Project description: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)
Project description:This dataset contains transcription profiles of TOP10 E.coli transformed with 85 rewired network plasmids first described in: Evolvability and hierarchy in rewired bacterial gene networks. Nature 452:840-5 (2008). The data are described and analysed in an accompanying paper Baumstark et al.,The propagation of perturbations in shuffled bacterial gene networks (Submitted, 2015). 260 raw data microarrays are provided in total, representing biological triplicates (a,b and c; independent colonies grown from the same transformation, under standard growth conditions; LB, 16h). This is done for each of 255 promoter-ORF constructs (e.g. appY-crp, etc.) and 5 control construct microarrays (empty plasmid; Co). Co controls are provided for comparison, to show the relative effect of the rewiring genetic perturbation. The final processed data compares the number of perturbed genes, comparing between the average expression values of each rewired construct and Co. Methods: The 85 rewiring plasmids (Isalan et al, 2008) were transformed into E. coli TOP10 cells and grown under standardised conditions: bacteria were freshly plated onto LB Agar plates (with 100 μg/ml Ampicillin and 50 μg/ml Streptomycin) and incubated overnight at 37oC to form colonies. Single colonies (<3 days old) were used to inoculate 2 ml of LB in 14 ml culture tubes, containing 100 μg/ml Ampicillin and 50 μg/ml Streptomycin. Constructs were grown for 16h at 37oC, at 220 rpm in an orbital shaker. 10 μg of extracted total bacterial RNA (integrity number > 7.0) was used with Affymetrix GeneChip E. coli Genome 2.0 Arrays. Key to names: RAW DATA samples 1-260 _Co_1a.CEL = Control Co, colony a _Co_1b.CEL = Control Co, colony b etc. appY_O_30a.CEL = appY-promoter only, colony a appY_O_30b.CEL = appY-promoter only, colony b etc. appY_crp_34a.CEL = rewired construct, appY-promoter expressing crp ORF, colony a appY_crp_34b.CEL = rewired construct, appY-promoter expressing crp ORF, colony b appY_crp_34b.CEL = rewired construct, appY-promoter expressing crp ORF, colony c etc. PROCESSED DATA sample 261: probe_set_expression_value_norm_all - normalised data for all samples, for all E. coli K12 genes sample 262: probe_set_expression_value_norm_MG1655 - normalised data for all samples, for E. coli MG1655 subset of genes
Project description:This SuperSeries is composed of the following subset Series: GSE17517: Microarray analysis of high Arctic soil bacterial response to hydrocarbon pollution and bioremediation GSE17532: RT-PCR analysis of high Arctic soil bacterial response to hydrocarbon pollution and bioremediation Refer to individual Series
Project description:This SuperSeries is composed of the following subset Series: GSE25137: Functional and cellular constraints that shaped the PPARg binding landscape in human and mouse macrophages: human expression GSE25426: Functional and cellular constraints that shaped the PPARg binding landscape in human and mouse macrophages: human ChIP-Seq Refer to individual Series
Project description:Whole Genome Metabolism of "Wigglesworthia glossinidia endosymbiont of Glossina morsitans morsitans (Yale colony)"
This is a whole genome metabolism model of Wigglesworthia glossinidia endosymbiont of Glossina morsitans morsitans (Yale colony).
This model has been automatically generated by the SuBliMinaL Toolbox
and libAnnotationSBML using information coming from from KEGG (release 66, April 2013, accessed via the resource's web services interface) and, where relevant, augmented with metabolic pathway information extracted from MetaCyc (version 17.0, March 2013).
This model has been produced by the path2models
project and is currently hosted on BioModels Database
and identified by: BMID000000141651
Other models with the same genus include BMID000000023675 BMID000000023676 BMID000000023677 BMID000000023678 BMID000000023679 BMID000000023680 BMID000000023681 BMID000000023682 BMID000000023683 BMID000000023684 BMID000000023685 BMID000000023686 BMID000000023687 BMID000000023688 BMID000000023689 BMID000000125385 BMID000000125386 BMID000000125387 BMID000000125388 BMID000000125389 BMID000000125390 BMID000000125391 BMID000000125392 BMID000000125393 BMID000000125394 BMID000000125395 BMID000000125396 BMID000000125397 BMID000000125398 BMID000000125399 BMID000000125400 BMID000000125401 BMID000000125402 BMID000000125403 BMID000000125404 BMID000000125405 BMID000000125406 BMID000000125407 BMID000000125408 BMID000000125409 BMID000000125410 BMID000000125411 BMID000000125412 BMID000000125413 BMID000000125414 BMID000000125415 BMID000000125416 BMID000000125417 BMID000000125418 BMID000000125419 BMID000000125420 BMID000000125421 BMID000000125422 BMID000000125423 BMID000000125424 BMID000000125425 BMID000000125426 BMID000000125427 BMID000000125428 BMID000000125429 BMID000000125430 BMID000000125431 BMID000000125432 BMID000000125433 BMID000000125434 BMID000000125435 BMID000000125436 BMID000000125437 BMID000000125438 BMID000000125439 BMID000000140879 .
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.