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Supplemental files for the publication of the dataset collection.
SEEK ID: https://fairdomhub.org/studies/711
Projects: SysMetEx
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Created: 23rd Jan 2020 at 12:01
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
Supplemental files for the publication
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
Links to additional gitlab repositories
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
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
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