Quick Introduction to the CAT Core and Workshop

The Center for Advanced Technology (CAT) operates within the Department of Biochemistry and Biophysics at the University of California, San Francisco. Our core mission is to facilitate and enhance research endeavors within UCSF laboratories by providing essential resources and hosting advanced instrumentation. While our primary focus remains on serving UCSF, we extend a welcoming invitation to other academic institutions and industry sectors. Collaboration knows no boundaries at CAT, as we strive to foster innovation and drive impactful discoveries.

Bioinformatics in the CAT

Bioinformatics is a new sevice (March 2024) the UCSF Center for Advanced Technology (CAT) is offering our users. We offer custom bioinformatic services to academic and private organizations, having a strong academic background with a focus on cutting edge, open source software. Bioinformatics workflow/piplines are at times replicated from community standards (best practices) when appropriate, and/or can develop novel applications and pipelines when needed, however will always emphasize the goals of biological interpretation as the point of data analysis.

Contacts

• The new CAT Website

  CAT Core

• General requests for genomics sequencing, library preperation, and consultation.

  catcore@ucsf.edu

• Request for data analysis services, consultations.

  catbioinformatics@ucsf.edu

• Bioinformatics training courses information

  (https://cat.ucsf.edu/bioinformatics/workshop)[https://cat.ucsf.edu/bioinformatics/workshop]

Workshop Materials

Workshop materials are all posted on github, and publicly available

https://github.com/UCSF-CAT-Bioinformatics

• This SCRNA-Seq Workshop

  https://ucsf-cat-bioinformatics.github.io/2024-08-SCRNA-Seq-Analysis/

Workshop Goals

• End-to-End understanding of Basics of SCRNA-Seq differential expression analysis
  • Discussions/lectures
  • Technologies
  • Experimental design
  • Cost estimation
  • Data reduction workflow
  • SCRNA data analysis
  • Visualizations

• To work through a complete experiment (mostly), discussion of raw data to counts tables (10X Cellranger), then in depth analysis of single cell using seurat through to Cell typing.

• Goal is 30-40% lecture/discussion 60-70% hands-on

Computing Resources

Not command line will be needed for this workshop and all will be done in R, I will work to try and meet you where you are, but may need to adjust as needed.

Patience

I ask for a little patience as I navigate how best to provide quality bioinformatics workshops to the UCSF community and are likely to have a wide background in workshop participants, but I are committed to providing you the best educational experience I can.