Molecular dynamics of the matrisome across sea anemone life history

B. Gideon Bergheim, Alison G. Cole, Mandy Rettel, Frank Stein, Stefan Redl, Michael W. Hess, Aissam Ikmi and Suat Özbek*

*Correspondence: suat.oezbek@cos.uni-heidelberg.de

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Supplementary Files

input_proteomes

FASTA files of complete proteomes used as basis for in silico matrisome generation

in_silico_matrisomes

from_literature

In silico matrisomes taken from the Matrisome Project webpage. IDs were looked up in the respective sequence data bases. For Bos Taurus (where no IDs were provided) genes were searched by gene name.

• Homo sapiens
• Mus musculus
• Bos taurus
• Danio rerio
• Coturnix japonica
• Drosophila melanogaster
• C. elegans
• Schmidtea mediterranea

in_this_publication

The following in silico matrisomes where generated with the methods described in Materials and Methods and used as representative members of different taxa.

Chordata

• Branchiostoma belcheri
• Branchiostoma floridae
• Branchiostoma lanceolatum

Choanozoa

• Monosiga brevicollis
• Salpingoeca rosetta

Cnidaria

• Acropora digitifera
• Exaiptasia diaphana
• Nematostella vectensis
• Porites asteroides
• Stylophora pistillata
• Xenia spec.
• Morbakka virulenta
• Clytia hemispherica
• Hydra vulgaris
• Thelohanellus_kitauei
• Aurelia aurita
• Calvadosia cruxmelitensis

Ctenophora

• Mnemiopsis leidyi
• Pleurobrachia bachei
• Beroe ovata

Placozoa

• Trichoplax spec. (H2)
• Tricoplax adhaerens

Porifera

• Amphimedon queenslandica
• Ephydatia muelleri

other_in_silico_matrisomes

In addition to the in silico matrisomes mentioned in this publication we also generated a number of additional in silico matrisomes using the same methods. These are not included in any of the analyses in the publication.

Annelida

• Capitella teleta (was excluded due to severe fragmentation)

Cnidaria (were excluded to avoid a Cnidarian bias as much as possible)

• Acropora cervicornis
• Acropora hyacinthus
• Acropora millepora
• Acropora muricata
• Actinia tenebrosa
• Montipora aequituberculata
• Montipora foliosa
• Pocillopora damicornis
• Pocillopora verrucosa
• Renilla reniformis
• Hydra viridissima
• Hydractinia echinata
• Hydractinia symbiolongicarpus
• Myxobolus honghuensis
• Cassiopea xamachana

orthofinder results

This directory contains most of the output of the orthofinder run used to identify orthogroups. An extensive overview over the files can be found on OrthoFinder Tutorial.

Source Code

This directory contains the python code which was used to generate the in silico matrisomes and the following analyses. Some of these rely on additional files found in suppl_code_files.

mass_spec_run

This directory contains the MS files and R analysis markdown files written by Frank Stein.

scRNA expression

This directory contains the R script for generating scRNA expression plots written by Alison G. Cole.