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Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT
Experimental data and all related material for the publication "Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT".
SEEK ID: https://fairdomhub.org/investigations/162
Projects: SysMetEx
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Created: 7th Nov 2017 at 14:44
Last updated: 7th Nov 2017 at 14:52
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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
This stores:
Processed data files
Links to raw data files
Links to repositories containing applied workflows
Person responsible: Malte Herold
Snapshots: No snapshots
Investigation: Multi -omics reveal lifestyle of acidophile, mi...
Assays: Experimental methods, Genomics, Proteomics, RNAseq
RNAseq data for L.ferriphilum samples
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Multi -omics reveal lifestyle of acidophile, mi...
Study: Omics_data_analysis
Organisms: No organisms
SOPs: No SOPs
Data files: LF_RNAseq_TPM_continuous, LF_RNAseq_TPM_mineral, LF_RNAseq_rawdata, LF_deseq_comparison, LF_omics_analysis, LF_omics_combined_Table
Proteomics data for L.ferriphilum samples (continuous and with mineral)
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Multi -omics reveal lifestyle of acidophile, mi...
Study: Omics_data_analysis
Organisms: No organisms
SOPs: No SOPs
Data files: LF_LFQ_comparison_ttest, LF_omics_analysis, LF_omics_combined_Table, LF_proteomics_LFQs_continuous, LF_proteomics_LFQs_mineral, LF_proteomics_LFQs_mineral_scaled, LF_proteomics_continuous_scaled, LF_proteomics_maxquant_perseus_filtered, LF_proteomics_maxquant_perseus_unfiltered, Perseus workflow t-test, Proteomics data comparing LXX cultures cultivat...
Genomics data, for L.ferriphilum
Sequencing of the genome and functional annotation
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Multi -omics reveal lifestyle of acidophile, mi...
Study: Omics_data_analysis
Organisms: No organisms
SOPs: No SOPs
Data files: Functional_annotation_repository, LF_functional_annotation_gbk, LF_omics_combined_Table, LF_sequencing_data
Collection for experimental SOPs
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Multi -omics reveal lifestyle of acidophile, mi...
Study: Omics_data_analysis
Organisms: No organisms
SOPs: 003 Biomolecular Extractions from LAO (Qiagen A..., SOP - Bioleaching in flasks (LNU), SOP - RNA/Protein sampling for continuous culture
Data files: No Data files
Filtering of data in Perseus and t-test between conditions
Perseus save file
Creator: Malte Herold
Submitter: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics
Maxquant output.
Proteomics data comparing LXX cultures cultivated on mineral and in continuous culture:
mineral samples:
LNU-LXX9-Si00-14B-P-B-Pr
LNU-LXX9-Si00-14B-P-C-Pr
LNU-LXX9-Si00-14B-P-D-Pr
conitnuous culture samples:
LNU-LXX9-Si00-CnA-P-B2-Pr
LNU-LXX9-Si00-CnA-P-B3-Pr
LNU-LXX9-Si00-CnA-P-B4-Pr
LNU-LXX9-Si00-CnA-P-B5-Pr
LNU-LXX9-Si00-CnA-P-B6-Pr
LNU-LXX9-Si00-CnA-P-B7-Pr
Creator: Mohamed El Hajjami
Submitter: Mohamed El Hajjami
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics
Creator: Malte Herold
Submitter: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics
Creator: Malte Herold
Submitter: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics
Creator: Malte Herold
Submitter: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics
Creator: Malte Herold
Submitter: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics
LFQ intensities from maxquant from combined search (mineral and continuous samples), filtered (at least 3 values in each condition), log-transformed
Creators: Malte Herold, Ansgar Poetsch, Mohamed El Hajjami, Ansgar
Submitter: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics
LFQ intensities from maxquant from combined search (mineral and continuous samples), log-transformed
Creators: Malte Herold, Ansgar Poetsch, Mohamed El Hajjami
Submitter: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics
Raw data and assembly for pacbio sequencing of L.ferriphilum.
Creator: Malte Herold
Submitter: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Genomics
Link to the repository for functional annotation
Creator: Malte Herold
Submitter: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Genomics
Genbank file for the L.ferriphilum chromosome, annotated with prokka 1.12beta
Creator: Malte Herold
Submitter: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Genomics
Table combining data for L.ferriphilum.
RNAseq data, Proteomics LFQs, Functional annotation
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Genomics, Proteomics, RNAseq
Comparison between axenic and planktonic readcounts with deseq2
Creator: Malte Herold
Submitter: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: RNAseq
Comparison for LFQs with t-test in Perseus
Creator: Malte Herold
Submitter: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics
Raw read files for samples
Creator: Malte Herold
Submitter: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: RNAseq
Normalized counts (tpm) for LF samples with mineral
Creator: Malte Herold
Submitter: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: RNAseq
Normalized counts (tpm) for L.ferriphilum samples from continuous culture.
Creator: Malte Herold
Submitter: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: RNAseq
Repository for omics data analysis
Creator: Malte Herold
Submitter: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics, RNAseq
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
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
Initial configuration and parameters of the Bioleaching
Creator: Stephan Christel
Submitter: Stephan Christel
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Experimental methods
Abstract (Expand)
Authors: Stephan Christel, Malte Herold, Sören Bellenberg, Mohamed El Hajjami, Antoine Buetti-Dinh, Igor V. Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mark Dopson
Date Published: 1st Feb 2018
Publication Type: Not specified
DOI: 10.1128/AEM.02091-17
Citation: Appl Environ Microbiol 84(3) : e02091-17