Resources
The resources we have created are hosted at FigShare, NCBI, GitHub and protocols.io.
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):
Wet Lab Protocols
Transcriptome sequencing of 19 diverse species of choanoflagellates. From Richter et al. (2018):
protocols.io, https://doi.org/10.17504/protocols.io.kwscxee