Transcriptomics,Genomics

Dataset Information

38

C. elegans genomic response to Konza Prairie Soil bacterial environment


ABSTRACT: Here we have compared adult wildtype (N2) C. elegans gene expression when grown on different bacterial environments/fod sources in an effort to model naturally occuring nematode-bacteria interactions at the Konza Prairie. We hypothesize that human-induced changes to natural environments, such as the addition of nitrogen fertalizer, have effects on the bacterial community in soils and this drives downstream changes in the structure on soil bacterial-feeding nematode community structure. Here we have used transcriptional profiling to identify candidate genes involved in the interaction of nematodes and bacteria in nature. Overall design: Here we have performed 36 microarrays and because channels were analyzed separately we have uploaded channels separately. We used six biological replicates of C. elegans grown in four bacterial environments (E. coli OP50, Micrococcus luteus, Bacillus megaterium, and Pseudomonas sp.). For each of those biological replicates we have performed three technical replicates because we made all six pair-wise comparisons amoungst the four bacterial environments. Dye swaps were performed. > Biological replicates (technical replicates) < Micrococcus luteus 1 (GSM399039,GSM399094,GSM399119) Micrococcus luteus 2 (GSM399426,GSM399431,GSM399459) Micrococcus luteus 3 (GSM399467,GSM399482,GSM399486) Micrococcus luteus 4 (GSM399489,GSM399493,GSM399500) Micrococcus luteus 5 (GSM399514,GSM399533,GSM399534) Micrococcus luteus 6 (GSM399539,GSM399544,GSM399547) E. coli OP50 1 (GSM399108,GSM399118,GSM399125) E. coli OP50 2 (GSM399427,GSM399428,GSM399465) E. coli OP50 3 (GSM399480,GSM399485,GSM399487) E. coli OP50 4 (GSM399490,GSM399492,GSM399495) E. coli OP50 5 (GSM399510,GSM399513,GSM399535) E. coli OP50 6 (GSM399541,GSM399542,GSM399546) Bacillus megaterium 1 (GSM399089,GSM399097,GSM399123) Bacillus megaterium 2 (GSM399429,GSM399437,GSM399458) Bacillus megaterium 3 (GSM399468,GSM399479,GSM399484) Bacillus megaterium 4 (GSM399496,GSM399498,GSM399505) Bacillus megaterium 5 (GSM399512,GSM399531,GSM399536) Bacillus megaterium 6 (GSM399538,GSM399543,GSM399549) Pseudomonas sp. 1 (GSM399029,GSM399082,GSM399113) Pseudomonas sp. 2 (GSM399432,GSM399457,GSM399464) Pseudomonas sp. 3 (GSM399481,GSM399483,GSM399488) Pseudomonas sp. 4 (GSM399491,GSM399494,GSM399509) Pseudomonas sp. 5 (GSM399511,GSM399532,GSM399537) Pseudomonas sp. 6 (GSM399540,GSM399545,GSM399548)

INSTRUMENT(S): WUSTL Caenorhabditis elegans Whole Genome 23k Oligo Array

SUBMITTER: Joseph Coolon 

PROVIDER: GSE15923 | GEO | 2009-05-02

SECONDARY ACCESSION(S): PRJNA116931

REPOSITORIES: GEO

altmetric image

Publications

Caenorhabditis elegans genomic response to soil bacteria predicts environment-specific genetic effects on life history traits.

Coolon Joseph D JD   Jones Kenneth L KL   Todd Timothy C TC   Carr Bryanua C BC   Herman Michael A MA  

PLoS genetics 20090605 6


With the post-genomic era came a dramatic increase in high-throughput technologies, of which transcriptional profiling by microarrays was one of the most popular. One application of this technology is to identify genes that are differentially expressed in response to different environmental conditions. These experiments are constructed under the assumption that the differentially expressed genes are functionally important in the environment where they are induced. However, whether differential e  ...[more]

Similar Datasets

2012-12-13 | PXD007681 | Pride
2016-03-31 | E-GEOD-60063 | ArrayExpress
2009-09-01 | GSE16596 | GEO
2010-05-06 | E-GEOD-16596 | ArrayExpress
2012-03-13 | E-GEOD-36413 | ArrayExpress
2012-03-21 | GSE36523 | GEO
2012-03-20 | E-GEOD-36636 | ArrayExpress
2012-09-24 | E-GEOD-38040 | ArrayExpress
2019-07-13 | E-MTAB-7272 | ArrayExpress
2012-03-21 | E-GEOD-36499 | ArrayExpress