SysMetEx - Dataset collection

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.

DOI: 10.15490/fairdomhub.1.investigation.292.2

Created at: 12th Feb 2020 at 13:50

Contents

Biofilms on chalcopyrite grains

No description specified

Microscopy imaging

No description specified

Biofilm Imaging

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

  • 2669113

SOP_Bioleaching_in_flasks_UDE

SOP for bioleaching experiments carried out for microscopy analysis at UDE

  • SOP_bioleaching_in_flasks_UDE.docx

Proteomics rawdata

No description specified

SAL_M Proteomics

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

  • PXD011503

SLX_M Proteomics

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

  • PXD011504

LXX_M Proteomics

Raw data for L.ferriphilum biofilm proteomics data

  • PXD012780

DNA, RNA, Protein extraction from mineral samples

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

  • Hot_Phenol_Protocol.docx

SOP - RNA-Prot sampling for bioleaching

sampling procedure for mineral containing leaching experiments

  • SOP_RNA-Prot_sampling_for_leaching.docx

Sample Identification Code

This file describes the naming system used to uniquely identify samples

  • sample_code_description.xlsx

In solution digestion part

Aceton precipitation and protein digestion for proteomic workflow

  • 20161024 Sysmetex P02_in-sol-digest3_SDS.docx

RNAseq rawdata

Rawdata for RNAseq derived from biofilms on chalcopyrite grains

Rawdata RNAseq

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

  • PRJEB30645

DNA, RNA, Protein extraction from mineral samples

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

  • Hot_Phenol_Protocol.docx

SOP - RNA-Prot sampling for bioleaching

sampling procedure for mineral containing leaching experiments

  • SOP_RNA-Prot_sampling_for_leaching.docx

Sample Identification Code

This file describes the naming system used to uniquely identify samples

  • sample_code_description.xlsx

Planktonic cells

No description specified

Proteomics rawdata

Raw proteomics data derived from planktonic cells in chalcopyrite leaching experiments

LXX_P Proteomics

Raw proteomics data for L. ferriphilum planktonic samples

  • PXD012783

SXX_P Proteomics

Raw proteomics data for S. thermosulfidooxidans samples

  • PXD011921

SAL_P Proteomics

Raw data for tertiary mixture, planktonic cells, proteomics

  • PXD011540

ASX_LSX_P Proteomics

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

  • PXD011502

SAX_P Proteomics

Raw proteomics data for St + Ac planktonic cells

  • PXD011506

AAS_P Proteomics

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

  • PXD011508

ASS_P Proteomics

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

  • PXD011509

003 Biomolecular Extractions from LAO (Qiagen AllPrep)

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.

  • 003_BIOMOLECULAR EXTRACTIONS FROM LAO (Qiagen AllPrep).docx

SOP - RNA-Prot sampling for bioleaching

sampling procedure for mineral containing leaching experiments

  • SOP_RNA-Prot_sampling_for_leaching.docx

Sample Identification Code

This file describes the naming system used to uniquely identify samples

  • sample_code_description.xlsx

In solution digestion part

Aceton precipitation and protein digestion for proteomic workflow

  • 20161024 Sysmetex P02_in-sol-digest3_SDS.docx

RNAseq rawdata

Link to RNAseq raw data

Rawdata RNAseq

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

  • PRJEB30645

003 Biomolecular Extractions from LAO (Qiagen AllPrep)

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.

  • 003_BIOMOLECULAR EXTRACTIONS FROM LAO (Qiagen AllPrep).docx

SOP - RNA-Prot sampling for bioleaching

sampling procedure for mineral containing leaching experiments

  • SOP_RNA-Prot_sampling_for_leaching.docx

Sample Identification Code

This file describes the naming system used to uniquely identify samples

  • sample_code_description.xlsx

Continuous cultures

No description specified

Proteomics rawdata

Proteomics data for samples derived from continuous cultures

AXX_Cn Proteomics

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

  • PXD011507

003 Biomolecular Extractions from LAO (Qiagen AllPrep)

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.

  • 003_BIOMOLECULAR EXTRACTIONS FROM LAO (Qiagen AllPrep).docx

SOP - RNA/Protein sampling for continuous culture

steps conducted to pellet cells for RNA and protein extraction

  • SOP_RNA-Prot_sampling.docx

Sample Identification Code

This file describes the naming system used to uniquely identify samples

  • sample_code_description.xlsx

In solution digestion part

Aceton precipitation and protein digestion for proteomic workflow

  • 20161024 Sysmetex P02_in-sol-digest3_SDS.docx

RNAseq rawdata

RNAseq raw data derived from continuous culture samples

Rawdata RNAseq

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

  • PRJEB30645

003 Biomolecular Extractions from LAO (Qiagen AllPrep)

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.

  • 003_BIOMOLECULAR EXTRACTIONS FROM LAO (Qiagen AllPrep).docx

SOP - RNA/Protein sampling for continuous culture

steps conducted to pellet cells for RNA and protein extraction

  • SOP_RNA-Prot_sampling.docx

Sample Identification Code

This file describes the naming system used to uniquely identify samples

  • sample_code_description.xlsx

Supplemental Files

Supplemental files for the publication of the dataset collection.

Supplemental Files

Supplemental files for the publication

Supplemental File 1 - maxquant parameters

Parameters used in maxQuant analysis

  • Supplemental_File1.mqpar.xml

Supplemental File 2 - qc raw reads

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

  • Supplemental_File2.multiqc_rawreads.html

Supplemental file 3 - qc processed reads

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

  • Supplemental_File3.multiqc_preprocessedreads.html

Supplemental File 4 - mapping statistics

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

  • Supplemental_File4.multiqc_mappings.html

Supplemental Table 1 - omics samples

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

  • Supplemental_Table1.Prot_RNAseq_data_accessions.xlsx

Links to code repositories

Links to additional gitlab repositories

Repository for data analysis

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

  • sysmetex_data_analysis

Repository for reference genomes

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

  • SysMetEx_ReferenceGenomes
Fingerprints

These checksums allow you to check a Snapshot you have downloaded hasn't been modified. For details on how to use these please visit this guide

MD5: 3a12fd9a9c2f9f9fa4352ab439a1d88e

SHA1: 5fa415af138c21895b8b372ab98117f2cb87ef70

Citation
Herold, M. (2020). SysMetEx - Dataset collection. FAIRDOMHub. http://doi.org/10.15490/FAIRDOMHUB.1.INVESTIGATION.292.2
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Snapshot 2 (12th Feb 2020) DOI
Snapshot 1 (23rd Jan 2020) DOI
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Created: 12th Feb 2020 at 13:50

Last updated: 12th Feb 2020 at 13:51

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