Embedded Files
Protocols and Recipes
Protocols and Recipes
RS, a fully defined medium for growing diverse protists. RS medium is composed of two components: non-nutrient medium (NNM) and nutrient medium (NM). The NM component is diluted into the NNM component in order to achieve the desired concentration of nutrients in the final medium.
Non-Nutrient Medium (NNM) component, featuring a natural pH buffer system, is designed to mimic the chemical composition of seawater: MediaDive, https://mediadive.dsmz.de/medium/P4
Nutrient Medium (NM) component, with a wide variety of nutrients to support growth: MediaDive, https://mediadive.dsmz.de/medium/P5
Transcriptome sequencing of 19 diverse species of choanoflagellates. From Richter et al. (2018):
protocols.io, https://doi.org/10.17504/protocols.io.kwscxee
Protist Cultures
Protist Cultures
We have strains in culture that we do not plan to pursue ourselves, but that might be useful to the community. Please contact us if you would like us to share them with you.
If you publish using one of these strains, we do not ask to be included in your publication, but we do ask you to agree to:
Deposit the strain in a public culture collection, on or before publication.
Make all data generated from the strain (sequences, assemblies, protein predictions, alignments, etc.) available in an appropriate public repository, on or before publication.
Publish a preprint and/or via open access, to ensure that anyone can read your work.
The list of strains in culture is available here, as a Google Sheet that we update regularly.
The majority of these cultures (indicated by BEAP IDs) contain more than one species of eukaryote (indicated by Within-Culture IDs: a, b, c, etc.). When two rows for a BEAP ID have the same Within-Culture ID, they represent forward and reverse 18S sequence reads that do not overlap.
Please note that we try to keep these cultures alive and growing, but there is always the chance that they may have died by the time you request them.
Data Sets
Data Sets
EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotic life. From: Richter et al. (2022):
EukRibo: a manually curated eukaryotic 18S rDNA reference database to facilitate identification of new diversity. From: Berney et al. (2022):
Global-scale surface ocean plankton biogeography: short read archive identifiers for Tara Oceans metagenomic and 18S V9 sequence reads, environmental measurements from sampling stations, metagenomic and 18S V9 community dissimilarity matrices, minimum travel time and geographic distance matrices, 18S V9 metabarcode and OTU tables and reference database. From Richter et al. (2022):
Transcriptome sequencing of 19 diverse species of choanoflagellates. From Richter et al. (2018):
Assembled contig and predicted protein sequences, annotations, and inferred ancestral gene content: FigShare, https://doi.org/10.6084/m9.figshare.5686984
Raw sequence reads and assembled contig sequences: NCBI, https://www.ncbi.nlm.nih.gov/bioproject/PRJNA419411
Raw sequence reads from Salpingoeca rosetta ATCC PRA-366, test of polyA selection to separate choanoflagellate from bacterial RNA: NCBI, https://www.ncbi.nlm.nih.gov/bioproject/PRJNA420352
Contigs and predicted proteins from the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP; Keeling et al., 2013), with cross-contamination detected and removed. From Marron et al. (2016):
Computer Code/Scripts
Computer Code/Scripts
oligoN-design: a pipeline to produce oligonucleotide candidates for fluorescence in situ hybridization (probes). Primers for PCR amplification can also be searched. It focuses on the rDNA operon (specifically the small subunit of the rDNA: 18S rDNA and 16S rDNA), but can potentially be used for other genes.
EukProt: data formatting scripts and eukaryote tree-related files (input/output for plotting the tree via iTOL) From: Richter et al. (2022):
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