Assays

What is an Assay?

18 Assays visible to you, out of a total of 38

Proteomics rawdata

SysMetEx

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

Created: 6th May 2019 at 15:14, Last updated: 12th Feb 2020 at 12:49

Proteomics rawdata

SysMetEx

No description specified

Submitter: Malte Herold

Assay type: Proteomics

Technology type: Technology Type

Investigation: SysMetEx - Dataset collection

Study: Biofilms on chalcopyrite grains

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

Created: 6th May 2019 at 15:05, Last updated: 12th Feb 2020 at 12:47

Proteomics rawdata

SysMetEx

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) (chemostat)

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

Created: 6th May 2019 at 15:24, Last updated: 12th Feb 2020 at 12:47

Microscopy imaging

SysMetEx

No description specified

Submitter: Malte Herold

Assay type: Experimental Assay Type

Technology type: Microscopy

Investigation: SysMetEx - Dataset collection

Study: Biofilms on chalcopyrite grains

SOPs: SOP_Bioleaching_in_flasks_UDE

Data files: Biofilm Imaging

Snapshots: No snapshots

Created: 6th May 2019 at 15:01, Last updated: 12th Feb 2020 at 12:42

RNAseq rawdata

SysMetEx

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

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

Created: 6th May 2019 at 15:26, Last updated: 23rd Jan 2020 at 12:14

Supplemental Files

SysMetEx

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

Created: 23rd Jan 2020 at 11:03, Last updated: 23rd Jan 2020 at 12:14

Links to code repositories

SysMetEx

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

Created: 23rd Jan 2020 at 11:13, Last updated: 23rd Jan 2020 at 12:14

RNAseq rawdata

SysMetEx

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

Study: Biofilms on chalcopyrite grains

SOPs: DNA, RNA, Protein extraction from mineral samples, SOP - RNA-Prot sampling for bioleaching, Sample Identification Code

Data files: Rawdata RNAseq

Snapshots: No snapshots

Created: 6th May 2019 at 15:10, Last updated: 23rd Jan 2020 at 12:14

RNAseq rawdata

SysMetEx

Link to RNAseq raw data

Submitter: Malte Herold

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: SysMetEx - Dataset collection

Study: Planktonic cells

SOPs: 003 Biomolecular Extractions from LAO (Qiagen A..., SOP - RNA-Prot sampling for bioleaching, Sample Identification Code

Data files: Rawdata RNAseq

Snapshots: No snapshots

Created: 6th May 2019 at 15:25, Last updated: 23rd Jan 2020 at 12:14

RNA data

SysMetEx

Data derived from RNAseq

Submitter: Malte Herold

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Reverse Engineering Directed Gene Regulatory Ne...

Study: Supplementary files

Organisms: No organisms

SOPs: No SOPs

Data files: Sample information, TPM counts

Snapshots: No snapshots

Created: 15th Apr 2019 at 06:09, Last updated: 17th Apr 2019 at 15:49

Proteome data

SysMetEx

Data derived from protein samples

Submitter: Malte Herold

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Reverse Engineering Directed Gene Regulatory Ne...

Study: Supplementary files

Organisms: No organisms

SOPs: No SOPs

Data files: LFQ intensities, Sample information

Snapshots: No snapshots

Created: 15th Apr 2019 at 06:10, Last updated: 17th Apr 2019 at 15:49

Simulations for network engineering

SysMetEx

Scripts for running network simulations

Submitter: Malte Herold

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: Reverse Engineering Directed Gene Regulatory Ne...

Study: Supplementary files

Organisms: No organisms

SOPs: No SOPs

Data files: TwinSensNet

Snapshots: No snapshots

Created: 15th Apr 2019 at 06:13, Last updated: 17th Apr 2019 at 15:49

Imaging of leaching cultures

SysMetEx

tbd

Submitter: Malte Herold

Assay type: Experimental Assay Type

Technology type: Confocal Laser Scanning Microscopy (CLSM)

Investigation: Deep Neural Networks Outperform Human Expert’s ...

Study: Deep Neural Networks Outperform Human Expert’s ...

Organisms: Acidithiobacillus caldus : Acidithiobacillus caldus ATCC 51756 (wild-type / wild-type) (batch), Leptospirillum ferriphilum : Leptospirillum ferriphilum DSM 14647 (wild-type / wild-type) (batch), Sulfobacillus thermosulfidooxidans : Sulfobacillus thermosulfidooxidans DSM 9293 (wild-type / wild-type) (batch)

SOPs: No SOPs

Data files: Images of mineral colonization

Snapshots: No snapshots

Created: 26th Feb 2019 at 12:42, Last updated: 14th Mar 2019 at 11:11

Code for image analysis

SysMetEx

tbd

Submitter: Malte Herold

Biological problem addressed: Model Analysis Type

Investigation: Deep Neural Networks Outperform Human Expert’s ...

Study: Deep Neural Networks Outperform Human Expert’s ...

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: Code for image analyses

Snapshots: No snapshots

Created: 26th Feb 2019 at 13:38, Last updated: 14th Mar 2019 at 11:11

RNAseq

SysMetEx

RNAseq data for L.ferriphilum samples

Submitter: Malte Herold

Assay type: Experimental Assay Type

Technology type: Technology Type

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

Snapshots: No snapshots

Created: 19th Jul 2017 at 23:51, Last updated: 8th Nov 2017 at 14:21

Proteomics

SysMetEx

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

Submitter: Malte Herold

Assay type: Experimental Assay Type

Technology type: Technology Type

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...

Snapshots: No snapshots

Created: 19th Jul 2017 at 23:59, Last updated: 8th Nov 2017 at 14:21

Genomics

SysMetEx

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

Submitter: Malte Herold

Assay type: Experimental Assay Type

Technology type: Technology Type

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

Snapshots: No snapshots

Created: 20th Jul 2017 at 00:04, Last updated: 8th Nov 2017 at 14:21

Experimental methods

SysMetEx

Collection for experimental SOPs

Submitter: Malte Herold

Assay type: Experimental Assay Type

Technology type: Technology Type

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

Snapshots: No snapshots

Created: 20th Jul 2017 at 00:12, Last updated: 8th Nov 2017 at 14:21

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