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Created: 6th May 2019 at 15:00
Last updated: 23rd Jan 2020 at 12:14
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Projects: SysMetEx
Institutions: University of Luxembourg
The main objective of the ERANET proposal Systems Biology Applications - ERASysAPP (app = application = translational systems biology) is to promote multidimensional and complementary European systems biology projects, programmes and research initiatives on a number of selected research topics. Inter alia, ERASysAPP will initiate, execute and monitor a number of joint transnational calls on systems biology research projects with a particular focus on applications - or in other words so called ...
Projects: SysVirDrug, SysMilk, SysMetEx, MetApp, IMOMESIC, WineSys, CropClock, SYSTERACT, XyloCut, RootBook, ROBUSTYEAST, LEANPROT, ErasysApp Funders
Web page: https://www.cobiotech.eu/about-cobiotech/erasysapp
Biomining is a biotechnological process carried out in many parts of the world that exploits acid loving microorganisms to extract metals from sulphide minerals. One industrial biomining method is called ‘heap bioleaching’ where typically copper containing minerals are piled into very large heaps, acid and microorganisms are added to the top and the soluble metal is collected at the heap base.
The role of the different types of microbes in the process is to speed up metal solubilisation by oxidising ...
Programme: ERASysAPP
Public web page: http://sysmetex.eu/index.html
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
Snapshots: Snapshot 1, Snapshot 2
Proteomics data for samples derived from continuous cultures
Submitter: Malte Herold
Assay type: Proteomics
Technology type: Technology Type
Investigation: SysMetEx - Dataset collection
Study: Continuous cultures
Organisms: Acidithiobacillus caldus : Acidithiobacillus caldus ATCC 51756 (wild-type / wild-type)
SOPs: 003 Biomolecular Extractions from LAO (Qiagen A..., In solution digestion part, SOP - RNA/Protein sampling for continuous culture, Sample Identification Code
Data files: AXX_Cn Proteomics
Snapshots: No snapshots
RNAseq raw data derived from continuous culture samples
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: SysMetEx - Dataset collection
Study: Continuous cultures
Organisms: Acidithiobacillus caldus : Acidithiobacillus caldus ATCC 51756 (wild-type / wild-type), Leptospirillum ferriphilum : Leptospirillum ferriphilum DSM 14647 (wild-type / wild-type), Sulfobacillus thermosulfidooxidans : Sulfobacillus thermosulfidooxidans DSM_9293 (wild-type / wild-type)
SOPs: 003 Biomolecular Extractions from LAO (Qiagen A..., SOP - RNA/Protein sampling for continuous culture, Sample Identification Code
Data files: Rawdata RNAseq
Snapshots: No snapshots
Umbrella study for all RNAseq rawdata Separate projects can be accessed under "component projects"
Creator: Malte Herold
Submitter: Malte Herold
Investigations: SysMetEx - Dataset collection
Studies: Biofilms on chalcopyrite grains, Continuous cultures, Planktonic cells
Assays: RNAseq rawdata, RNAseq rawdata, RNAseq rawdata
Pride project for raw and search data for AXX-Cn samples: LNU-AXX-Si00-CnB-P-B6ST-Pr_180min LNU-AXX-Si00-CnB-P-B7ST-Pr_180min LNU-AXX-Si00-CnB-P-B8ST-Pr_180min
Creator: Malte Herold
Submitter: Malte Herold
Investigations: SysMetEx - Dataset collection
Studies: Continuous cultures
Assays: Proteomics rawdata
Aceton precipitation and protein digestion for proteomic workflow
Creators: Malte Herold, Mohamed El Hajjami
Submitter: Malte Herold
Investigations: SysMetEx - Dataset collection
Studies: Biofilms on chalcopyrite grains, Continuous cultures, Planktonic cells
Assays: Proteomics rawdata, Proteomics rawdata, Proteomics rawdata
steps conducted to pellet cells for RNA and protein extraction
Creator: Stephan Christel
Submitter: Stephan Christel
Investigations: Multi -omics reveal lifestyle of acidophile, mi..., SysMetEx - Dataset collection
Studies: Continuous cultures, Omics_data_analysis
Assays: Experimental methods, Proteomics rawdata, RNAseq rawdata
This file describes the naming system used to uniquely identify samples
Creator: Stephan Christel
Submitter: Stephan Christel
Investigations: SysMetEx - Dataset collection
Studies: Biofilms on chalcopyrite grains, Continuous cultures, Planktonic cells
Assays: Proteomics rawdata, Proteomics rawdata, Proteomics rawdata, RNAseq rawdata, RNAseq rawdata, RNAseq rawdata
Protocol for the extraction of biomolecules (DNA,RNA,protein,metabolties) from the same sample. Originally intended for lipid accumulating organisms (LAO) from wastewater treatment plant samples. So far succesfully used for pelleted cells from planktonic cultures.
Creator: Malte Herold
Submitter: Malte Herold