# Gene expression, Epigenetics and Bioinformatics Core

> **NIH NIH P01** · UNIVERSITY OF FLORIDA · 2022 · $337,142

## Abstract

PROJECT SUMMARY / ABSTRACT
Core C (Pipkin)
The overarching goal of Core C is to provide standardized, uniform and innovative next generation sequencing
(NGS) and computational approaches to address the genome-scale experiments proposed in Projects 1-3. The
individual Projects goals are to analyze pooled in vivo screens, gene expression, transcription and chromatin
structure and to discern the basic molecular regulation of T and B cell mediated immunity. Core C will facilitate
these objectives by using NGS approaches to analyze (1) pooled in vivo gene loss-of-function screens by
sequencing, (2) expression of chromatin-associated RNA (nascent RNA), and mature mRNA from limiting ex
vivo cell numbers, and single cells (scRNA-seq) using RNA-seq; (3) chromatin accessibility via the assay for
transposase-accessible chromatin followed by sequencing (ATAC-seq), and nucleosome organization (MNase-
seq and BEM-seq); and (4) CRF and TF binding to near base-pair resolution after chromatin immunoprecipitation
from small numbers of primary lymphocytes using ChIP-exo (Aims 1 and 2). Core C has demonstrated
experience in developing and applying all of these approaches. In addition, Core C has established a centralized,
interlinked and documented framework for the storage, analysis and sharing of these large datasets between
Projects 1-3 (Aim 3), and will apply available algorithms in creative arrangements that comprise computational
approaches to identify and define operational cis-regulatory regions based on chromatin accessibility,
nucleosome organization and histone modifications, and to infer utilized TF binding site motifs within these
regions and predict their cognate TFs. Furthermore, these observations will be correlated with transcriptional
activity (nascent RNA expression) and RNA Pol II activity (ChIP-seq) and TF and CRF binding events (ChIP-
exo), and overall gene expression (mRNA) in the context of gene-perturbations to clarify functionally how gene
regulatory networks drive T cell differentiation and function during immune responses in vivo.

## Key facts

- **NIH application ID:** 10488585
- **Project number:** 5P01AI145815-04
- **Recipient organization:** UNIVERSITY OF FLORIDA
- **Principal Investigator:** Matthew Eugene Pipkin
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $337,142
- **Award type:** 5
- **Project period:** 2020-08-01 → 2025-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10488585

## Citation

> US National Institutes of Health, RePORTER application 10488585, Gene expression, Epigenetics and Bioinformatics Core (5P01AI145815-04). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10488585. Licensed CC0.

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