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- Biofilms on chalcopyrite grains

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Created: 6th May 2019 at 16:59
Last updated: 23rd Jan 2020 at 13:14
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Projects: SysMetEx
Institutions: University of Luxembourg
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
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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.
Snapshots: Snapshot 1, Snapshot 2
Submitter: Malte Herold
Assay type: Proteomics
Technology type: Technology Type
Snapshots: No snapshots
Investigation: SysMetEx - Dataset collection
Study: Biofilms on chalcopyrite grains
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: DNA, RNA, Protein extraction from mineral samples, In solution digestion part, SOP - RNA-Prot sampling for bioleaching, Sample Identification Code
Data files: LXX_M Proteomics, SAL_M Proteomics, SLX_M Proteomics
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Microscopy
Snapshots: No snapshots
Investigation: SysMetEx - Dataset collection
Study: Biofilms on chalcopyrite grains
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: SOP_Bioleaching_in_flasks_UDE
Data files: Biofilm Imaging
Rawdata for RNAseq derived from biofilms on chalcopyrite grains
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: SysMetEx - Dataset collection
Study: Biofilms on chalcopyrite grains
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: DNA, RNA, Protein extraction from mineral samples, SOP - RNA-Prot sampling for bioleaching, Sample Identification Code
Data files: Rawdata RNAseq
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
Raw data for mixed culture biofilm proteomics
Samples:
UDE-SAL8-7O-M-B-Pr-2
UDE-SAL8-7O-M-B-Pr
UDE-SAL7-Pc20-7M-P-B-Pr_2uL
UDE-SAL7-A7-M-B-Pr
UDE-SAL7-7C-M-B-Pr
UDE-SAL7-7A-M-B-Pr
Creator: Malte Herold
Submitter: Malte Herold
Investigations: SysMetEx - Dataset collection
Studies: Biofilms on chalcopyrite grains
Assays: Proteomics rawdata
Microscopy images of A.Caldus (A), L.ferriphilum (L), S.thermosulfidooxidans (S) biofilms on chalcopyrite particles. (individual,e.g. SXX or mixed, e.g. SAL, cultures)
Timepoints: Day1, Day3, Day7, Day14, Day21
Creators: Malte Herold, Soeren Bellenberg
Submitter: Malte Herold
Investigations: SysMetEx - Dataset collection
Studies: Biofilms on chalcopyrite grains
Assays: Microscopy imaging
Raw data for mixed cultures of S. thermosulfidooxidans and L.ferriphilum
Creator: Malte Herold
Submitter: Malte Herold
Investigations: SysMetEx - Dataset collection
Studies: Biofilms on chalcopyrite grains
Assays: Proteomics rawdata
Raw data for L.ferriphilum biofilm proteomics data
Creator: Malte Herold
Submitter: Malte Herold
Investigations: SysMetEx - Dataset collection
Studies: Biofilms on chalcopyrite grains
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
SOP for bioleaching experiments carried out for microscopy analysis at UDE
Creators: Malte Herold, Soeren Bellenberg
Submitter: Malte Herold
Investigations: SysMetEx - Dataset collection
Studies: Biofilms on chalcopyrite grains
Assays: Microscopy imaging
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
SOP for extracting DNA, RNA and Proteins from the mineral pellet of a bioleaching culture using hot acidic phenol.
Current draft.
Creators: Malte Herold, Mario Vera, Soeren Bellenberg
Submitter: Malte Herold
Investigations: SysMetEx - Dataset collection
Studies: Biofilms on chalcopyrite grains
Assays: Proteomics rawdata, RNAseq rawdata
sampling procedure for mineral containing leaching experiments
Creator: Stephan Christel
Submitter: Stephan Christel
Investigations: SysMetEx - Dataset collection
Studies: Biofilms on chalcopyrite grains, Planktonic cells
Assays: Proteomics rawdata, Proteomics rawdata, RNAseq rawdata, RNAseq rawdata