The Hubcap

The HubCap Quarterly Newsletter

This year was an exciting year in genomics and much of it is reflected in Hub activities.  Just  to mention a few: staff worked collaboratively with a few companies and UCI faculty to do comparative testing of several single cell spatial platforms. This concluded with the choice of the 10X Genomics Xenium platform in which to invest in late fall with installation and training completed in December. Xenium joins the NanoString GeoMx instrument previously acquired for spatial transcriptomics. Faculty Kessenbrock and Lawson have also used 10X products and were able to have early access to this technology and advise the Hub.   There will be several workshops on different applications of this technology in 2024. Because it is probe based, the choices are to go with present panels or potentially identify other users with similar target interests in order to design custom probe sets.

Transcriptomics has transitioned from bulk to major focus on single cell. More groups are using both the Parse high throughput system in which up to a million cells can be accessed to support one or more experiments and also multi-omics, mostly empowered by 10X Genomics.   Using this tool there have been multiple publications particularly from skin and cancer research groups.  Novel software tools such as CellChat developed in the Nie group in order to predict cell-cell interactions were extended to enable incorporation of spatial insights.

Many more groups are interested in long read sequencing to enable understanding cell type/state specific isoforms.  MAS technology enables read outs of single cell RNA and the long reads also capture haplophasing of the DNA. With addition off Chrangrui Xiao and Eric Villain  to the genetics team, Min Zhang and Wei Li on the bioinformatics end, human genome sequencing is beginning to take off at UCI.

Workshops to stay current with emerging technologies play an ever more important role in Hub activities.  Next year wetbench training sessions will be held to facilitate adoption of the Xenium system. Look out for these announcements!  In addition, this year Bioinformatics workshops were held on a regular bimonthly basis taught mainly by Jenny Wu and Ivan Chang with guest appearances by RCIC director Phil Papadopoulos and Eduard Mas, postdoctoral fellow.

Finally, there were grant applications for a cancer P01, Skin P30, and Shared Instruments.  These are all waiting to be reported out. The Hub is very grateful to the campus Office of Research, Schools, especially Biological Sciences and Medicine, ORU/SRP directors, and Departments for providing significant support to allow these investments in emerging technologies.

From the entire staff of the GRT Hub, we wish you the best holiday season and a Happy New Year!!

Suzanne Sandmeyer, Ph.D.
GRT Hub Director