# A Comprehensive Resource for Escherichia coli Genomic Data and Tools

> **NIH NIH R01** · BOSTON UNIVERSITY (CHARLES RIVER CAMPUS) · 2022 · $371,226

## Abstract

ABSTRACT
Escherichia coli is the single most utilized cell in biology. It is the cornerstone of the biotechnology revolution,
and the principal model organism for our understanding of bacterial molecular and cellular physiology. Despite
its central importance, there is no single resource providing access to the growing body of E. coli genomics
data. RegulonDB is already the primary portal for curated knowledge of E. coli gene regulation. We propose to
expand RegulonDB to be a critically needed portal for E. coli genomic data in three key ways: (1) We will
curate all available E. coli highthroughput genomic data sets, analyze these data sets in a consistent fashion,
and integrate the data into RegulonDB with tools for access, query, visualization, and analysis. The datasets
will include the first comprehensive map of the E. coli regulatory network based on ChIP-Seq and RNA-seq
currently being generated by two of the PIs. (2) We will extend RegulonDB with comparative genomic data
spanning the Enterobacteriaceae. This will include genomic data for representatives of all major
Enterobacteriaceae genera. It will also include deep manual curation of the literature and genomic data sets for
three key pathogens related to E. coli: Salmonella enterica, Klebsiella pneumoniae, and Yersinia pestis. In
addition, we will perform the first comparative ChIP-Seq mapping in a set of conserved TFs in these three
species and E. coli. This will provide the first broad view of the evolution of regulation between E. coli and
these pathogens based on the comprehensive mapping of binding sites in conserved TFs. It will also provide a
framework for generating complete regulatory maps in these and other Enterobacteriaceae species. (3) We will
provide an online server for bacterial ChIP-Seq analysis. The server will be specifically tailored to the unique
characteristics and pitfalls of ChIP-Seq in bacteria. The server will enable a new generation of microbiologists
access to the power of ChIPSeq for the comprehensive mapping of transcription factor-DNA binding.

## Key facts

- **NIH application ID:** 10359688
- **Project number:** 5R01GM131643-04
- **Recipient organization:** BOSTON UNIVERSITY (CHARLES RIVER CAMPUS)
- **Principal Investigator:** Julio Collado-Vides
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $371,226
- **Award type:** 5
- **Project period:** 2019-06-01 → 2024-02-29

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10359688

## Citation

> US National Institutes of Health, RePORTER application 10359688, A Comprehensive Resource for Escherichia coli Genomic Data and Tools (5R01GM131643-04). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10359688. Licensed CC0.

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