# Core C - Functional Genomics and Computational Biology Core

> **NIH NIH P01** · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · 2021 · $210,738

## Abstract

CORE SUMMARY
The overall goal of this PPG application is to compare and contrast the mechanisms by which the inhibitory
receptors PD1 and LAG3 operate on T cells in the context of tolerance and autoimmunity, cancer, and chronic
infection. One major approach to be used throughout the studies is the application of genome-wide
transcriptional profiling. The purpose of the Functional Genomics and Computational Biology Core (Core C) is
to provide essential and centralized sequencing-based genomics services for all three Projects in this Program.
In addition, this Core will operate provide the service of a retroviral (RV)-enforced expression and knockdown
platform that can directly test in vivo individual genes and pathways identified from computational analyses. Thus,
Core C will provide integrated bioinformatic and computational analytical platforms and data integration services
coupled to downstream RV-enforced expression and knockdown as well as in vivo CRISPR/Cas9-focused
genetic screening. The Aims are:
AIM 1: To provide initial data hosting, normalization, preprocessing, and analysis as well as perform
cross-Project data integration and computational network modeling for bulk and single-cell
transcriptomic and epigenetic datasets. Core C will (i) provide raw data QC, data cleaning, pre-processing,
and generation of files for downstream analyses as well as operate a web portal interface for user exploration of
the data; (ii) perform primary and secondary genomics data analyses; and (iii) perform network and integrated
analyses including. The Core also will support and/or develop new analytical tools as technologies become
available (as for scRNA-seq in the last cycle).
AIM 2: To enable in vivo CRISPR/Cas9 screening and provide an RV-enforced expression and
knowckdown platform for downstream in vivo interrogation of genes and pathways regulated by PD-1
and/or LAG3. Core C will aid in design of CRISPR screening libraries for in vivo CRISPR screening platforms
by the Projects as well as downstream data analysis. Core C will also provide an in vivo retroviral platform to
enforce expression or shRNA knock-down of high-priority GOIs.
By its nature, Core C is highly interactive with other components of this PPG. Samples from Projects 1, 2, and
3 will enter Core C, which will analyze samples with input from the Projects and integrate results among the
three Projects. Core C will interact heavily with Cores A, B, and D for administrative support and to identify gene
targets for novel mouse strains and immunostaining analysis.

## Key facts

- **NIH application ID:** 10239108
- **Project number:** 5P01AI108545-07
- **Recipient organization:** UNIVERSITY OF PITTSBURGH AT PITTSBURGH
- **Principal Investigator:** E. John Wherry
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $210,738
- **Award type:** 5
- **Project period:** 2015-05-15 → 2025-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10239108

## Citation

> US National Institutes of Health, RePORTER application 10239108, Core C - Functional Genomics and Computational Biology Core (5P01AI108545-07). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10239108. Licensed CC0.

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