Assays

Supplementary Information linked together

Short Name: 08_centrifuge_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: Centrigufe pan-transcriptome sequence classification Description: Classify cv rep transcripts and pan-transcriptome singletons based on taxonomy pISA Assay creation date: 2020-03-11 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Short Name: 03_components_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: components Description: representative and alternative pan-transcriptome CDS and polypeptide fasta files pISA Assay creation date: 2020-03-10 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Short Name: 04_BUSCO_3cvs-GFFmerged Assay Class: DRY Assay Type: GFFmerged Title: BUSCOs Description: BUSCO on ITAG, PGSC, ITAG/PGSC merged, pan-transcriptome representatives, pan-transcriptome alternatives, and pan-transcriptome pISA Assay creation date: 2020-03-10 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: Data:

Plant material The same plant material used for transcriptome analysis in (Flis et al., 2016) was the basis of our proteome study. Briefly, Arabidopsis thaliana Col-0 plants were grown on GS 90 soil mixed in a ratio 2:1 (v/v) with vermiculite. Plants were grown for 1 week in a 16 h light (250 μmol m−2 s−1, 20 °C)/8 h dark (6 °C) regime followed by an 8 h light (160 μmol m−2 s−1, 20 °C)/16 h dark (16 °C) regime for one week. Plants were then replanted with five seedlings per pot, transferred for ...

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Here would be the results from the Analysis part of the Simulation foundry. For the newest version, which was improved based on reviewers comments to represent best practices, of the Simulation Foundry for Methanol-Water mixtures no such results exist yet.

Assay: _A_03.1_filtering Short Name: 03.1_filtering Assay Class: DRY Assay Type: filtering Title: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs Description: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Assay: _A_02.2_assembly-contribution-count Short Name: 02.2_assembly-contribution-count Assay Class: DRY Assay Type: count Title: assembly contribution count Description: assembly contribution count, input/output tr2aacds pISA Assay creation date: 2019-10-22 pISA Assay creator: Maja Zagorscak Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt

Raw proteomics data derived from planktonic cells in chalcopyrite leaching experiments

Proteomics data for samples derived from continuous cultures

Extraction of causalities from transcription and translation reactions from the Reactome pathway database.

Curation guidelines for molecular interaction causal statements

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

Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, without Mn2+ added, but with NAD recycling, metabolites measured enzymatically. https://jjj.bio.vu.nl/models/experiments/shen2020_fig4d/simulate

Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, with 0.15 mM Mn2+ added, but no NAD recycling, metabolites measured enzymatically. https://jjj.bio.vu.nl/models/experiments/shen2020_fig4c/simulate

Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, with 0.15 mM Mn2+ added, and with NAD recycling, metabolites measured enzymatically. https://jjj.bio.vu.nl/models/experiments/shen2020_fig4b/simulate