Data files

To focus our investigation of omega-3 metabolism, we are compiling a list of relevant genes. As a start, we selected seven KEGG pathways, but eventually we’ll also include Reactome’s equivalent pathways. Unfortunately, the KEGG pathways include only enzymes, not regulators or transporters (SREBP, LXR, FABP’s etc.), so we’ll have to add the latter manually. (Reactome might have them.) The gene list below is a large, autogenerated table showing

Various identifiers for each gene.
The most similar
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Reference genome of Sulfolobus solfataricus P2 used for mapping of RNA-seq results. Based on NCBI genome of Sulfolobus solfataricus.

RNA-Seq raw data: Sulfolobus solfataricus P2 grown on casaminoacids and d-glucose.

RNA-Seq mapping results (part2): Sulfolobus solfataricus P2 grown on casaminoacids and d-glucose, mapped using bowtie2 against reference sequence of Sulfolobus solfataricus P2 (NBCI, see other data files of experiment).

RNA-Seq mapping results (part1): Sulfolobus solfataricus P2 grown on casaminoacids and d-glucose, mapped using bowtie2 against reference sequence of Sulfolobus solfataricus P2 (NBCI, see other data files of experiment).

Supplementary file required by main Zip archive file for file extraction.

Cells of S. solfataricus were grown on either caseinhydrolysate or D-glucose (reference) as sole carbon source.

The distribution of enzymes involved in oxidative Stickland reactions among archaea was estimated using BLAST searches (BLOSUM62) with the protein sequences of acetate-CoA ligase (EC 6.2.1.13, ACS), ketoisovalerate oxidoreductase (EC 1.2.7.7, BC-OR) and indolepyruvate oxdoreductase (EC 1.2.7.8, AR-OR) from Pyrococcus furiosus (Pfu) and Sulfolobus solfataricus (Sso) against all archaea. Positive results are indicated by a '+' (homologue found, e-value < 1e-20) and negative results by a '-' (no
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The calculation of amino acid uptake rates for cells of Sulfolobus solfataricus P2 grown on caseinhydrolysate was performed based on the relative consumption of individual amino acids from the growth medium and the previously published absolute concentration of amino acids in the used growth medium.

Protein, RNA and DNA content during the logarithmic growth phase were investigated in this study. The values represent the average of at least three independent experiments. Errors represent the standard deviation between the experiments.

Sulfolobus solfataricus P2 was cultivated on 1 % Caseinhydrolysate. Samples of the culture supernatants were taken at regular intervalls and analyzed by GC-MS. To evaluate the stability of amino acids under cultivation conditions an additional non-inoculated control culture was also analyzed.

Intracellular metabolome analysis of S. solfataricus P2 grown on caseinhydrolysate or D-glucose as sole carbon source.
Samples were analyzed with GC-MS. CoA derivatives were analyzed with LC-MS.

These files contain the output results from Phenyx searching, providing all necessary information for matching MS data with protein database.

This file contains the results from proteome analysis of Sulfolobus solfataricus grown on Caseinhydrolysate as carbon source (growth on D-glucose served as reference condition).

Raw MS data files of the comparison of Sulfolobus solfataricus grown on either caseinhydrolysate or D-glucose. The numbers represents the fractions collected from the HPLC run (e.g. 22 indicates that this sample was collected from 21 min to 22 min). For MS analysis every two fractions were combined, indicated by double numbers (e.g. 80-81: combined fractions 80 and 81). Furhter all combined fractions were run twice on the MS.
Zip archive. Requires the supplementary .z01, .z02 and .z03 files for
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Supplementary file required by main Zip archive file for file extraction.

Supplementary file required by main Zip archive file for file extraction.

Master file, aggregates metabolite concentrations inside and outside the cell, protein copy number and flux estimates for metabolites in the core model. Based on all internal metabolite concentrations, external metabolite concentrations from growth curve data, flux of glucose, lactate and acetate based on growth curve data and protein copy number data for enzyme concentrations. Combines absolute and relative measurements and metabolomics measurements from different experiment to get an as complete
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Protein copy number estimates, Mean and SD based on multiple proteomics experiments.
Compatible with internal and external metabolite measurements for Growth curve A.
Used as training data for the model

A dummy file used to test programmatic download from SEEK.

test file

test file

test file

test file

Lists containing sample identifiers and relationships between samples.

Also see SOP for sample identifiers: https://fairdomhub.org/sops/242

Alterations to SOP:
Block1: LNU1/LNU2 -> LNU
Block 4: Continuous cultures -> Cn, Batch cultures -> #days, replicates -> A-Z refer to CULTURE REPLICATES
Block 6: biosample + REPLICATE , B1,B2 ...
Block 7: Sample Type + Replicate , RNA: R1,R2,... DNA: D1... Protein: Pr

Header: Bold -> mandatory, other fields are either for additional information or redundant
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Chalcopyrite leaching data of cultures with our combinations of the three species (A, L, S, ALS, AL, AS, LS, SA, SL, SAL)

Including development of planktonic and sessile cell population, pH, EH, [ferrous iron], [total iron], [total copper] within 21 days of incubation at 37 C° with 160 rpm shaking after inoculation with 1e7 cells/mL (per species).