Dataset: NCBI accession numbers from a study of two tintinnid ciliate species, Schmidingerella arcuata and Schmidingerella meunieri

This project required sequencing whole genomes and transcriptomes from single cells picked from two cultures. One was Schmidingerella arcuata (urn:lsid:marinespecies.org:taxname:732664), isolated from the East Coast of the United States in Long Island Sound; the other was Schmidingerella meunieri (urn:lsid:marinespecies.org:taxname:732864), isolated by S. Strom from Puget Sound on the West Coast of the United States. S. arcuata was collected from the surface waters of northeastern Long Island Sound, CT (41.31°N, 72.06°W), using a 20-micrometer (µm) mesh plankton net. Single cells were isolated with drawn capillaries and moved to six-well culture plates with 0.2-µm-filtered sample water. The goal was to quantify the degree of difference in genome architecture for these two close congeners.

The cultures were grown in filtered seawater at 18 degrees Celsius (°C) on a 12:12 light cycle and fed the dinoflagellate Heterocapsa triquetra and the prymnesiophyte Isochrysis galbana. Individual cells were picked with a drawn capillary pipette and processed for sequencing as detailed below (from Smith et al 2020).

The SMART-Seq2 v4 Ultra Low input RNA kit (Cat: 634889; Takara, Mountain View, CA) was used for whole transcriptome amplification (WTA) following the manufacturer's protocols, with the exception that we quartered the reaction volumes. For whole-genome amplification (WGA), the Repli-g single-cell kit (Cat: 150343; Qiagen, Hilden, Germany) was used following the manufacturer’s protocols. The products (cDNA for WTA, gDNA for WGA) were quantified with the dsDNA Qubit assay (Invitrogen, Waltham, MA) and polymerase chain reaction-checked with eukaryotic 18S rDNA and genus-specific ITS primers. Minimum bacterial contamination was confirmed by polymerase chain reaction with 16S rDNA primers Sequencing libraries were prepared with the Illumina Nextera XT kit (Cat: FC1311096; Illumina, San Diego, CA), then processed with Illumina HiSeq 2500 at Macrogen Sequencing (Geumcheon-gu, Seoul, South Korea).

The isolation/cultivation was done in 2014-2015. The sequencing work was all completed and analyzed by the suummer of 2020.