Data files

• Calculations of predictions of all identified proteins of P. cordatum
• Calculations of fold-changes of all identified proteins (cell vs. nuclei fraction) of P. cordatum
• Calculations of predictions of proteins of unknown function of_ P. cordatum_
• Calculations of fold-changes of unknowns (cell vs. nuclei fraction) of P. cordatum

Tab color: all identified proteins, purple; unkowns, green

Content:

• Nuclear protein fractions: NSP, NMP and NTP R1-R3 (Peptide counts)
• Summary nuclear proteins geLC
• Cellular protein fractions: CSP, CMP R1-R3 (Peptide counts)
• Summary cellular proteins geLC
• Summary nuclear protein fractions NSP R1-R3 (iBAQs)
• Summary cellular protein fractions CSP R1-R3 (iBAQs)
• 15 columns annotation
• Final summary of protein data
• Prediction results
• Annotation (biological processes and categories)

Tab color: raw data, green; summarized data, orange; final ...

• Summary of functional categorization of all identified proteins of P. cordatum
• Calculations of general functions (Fig. 5, left panel)
• Calculations of nuclear functions (Fig. 5, right panel)
• Categories in separate sheets

Tab color: Summarized data, purple; calculations, organge; functional categories, green

• Summary of nuclear proteins
• Separate sheets of nuclear processes (MBNP_Histones, DNA replication, DNA repair, RNA processing (rRNA and mRNA processing), transcription, import and export, ubiquitylation, proteasome, biogenesis ribosomes)
• Ribosomes (category translation)

Tab color: Summary, purple; nuclear processes, green; ribosomes, orange

Prepared (sub-)cellular fractions were separated by gradient SDS-PAGE and entire sample lanes cut into pieces prior to in-gel digest and nanoLC separation coulpled to iontrap MS/MS detection.

Supplementary movie of the distribution of nuclear pores in the nuclear envelope of P. cordatum

Movie of the chromosomal packing in the nucleus of P. cordatum MPEG format (mp4)

• Amira raw data of nuclear structures of P. cordatum
• Volume calculations of nuclear structures of_ P. cordatum _

• raw data tif-file, stacked image for 3D reconstruction of the nucleus of P. cordatum

This file provides a full list of the PubMed IDs used as input to our survey of SARS-CoV2 enrichment analysis results

A list of the search terms used for identifying SARS-CoV2 studies involving enrichment analysis. A random sample of 100 papers were used as input to the experiment.

Summary of identified ribosomal proteins of P. cordatum.

Summary table of identified pigment binding proteins with relative shares in % and calculations of total amount of pigment binding proteins in the different data sets.

Comparative flux balance analysis file. All values are given in mmol/g/h. Fluxes were optimized to maximize BIOMASS.

Uptake and growth rates, and biomass yields are compared in vivo and in silico.

The metano scenario file for aerobic growth on 3-Hydroxybenzoate.

The metano scenario file for anaerobic growth on 3-Hydroxybenzoate.

The metano scenario file for aerobic growth on 4HPP.

The metano scenario file for anaerobic growth on 4HPP.

The metano scenario file for aerobic growth on acetate.

The metano scenario file for anaerobic growth on acetate.

The metano scenario file for aerobic growth on Benzoate.

The metano scenario file for anaerobic growth on benzoate.