Learning about omics: a visit to the Roslin Institute

Written by Dr Rose Ruiz Daniels, Lecturer in Aquaculture Genomics.

As part of my ongoing work investigating cells in their natural habitats (tissues), I have been optimizing protocols using a method I developed during my time as a research fellow at the Roslin Institute (Ruiz Daniels et al., 2023) in order to take nuclei out of cells to sequence them. I took my soon-to-be PhD student, France, and my MSc student, Anthony, to the Roslin Institute to visit the genomics facility and gain an understanding of how to optimize NGS protocols. This was an incredible experience for me as a new lecturer, teaching something I had developed to students. I feel passionate about knowledge exchange, and as they learned about omics, I learned about how my students interact with the work and how best to make omics more accessible. We will be applying these technologies to solve problems facing aquaculture now and in the future. I am hoping this paves the way for more collaborative efforts and helps to instil a love of omics in the next generation of aquaculture researchers.

Antony, Rose, and France with Dolly the sheep in the Roslin institute.

France Chaiyasut (Eastbio PhD student starting October 2024), working on the topic Understanding the role of mesenchymal stromal cells in Atlantic salmon during disease and regeneration:

“To have laboratory training in single-nucleus RNA sequencing is an opportunity that rarely comes by, especially the opportunity to be trained at the cutting-edge facilities at the Roslin Institute. This experience has not only allowed me to have a glimpse into the workings of their laboratory but also the working environment of the students and staff. The laboratory infrastructure and the friendly yet professional atmosphere there have inspired me to reflect on my laboratory practices as well as reminded me of the importance of communication between colleagues. This learning experience will surely benefit my PhD project. For such a wonderful opportunity, I would love to offer my sincere gratitude to Dr. James Furniss, manager of the Genomics Platform, and Dr. Rose Ruiz Daniels, my supervisor, as well as to everyone at the Roslin Institute.”

Dr Ruiz Daniels running the Chromium X for the first time, making successful snRNA-seq libraries after 2 days of protocol optimisation and many weeks of plans.

Anthony Anakwe (DVM, MSc Aquatic Veterinary Studies candidate), working on the topic The cellular dynamics of the gills of Atlantic salmon infected with Aeromonas salmonicida:

“It was amazing experience to have actively participated, in a very educative training in single-nucleus RNA sequencing (snRNA -seq) technique at the famous Roslin Institute on the 9th of May 2024.  Under the supervision/support of my supervisor (Dr Rose Ruiz Daniels) and our Roslin host (Dr. James Furniss), we had an exciting time extracting/isolating nuclei from frozen gonadal tissues of Atlantic salmon. This nuclei isolation step which is pivotal to the success of any snRNA-seq protocol was performed by firstly mincing the tissues in a 6-well tissue culture plate (on dry ice) containing a Tri-Salt Tween -PBS BSA buffer mix followed by filtration with a 40-um cell strainer. Then, after centrifugation at 4°C, we loaded the lysate unto a haemocytometer and viewed under a light microscope to perform a manual nuclei count. It was also a great privilege networking with some experts and fellows in the Molecular Biology and Bioinformatics fields over there. Exciting times indeed!”

Anthony, France, and Carl. Carl Milton is a PhD student in Dan Macqueen’s lab at the Roslin Institute. He is working with us to create a cell atlas of the Atlantic salmon gill to understand how different immune cells respond to infection.

Thanks to the Roslin Institute for access to their genomics facilities and Dr James Furniss, the facilities manager.

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