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Frequently Asked Questions (FAQs): ENCODE Data Analysis Center (DAC) U24 (RFA HG 16 006)

What is this funding opportunity?

This opportunity funds the ENCODE Data Analysis Center (DAC) through a U24 cooperative agreement mechanism. It is listed as RFA HG 16 006 under the National Institutes of Health (NIH) (HHS-NIH11) and is focused on strengthening the analysis backbone of the ENCyclopedia Of DNA Elements (ENCODE) project.

What is the overall purpose of the ENCODE DAC?

The DAC is intended to be a single, centralized center that provides high-level leadership and deep computational expertise to transform ENCODE-generated datasets into consistent, high-quality, integrative scientific products that the broader research community can use.

How does this DAC support the ENCODE project specifically?

The DAC is expected to lead ENCODE data analysis and continually define, maintain, and improve the computational workflows that make ENCODE data usable at scale. This includes setting technical standards so ENCODE outputs remain reliable, reproducible, and interoperable across labs and platforms over time.

Is the DAC expected to be a centralized award or multiple awards?

The solicitation indicates an expected single award. NIH intended to fund one central DAC to provide consistent analysis leadership rather than distributing the DAC role across multiple independent sites.

What are the primary responsibilities of the DAC?

Based on the opportunity description, key responsibilities include:

• Leading the analysis of ENCODE data.
• Defining, maintaining, and improving computational workflows used across ENCODE.
• Specifying and updating standardized data processing pipelines for major ENCODE assay types.
• Defining and updating quality metrics used to evaluate whether data meet consortium expectations.
• Conducting integrative analyses across many ENCODE datasets to produce coherent, high-value scientific products.

What does it mean that the DAC will define standardized pipelines and quality metrics?

It means the DAC is expected to set the rules and technical standards for how ENCODE data should be processed, assessed, and compared across laboratories and platforms. The goal is to ensure that datasets are processed consistently and evaluated against agreed-upon quality measures so results are comparable and reproducible.

What is meant by refining the "Encyclopedia" as a deliverable?

The "Encyclopedia" is described as a primary ENCODE product for the research community. The DAC is expected to continually refine and update it by performing integrative analyses that combine signals from different ENCODE experimental modalities as new data arrive, producing improved annotations and interpretations grounded in the evolving evidence base.

Does the DAC role go beyond running routine data processing?

Yes. The description emphasizes that the DAC is not limited to single-assay processing. It is expected to perform synthesis work: integrating across datasets, extracting biological meaning, and producing coherent annotations and interpretations that reflect combined evidence across ENCODE.

What is the DAC expected to do regarding ENCODE samples and biological coverage?

The DAC is tasked with strategic oversight of the ENCODE sample portfolio. This includes developing a scientific strategy to characterize what samples ENCODE has studied, identifying what remains underexplored, and helping prioritize which new data should be collected next (for example, tissues, cell types, or conditions likely to yield the highest value).

What is meant by assessing ENCODE coverage across "sample space"?

In this opportunity, "sample space" refers to the broader range of biological contexts (such as different tissues, cell types, and conditions). The DAC is expected to assess how comprehensive ENCODE coverage is across this range and to help identify gaps where ENCODE has not adequately examined key biological contexts.

How does the DAC relate to the ENCODE Data Coordinating Center (DCC)?

The DAC is designed to work closely with a separate ENCODE component, the Data Coordinating Center (DCC), which is solicited under a companion announcement (RFA-HG-16-005). Together, the DAC and DCC are expected to form an integrated ENCODE Data Coordination and Analysis Center (EDCAC).

What is the ENCODE Data Coordination and Analysis Center (EDCAC)?

EDCAC refers to the integrated structure formed by the DAC and the DCC working together. The DAC provides analysis leadership and technical direction (pipelines, metrics, integrative interpretation), while coordinating tightly with DCC functions supporting coordination, data handling, and consortium-facing infrastructure.

Is the DAC expected to work independently or as part of a consortium?

The DAC is explicitly not meant to operate in isolation. The opportunity expects close coordination with the DCC and participation in broader ENCODE Consortium efforts, including helping coordinate consortium activities as needed.

What type of funding mechanism is used for this award?

The opportunity uses a U24 cooperative agreement mechanism and is described as a discretionary, health-related cooperative agreement.

What does "cooperative agreement" imply in this context?

The posting notes that cooperative agreement funding typically implies substantial programmatic involvement from NIH compared with a standard research grant. This reflects the consortium-scale coordination, shared standards, and ongoing alignment required for ENCODE.

Who is eligible to apply?

Eligibility is described as broad and includes:

• Various levels of government entities
• Public and private institutions of higher education
• Nonprofit organizations (including those with and without 501(c)(3) status)
• For-profit organizations (other than small businesses)
• Small businesses
• Tribal governments and tribal organizations
• Public housing authorities / Indian housing authorities
• Other organizations as described in the full eligibility text

What is the CFDA number associated with this opportunity?

The opportunity is associated with CFDA number 93.172 (and also lists 93.172 in the provided data).

What was the application closing date listed for this opportunity?

The posting lists a closing date of March 21, 2016.

What kind of expertise is the DAC expected to provide?

The DAC is expected to provide high-level leadership and deep computational expertise, with the ability to define and maintain processing standards, run and improve large-scale analysis workflows, perform integrative analyses across diverse datasets, and produce community-facing scientific products.

What kinds of outputs is the DAC expected to produce for the broader community?

The opportunity emphasizes producing consistent, high-quality, integrative scientific products that the broader research community can use, including ongoing improvements to the ENCODE "Encyclopedia" and other integrative analyses and annotations that make ENCODE data interpretable and usable at scale.

How does this opportunity help ensure ENCODE data remain reproducible and interoperable?

By requiring the DAC to specify and update standardized processing pipelines and to define and maintain quality metrics, the opportunity aims to ensure that ENCODE datasets can be processed consistently and evaluated uniformly, supporting reproducibility and interoperability across time, labs, and platforms.

What is the relationship between data collection priorities and the DAC's role?

The DAC is expected to provide portfolio-level scientific strategy on ENCODE sampling. That includes helping identify underexplored samples and guiding priorities for what new datasets should be collected next, with an emphasis on using data-collection resources wisely while improving coverage across biological contexts.

What NIH program area is this opportunity tied to?

The opportunity is an NIH funding opportunity under HHS-NIH11 and is tied to the ENCODE project, which is a community-facing effort to map and interpret functional elements in the human genome.