In the prior funding period, the Biospecimen and Bioinformatics Core (Core C) was extremely productive in its development of new methods and provision of an essential core resource for the processing, storage, and distribution of biospecimens collected from the clinical studies and advanced Bioinformatics support for ?Type 2 inflammatory phenotyping? and genomic analyses. In this funding period, the Biospecimen and Bioinformatics Core will continue to provide essential processing, storage, and distribution of biospecimens collected from the clinical studies funded by this grant and will refine mass cytometry (CyTOF protocols) and perform new services related to mass cytometry (CyTOF). These CyTOF services include development and validation of CyTOF panels and CyTOF staining of the experimental samples. The Core?s Bioinformatics resource also has optimized pipelines for handling the new data analysis challenges related to CyTOF and will provide specialized cross- investigator integrated analyses of bulk RNA-seq, single cell sequencing, ATAC-seq and DNA methylation studies proposed in the projects. Core C will integrate these analyses using scientific input from all 3 projects and perform iterative analyses across experiments and experimental groups. Finally, this core will share banked samples from the IRB-approved existing UCSF Airway Tissue Bank to the Projects of this P01. The Bioinformatics Core will have an extension at National Jewish Health led by Max A. Seibold, who is also a Co-I for Project 3. It will also have expert input on CyTOF from Dr. Matthew Spitzer (a Co-I on the Core) and expert input on single cell RNA-seq analyses from Dr. David Erle (a consultant/collaborator).

Public Health Relevance

The proposed research is relevant to public health because asthma is a common medical condition, severe asthma accounts for great public health burden and cost, and further advancing effective treatment of severe asthma will depend on identifying the biological mechanisms underlying the persistence of type 2 inflammation in the airway. Successful completion of the work proposed in this Core will provide each of the associated projects with the clinical samples, perform advanced cell staining protocols (CyTOF) and provide advanced biostatistical support for genomics analyses.

Agency
National Institute of Health (NIH)
Institute
National Heart, Lung, and Blood Institute (NHLBI)
Type
Research Program Projects (P01)
Project #
2P01HL107202-06A1
Application #
9705661
Study Section
Heart, Lung, and Blood Initial Review Group (HLBP)
Program Officer
Noel, Patricia
Project Start
Project End
2024-07-31
Budget Start
2019-04-01
Budget End
2020-03-31
Support Year
6
Fiscal Year
2019
Total Cost
Indirect Cost
Name
University of California San Francisco
Department
Type
DUNS #
094878337
City
San Francisco
State
CA
Country
United States
Zip Code
94118
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