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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Targeted experimentation to increase functional coverage in omics dataset

ABSTRACT: To increase the GO coverage of Ecomics, we investigated which new conditions would lead to the most informative transcriptional profiles. We first transcriptionally profiled and included in the compendium 9 KO experiments that we had identified before as being highly informative for both GO coverage and model performance. We assumed that a GO term is represented in the compendium if the compendium has profiles where one or more genes that include that GO term have been perturbed. We identified the gene rank iteratively under the assumption that all genes of higher rank have been perturbed. Based on the resulting ranked list, we performed transcriptional profiling for the top 16 genetic perturbations (in triplicate; 48 profiles total), which led to an increase in coverage by 19.8% for KEGG, 24.3% for BP and 63.9% for MF. Genome-wide expression profiling of 25 single-gene knockouts for BW25113 and its wild-type grown with either LB or M9 media supplemented with glucose (total 87 samples).

ORGANISM(S): Escherichia coli BW25113

SUBMITTER: Ilias Tagkopoulos

PROVIDER: E-GEOD-73672 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Targeted experimentation to increase functional coverage in omics dataset

Project description:To increase the GO coverage of Ecomics, we investigated which new conditions would lead to the most informative transcriptional profiles. We first transcriptionally profiled and included in the compendium 9 KO experiments that we had identified before as being highly informative for both GO coverage and model performance. We assumed that a GO term is represented in the compendium if the compendium has profiles where one or more genes that include that GO term have been perturbed. We identified the gene rank iteratively under the assumption that all genes of higher rank have been perturbed. Based on the resulting ranked list, we performed transcriptional profiling for the top 16 genetic perturbations (in triplicate; 48 profiles total), which led to an increase in coverage by 19.8% for KEGG, 24.3% for BP and 63.9% for MF.

2016-09-03 | GSE73672 | GEO

Transcriptome profiling of 15 conditions for Escherichia coli selected from optimal experiment design, and targeted experimentation to increase functional coverage in omics dataset

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-09-03 | E-GEOD-73673 | biostudies-arrayexpress

Transcription profiling of yeast transcription factor knockout compendium

Project description:We reprocessed a recently published microarray compendium of 269 regulator knockouts that contains most known TFs and many epigenetic regulators for the yeast \italic{Saccharomyces cerevisiae} (Hu et al 2007). Using sensitive microarray analysis tools, we gained nearly 10 times more differentially expressed genes and recovered 90\% of previously described targets. We validated our analysis using Gene Ontology (GO), DNA-protein interactions, TF binding sites and protein-protein interactions. Our validation underlines the advantages of our sensitive analysis. The original data files for this submission can be found in E-MTAB-109.additional.zip

2010-03-22 | E-MTAB-109 | biostudies-arrayexpress

Pseudomonas aeruginosa Heme Metabolites Biliverdin IX and IX are Integral to Lifestyle Adaptations Associated with Chronic Infection

Project description:Pseudomonas aeruginosa is a versatile opportunistic pathogen requiring iron for its survival and virulence within the host. The ability to switch to heme as an iron source provides an advantage in chronic infection. We have recently shown the extracellular heme metabolites biliverdin IX (BVIX) and/or BVIX positively regulate the heme dependent cell surface signaling cascade. We further investigated the role of BVIX and BVIX in cell signaling utilizing allelic strains lacking a functional HemO (hemOin), or one reengineered to produce BVIX (hemO). Compared to PAO1 both strains show a heme dependent growth defect, decreased swarming and twitching and less robust biofilm formation. Interestingly, the motility and biofilm defects were partially rescued on addition of exogenous BVIX and BVIX. Utilizing LC-MS/MS we performed a comparative proteomics and metabolomics analysis of PAO1 versus the allelic strains in shaking and static conditions. In shaking conditions, the hemO allelic strains showed a significant increase in proteins involved in quorum sensing (QS), phenazine production and chemotaxis.Metabolite profiling further revealed increased levels of PQS and phenazine metabolites. In static conditions we observed a significant repression of chemosensory pathways and Type IV pili (TFP) biogenesis proteins as well as several phosphodiesterases associated with biofilm dispersal. We propose BVIX metabolites function as signaling and chemotactic molecules integrating heme utilization as an iron source into the adaptation of P. aeruginosa from a planktonic to sessile lifestyle.

2024-01-19 | PXD045835 | Pride

Dynamic 3D proteomes reveal functional pathway alterations in situ

Project description:Many biological processes are regulated via molecular events, such as intermolecular interactions and chemical modifications, which do not affect protein levels and escape detection in classical proteomic screens. Reasoning that these events affect protein structure, we propose here that a global protein structural readout could detect many functional alterations simultaneously and in situ. We test this idea using limited proteolysis-mass spectrometry (LiP-MS), which monitors structural changes in thousands of proteins within a native-like environment. In bacteria undergoing nutrient adaptation and in yeast responding to acute stress, this global structural readout captures enzyme activity changes, allosteric regulation, phosphorylation, protein aggregation and protein complex formation, with sufficiently high resolution to identify alterations of single functional sites such as active site occupancy and binding interfaces. Comparison with prior knowledge, including flux, phosphoproteomics and metabolomics data, shows that LiP-MS captures most known enzyme functional alterations and suggests novel metabolite-protein binding events, enabling identification of a fructose-1,6-bisphosphate-based regulatory mechanism of glucose uptake in E. coli. The structural readout dramatically increases classical proteomics screen coverage and generates mechanistic hypotheses, thus better linking holistic and reductionist approaches and paving the way for a new in situ structural systems biology.

2020-11-02 | PXD022297 | Pride

Expression data from Pseudomonas putida KT2440 (RNA-Seq data)

Project description:We used cDNA generated from total mRNA for RNA-Seq analysis (Genome Analyzer II at GATC Biotech AG) to monitore the gene expression of P. putida after a cold shock from 30M-BM-0C to 10M-BM-0C Culture was grown in minimal medium supplemented with succinate at 30M-BM-0C. In mid-exp. phase cells were harvested for subsequent RNA extraction (standard condition) and medium was cooled down to 10M-BM-0C. Two hrs after reaching the temperature, cells were again harvested for RNA extraction.

2011-02-01 | E-GEOD-24175 | biostudies-arrayexpress

Expression data from Pseudomonas putida KT2440: Fuelling the central metabolism with aromatic compounds

Project description:We used Progenika oligonucleotide arrays to monitore the gene expression of P. putida during carbon source stimulus experiments. After ensuring steady state conditions on benzoate, the stimuli were introduced by changing the carbon source from benzoate to glucose, from glucose to fructose and from fructose to benzoate, respectively. The single stimuli were monitored over a time period from 10 to 120 minutes after changing the carbon source by three representative timepoints. Moreover, the steady state conditions were compared among each other. Supplementary file: Individual normalized signal intensity VALUES for each channel of each array are provided in the FullNormalizedMatrix.txt file.

2014-02-01 | E-GEOD-26785 | biostudies-arrayexpress

Expression data from Pseudomonas putida KT2440 (Progenika oligo array data)

Project description:We used Progenika oligonucleotide arrays to monitore the gene expression of P. putida after a cold shock from 30°C to 10°C Culture was grown in minimal medium supplemented with succinate at 30°C. In mid-exp. phase cells were harvested for subsequent RNA extraction (standard condition) and medium was cooled down to 10°C. Two hrs after reaching the temperature, cells were again harvested for RNA extraction. Data from four replicate hybridizations (two dye-swaps) were combined into a single ratio value. Individual normalized signal intensity VALUES for each channel of each array are provided in the FullNormalizedMatrix.txt file available on the Series record.

2011-03-24 | E-GEOD-24174 | biostudies-arrayexpress

Project description:informAtive

| PRJEB19813 | ENA

Expression data from Pseudomonas putida KT2440 (Affymetrix data)

Project description:We used Affymetrix microarrays to monitore the gene expression of P. putida after a cold shock from 30°C to 10°C Culture was grown in minimal medium supplemented with succinate at 30°C. In mid-exp. phase cells were harvested for subsequent RNA extraction (standard condition) and medium was cooled down to 10°C. Two hrs after reaching the temperature, cells were again harvested for RNA extraction.

2011-03-24 | E-GEOD-24173 | biostudies-arrayexpress

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