Investigations
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Submitter: Jurgen Haanstra
Studies: Inhibition with Sulfasalazine (SSZ), Measurements of metabolism of HepG2 cells at 0 mM, 6 mM or 22 mM externa..., protein per cell for HepG2 cells
Assays: Cell counts and BCA Protein, Cell counts and metabolite levels, Inhibition experiment for the effect of SSZ on HepG2 metabolism
The raw data generated in the scope of the SysMetEx project for RNAseq, proteomics, and imaging analysis. The data was generated on single and mixed species cultures of A. Caldus, L.ferriphilum, and/or S.thermosulfidooxidans. Raw RNA data is combined in an ENA umbrella study summarising all short read data generated in the project. Raw proteomics data is provided for distinct conditions at the pride repository. Imaging data is provided for distinct conditions at a zenodo repository.
Submitter: Malte Herold
Studies: Biofilms on chalcopyrite grains, Continuous cultures, Planktonic cells, Supplemental Files
Assays: Links to code repositories, Microscopy imaging, Proteomics rawdata, Proteomics rawdata, Proteomics rawdata, RNAseq rawdata, RNAseq rawdata, RNAseq rawdata, Supplemental Files
Supplementary files for the submission: Reverse Engineering Directed Gene Regulatory Networks from Transcriptomics and Proteomics Data of Biomining Bacterial Communities with Approximate Bayesian Computation and Steady-State Signalling Simulations
Submitter: Malte Herold
Studies: Supplementary files
Assays: Proteome data, RNA data, Simulations for network engineering
Supplementary files for the publication: Deep Neural Networks Outperform Human Expert’s Capacity in Characterizing Bioleaching Bacterial Biofilm Composition
Publication data made available for Biotechnology Reports, supplementary data
Submitter: Antoine Buetti-Dinh
Studies: Deep Neural Networks Outperform Human Expert’s Capacity in Characterizin...
Assays: No Assays
Experimental data and all related material for the publication "Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT". changed ID
Experimental data and all related material for the publication "Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT".
Submitter: Malte Herold
Studies: Omics_data_analysis
Assays: Experimental methods, Genomics, Proteomics, RNAseq
Gene co-epxression network analyses are common in the study of large scale biological data sets. In this study, we have developed a methodology for the comparison of pairs of co-expression networks using the s-core network peeling approach. We apply the methodology to gene-expression data for human and mouse.
Antibiotics are made during the second phase of growth when there is a transition in metabolism from primary to secondary metabolism. Primary metabolism is growth related and involves all the normal cellular activities associated with cell growth and division. Whereas secondary metabolism is non-growth linked and is non-essential but many important activities occur during this phase which help the bacterium survive.
One of these activities is antibiotic production and is widespread in streptomycetes ...
Submitter: Jay Moore
Studies: ScoCyc metabolic pathway curation, Timeseries 1
Assays: Metabolic pathway curation, Online/offline measurements, metabolomics, proteomics, transcriptomics
