# ImmGen: Gene Expression and Regulation in Immune Cells

> **NIH NIH R24** · HARVARD MEDICAL SCHOOL · 2021 · $1,673,172

## Abstract

The Immunological Genome Project (ImmGen) is a collaborative group of 15 Immunology and
Computational Biology laboratories who perform, under standardized conditions, a thorough dissection of gene
expression and its regulation in the mouse immune system. We also investigated how these respond to
cytokines and immunologic challenges, how immune gene expression relates to chromatin configuration, and
used cutting-edge computational algorithms to deduce regulatory connections. ImmGen data are publicly
available on dedicated web and smartphone supports, using interactive graphic displays that make the results
intuitive to users. These are now frequently used by the Immunology research community. The proposed
continuation will harness the collective expertise of the ImmGen group to further develop this important public
resource. (1) Expand and deepen the compendium, applying single-cell RNAseq to define very broadly the
cast of cell-types at play in the immune system, their trajectories of differentiation, and their adaptation to
specific organismal locations This effort will be complemented by deeper bulk profiling of cell-types thus
identified. We will expand the analysis of cytokine signatures, continue to chart non-coding RNA (circRNAs),
and persue the “OpenSource” program of coordinated sample contributions from the community. (2)
Mechanistic Dissection of Immunogenomic Regulatory Networks focusing on a Core Set of 14 cell-types
that represent all the major immunological lineages. We will generate high-resolution maps of transcription
factor footprints by ultra-deep ATACseq; map 3D architectures by HiC chromosome conformation capture;
apply ChIPseq to define enhancers and super-enhancers, chromatin modification domains and structural
anchors; use machine learning approaches to integrate these complementary data into a comprehensive
regulatory plan which spans from fine TF footprints to topologically associated domaiins; validate these
inferences by collaborating with the KOMP project to analyze Core Set transcriptomes and chromatin
configuration in mice with mutations in transcription factors that determine functionally relevant facets of
immunocyte activity. (3): Public Display. ImmGen data have become a widely used resource in Immunology
research, which will be maintained and curated. For scalability, cost-effectiveness, and to enable facile
computation, we will develop and deploy cloud-based data storage and access solutions, compliant with NIH
Commons guidelines. We will add to the existing databrowsers to allow users to query different facets of the
expanding data (differential expression, regulatory network, chromatin states and architecture, cytokine
signatures), increasing connectivity to other data sources. We will continue developing the popular mobile app,
and explore the particular uses of that medium. ImmGen has positively impacted immunological research in
the current decade, providing detailed and rigorous genomic resolution of imm...

## Key facts

- **NIH application ID:** 10245033
- **Project number:** 5R24AI072073-15
- **Recipient organization:** HARVARD MEDICAL SCHOOL
- **Principal Investigator:** CHRISTOPHE O. BENOIST
- **Activity code:** R24 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $1,673,172
- **Award type:** 5
- **Project period:** 2007-09-18 → 2022-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10245033

## Citation

> US National Institutes of Health, RePORTER application 10245033, ImmGen: Gene Expression and Regulation in Immune Cells (5R24AI072073-15). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10245033. Licensed CC0.

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