Data files

Content:

• Compiled 15 columns annotation of P. cordatum (Dougan et al. 2022)
• Summary of predicted unknown proteins of P. cordatum
• Calculations of predicted unknown proteins of P. cordatum

Tab color: annotation, purple; unknowns, green

• 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

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.