Caenorhabditis elegans, have recently been reinterpreted as a subtle thermal effect caused by very slight heating. This study used a microwave exposure system (1.0 GHz, 0.5 W power input; SAR 0.9-3 mW kg-1 for 6-well plates) that minimises the temperature differential between sham and exposed conditions to ≤ 0.1°C. Comparable measurement and simulation studies of SAR distribution within this exposure system are presented. We compared 5 Affymetrix gene-arrays of pooled triplicate RNA populations from sham-exposed L4/adult worms against 5 gene-arrays of pooled RNA from microwave-exposed worms (taken from the same source population in each run). Few genes showed consistent expression changes across all 5 comparisons, and all such expression changes appeared modest after applying standard normalisation procedures (≤ 30% up- or down-regulated). The number of statistically significant differences in gene expression (846) was less than the false-positive rate expected by chance (1131). As one example, an apparent up-regulation of the vit-3 vitellogenin gene by microwave exposure was not mirrored by similar changes affecting the other co-regulated members of the same vit gene family. We conclude that the pattern of gene expression in L4/adult C elegans is not substantially perturbed by low-intensity microwave radiation, and that the minor changes observed in this study may well be explicable as false positives. As a check on the sensitivity of the Affymetrix gene-arrays used, we also compared RNA samples from N2 worms subjected to a sub-heat-shock treatment (28ºC) against controls kept at 26 ºC (but using only 2 gene arrays per condition). After similar normalisation, many more genes (3712) showed substantial expression changes (i.e. > 2-fold at p < 0.05), including a group of six heat-shock genes which were strongly but unexpectedly down-regulated (by > 10-fold). However, further replication and confirmation by real-time RT-PCR would be needed to establish how many of these changes might also be false positives. Experimenter name: Adam Dawe; Experimenter phone: +27 21 959 2364; adam@sanbi.ac.za; Experimenter institute: South African National Bioinformatics Institute; Experimenter address: University of Western Cape, Old Chemistry Building, University of Western Cape, Modderdam Road, Bellville 7530, Capetown; Experimenter zip/postal_code: 7530; Experimenter country: South Africa Experiment Overall Design: 14 samples were used in this experiment

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Whole-genome expression profiling of C. elegans larvae and adults

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