Sequencing at sea.PNGDr. Leonid Moroz is a researcher of comparative neurobiology at the University of Florida. Among his research interests is the use of the sea slug Aplysia Californica as a model for simple neuronal differentiation which then can be compared to high-order mollusks. He hypothesizes that parallel evolution of several ancestral cell lineages unite to form a brain in higher-order invertebrates. A collaborator spoke about their single-cell transcriptome sequencing work at the February 2014 Advances in Genome Technology and Biology meeting in Marco Island, Florida, where a poster was also presented. Dr. Moroz has also published a methods paper on single-cell RNA-Seq using semiconductor sequencing.

 

Another interest of Dr. Moroz is neurological regeneration in ctenophores (colloquially known as ‘comb jellies’), which regenerate their primitive brain in its entirety after only a few days.

 

In a novel approach, Dr. Moroz installed an Ion PGM™ system on a donated research vessel, collected samples in the open ocean, did his dissections and RNA purifications on-board, then constructed RNA-Seq libraries and sequenced them on Ion 318 chips. (His laboratory technicians note the difficulty of handling their pipettes while the ship is pitching and rolling in rough seas.)

 

Previously Dr. Moroz determined that he could get 85% of the genes detected from his samples with only 300,000 reads per sample, so using the Ion PGM™ system instead of the Ion Proton™ system made sense, multiplexing up to 16 samples per Ion 318™ Chip. After base-calling and mapping to reference (on the ship) with Torrent Suite™ software on an Ion server, he used a satellite uplink to transfer the BAM files back to the University of Florida, where a supercomputer carried out the differential gene analysis. He was then able to examine the analyzed data while still at sea.

 

His Ion PGM™ system easily accommodated sequencing on the open ocean since it is a solid-state, semiconductor-based sequencing system. He did put the Ion PGM™ system on a vibration table to shield it against the sharpest bumps, but this is an instance where an optical system simply would not work effectively.

 

See this video of Dr. Moroz in action on the ship, as well as a recent Associated Press story about his work.

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