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.
SEEK ID: https://fairdomhub.org/investigations/292
Projects: SysMetEx
Investigation position:
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Created: 6th May 2019 at 14:58
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
Submitter: Malte Herold
Investigation: SysMetEx - Dataset collection
Assays: Microscopy imaging, Proteomics rawdata, RNAseq rawdata
Snapshots: No snapshots
Submitter: Malte Herold
Investigation: SysMetEx - Dataset collection
Assays: Proteomics rawdata, RNAseq rawdata
Snapshots: No snapshots
Submitter: Malte Herold
Investigation: SysMetEx - Dataset collection
Assays: Proteomics rawdata, RNAseq rawdata
Snapshots: No snapshots
Supplemental files for the publication of the dataset collection.
Submitter: Malte Herold
Investigation: SysMetEx - Dataset collection
Snapshots: No snapshots
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Microscopy
Investigation: SysMetEx - Dataset collection
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
Snapshots: No snapshots
Submitter: Malte Herold
Assay type: Proteomics
Technology type: Technology Type
Investigation: SysMetEx - Dataset collection
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
Snapshots: No snapshots
Rawdata for RNAseq derived from biofilms on chalcopyrite grains
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: SysMetEx - Dataset collection
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
Snapshots: No snapshots
Raw proteomics data derived from planktonic cells in chalcopyrite leaching experiments
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: SysMetEx - Dataset collection
Study: Planktonic cells
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..., In solution digestion part, SOP - RNA-Prot sampling for bioleaching, Sample Identification Code
Data files: AAS_P Proteomics, ASS_P Proteomics, ASX_LSX_P Proteomics, LXX_P Proteomics, SAL_P Proteomics, SAX_P Proteomics, SXX_P Proteomics
Snapshots: No snapshots
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
Link to RNAseq raw data
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: SysMetEx - Dataset collection
Study: Planktonic cells
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-Prot sampling for bioleaching, Sample Identification Code
Data files: Rawdata RNAseq
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
Supplemental files for the publication
Submitter: Malte Herold
Biological problem addressed: Model Analysis Type
Investigation: SysMetEx - Dataset collection
Study: Supplemental Files
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Supplemental File 1 - maxquant parameters, Supplemental File 2 - qc raw reads, Supplemental File 4 - mapping statistics, Supplemental Table 1 - omics samples, Supplemental file 3 - qc processed reads
Snapshots: No snapshots
Links to additional gitlab repositories
Submitter: Malte Herold
Biological problem addressed: Model Analysis Type
Investigation: SysMetEx - Dataset collection
Study: Supplemental Files
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Repository for data analysis, Repository for reference genomes
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
Overview of the quality control for the RNAseq short read data after quality filtering of the reads
Creator: Malte Herold
Submitter: Malte Herold
Investigations: SysMetEx - Dataset collection
Studies: Supplemental Files
Assays: Supplemental Files
Overview for quality control of mapping statistics, after mapping processed reads to reference genomes
Creator: Malte Herold
Submitter: Malte Herold
Investigations: SysMetEx - Dataset collection
Studies: Supplemental Files
Assays: Supplemental Files
Repository for code used in data analysis (mainly for RNAseq) and for generating summary tables and overviews.
Creator: Malte Herold
Submitter: Malte Herold
Investigations: SysMetEx - Dataset collection
Studies: Supplemental Files
Assays: Links to code repositories
Files for the reference genomes utilized in the analysis are summarised in this repository.
Creator: Malte Herold
Submitter: Malte Herold
Investigations: SysMetEx - Dataset collection
Studies: Supplemental Files
Assays: Links to code repositories
Overivew of RNAseq and proteomics samples with respective accessions to access the raw data on ENA or PRIDE respectively.
Creator: Malte Herold
Submitter: Malte Herold
Investigations: SysMetEx - Dataset collection
Studies: Supplemental Files
Assays: Supplemental Files
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
Raw proteomics data for L. ferriphilum planktonic samples
Creators: Malte Herold, Mohamed El Hajjami
Submitter: Malte Herold
Raw proteomics data for S. thermosulfidooxidans samples
Creator: Malte Herold
Submitter: Malte Herold
Raw data for tertiary mixture, planktonic cells, proteomics
Creator: Malte Herold
Submitter: Malte Herold
Raw data for , Ac + St or Lf + St planktonic cells from leaching experiments
Creator: Malte Herold
Submitter: Malte Herold
Raw proteomics data for St + Ac planktonic cells
Creator: Malte Herold
Submitter: Malte Herold
Raw data for Ac + St leaching experiments proteomics data, with Ac 10x inoculum sizing
Creator: Malte Herold
Submitter: Malte Herold
Raw data for Ac+St planktonic cells, leaching experiments with St 10x incoulum sizing
Creator: Malte Herold
Submitter: Malte Herold
Parameters used in maxQuant analysis
Creator: Malte Herold
Submitter: Malte Herold
Investigations: SysMetEx - Dataset collection
Studies: Supplemental Files
Assays: Supplemental Files
Overview of the quality control for the RNAseq short read data before quality filtering of the reads
Creator: Malte Herold
Submitter: Malte Herold
Investigations: SysMetEx - Dataset collection
Studies: Supplemental Files
Assays: Supplemental Files
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
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
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
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
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