SysMetEx

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.

Supplementary files for the submission:
Reverse Engineering Directed Gene Regulatory Networks from
Transcriptomics and Proteomics Data of Biomining Bacterial
Communities with Approximate Bayesian Computation and
Steady-State Signalling Simulations

Supplementary files for the publication:
Deep Neural Networks Outperform Human Expert’s Capacity in Characterizing Bioleaching Bacterial Biofilm Composition

Publication data made available for Biotechnology Reports, supplementary data

Experimental data and all related material for the publication "Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT".
changed ID

Experimental data and all related material for the publication "Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT".

Supplemental files for the publication of the dataset collection.

Proteomics and transcriptomics data tables, sample IDs and description, source code

edit later

Publication data made available for Biotechnology Reports, supplementary data

This stores:
Processed data files
Links to raw data files
Links to repositories containing applied workflows

Raw proteomics data derived from planktonic cells in chalcopyrite leaching experiments

Proteomics data for samples derived from continuous cultures

RNAseq raw data derived from continuous culture samples

Supplemental files for the publication

Links to additional gitlab repositories

Rawdata for RNAseq derived from biofilms on chalcopyrite grains

Link to RNAseq raw data

Data derived from RNAseq

Data derived from protein samples

Scripts for running network simulations

tbd

tbd

RNAseq data for L.ferriphilum samples

Proteomics data for L.ferriphilum samples (continuous and with mineral)

Genomics data, for L.ferriphilum
Sequencing of the genome and functional annotation

Collection for experimental SOPs

Umbrella study for all RNAseq rawdata
Separate projects can be accessed under "component projects"

Overview of the quality control for the RNAseq short read data after quality filtering of the reads

Overview for quality control of mapping statistics, after mapping processed reads to reference genomes

Repository for code used in data analysis (mainly for RNAseq) and for generating summary tables and overviews.

Files for the reference genomes utilized in the analysis are summarised in this repository.

Overivew of RNAseq and proteomics samples with respective accessions to access the raw data on ENA or PRIDE respectively.

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

Raw proteomics data for L. ferriphilum planktonic samples

Raw proteomics data for S. thermosulfidooxidans samples

Raw data for tertiary mixture, planktonic cells, proteomics

Raw data for , Ac + St or Lf + St planktonic cells from leaching experiments

Raw proteomics data for St + Ac planktonic cells

Raw data for Ac + St leaching experiments proteomics data, with Ac 10x inoculum sizing

Raw data for Ac+St planktonic cells, leaching experiments with St 10x incoulum sizing

Parameters used in maxQuant analysis

Overview of the quality control for the RNAseq short read data before quality filtering of the reads

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

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

Raw data for mixed cultures of S. thermosulfidooxidans and L.ferriphilum

Raw data for L.ferriphilum biofilm proteomics data

Aceton precipitation and protein digestion for proteomic workflow

SOP for bioleaching experiments carried out for microscopy analysis at UDE

steps conducted to pellet cells for RNA and protein extraction

This file describes the naming system used to uniquely identify samples

SOP for extracting DNA, RNA and Proteins from the mineral pellet of a bioleaching culture using hot acidic phenol.
Current draft.

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.

sampling procedure for mineral containing leaching experiments

Initial configuration and parameters of the Bioleaching

TATAA biocenter workshop lecture

about Mark

Workshop by the fairdomhub team on reproducible and citable data and models

Stephan's poster for presentation at IBS 2015