# Project-001

> **NIH NIH U19** · COLD SPRING HARBOR LABORATORY · 2021 · $6,278,950

## Abstract

The BRAIN initiative cell census network calls for large-­scale, comprehensive approaches to define the
composition of the mammalian brain at the cellular level and using an overall strategy that integrates multimodal
information (morphology, connectivity, molecules etc..) within a Common Coordinated Framework (CCF) to
enable distribution, validation, integration and use of the atlas by the community. The BICCN challenge is
enormous and remains a scientific problem requiring new discovery, continuous innovation in methods,
technologies and pipeline of analysis. Given the unparalleled cellular diversity of the mouse brain and the
need for an informed cell classification scheme, we propose here an ambitious project that addresses both the
need for scale (coverage of millions of cells) and depth of analysis of each cell and, further, that integrates
molecular and anatomical information. To address this challenge, we have assembled a collaborative group of
key knowledge leaders and innovators across various fields of neuroscience, genomics, and technology. First,
we will apply transformative new droplet scRNA sequencing technologies and next-­generation computational
methods and data processing pipelines to compile a whole brain cell transcriptome atlas on a massive scale
(millions of single cells and nuclei collected brainwide). This effort will generate an unprecedented inventory of
cell type composition and distribution for the mouse brain within the CCF. Second, we will generate a forebrain
neuronal atlas that will integrate detailed molecular information (to saturation) of anatomically defined
populations with high-­resolution morphological and connectivity information to provide an in-­depth picture of a
core portion of the mammalian brain. We will also generate highly specific driver lines for precise marking of cell
types and to enable adaptive methods that refine cell sampling to achieve completeness. Finally, realizing the
need for innovation in technology to enable work that is made difficult because it requires both scale and
precision, we will devote key effort to develop new integrated technological platforms that combine multiple
methods to relate neuronal connectivity with transcriptomes and cellular distribution at an unprecedented scale.
Our Data Core will integrate, store, and manage multi-­modal datasets and provide bioinformatics and
computational expertise;; and our Administrative Core, will coordinate and oversee Center-­wide activities. Our
effort is unprecedented for scale and coverage, and it relies on a team of investigators with demonstrated
academic track records of innovation in technology and neurobiology, working in an environment that allows for
implementation of massive pipelines for production workflow. This will guarantee progressive evolution and
innovation of methods, experimental design and analysis to meet future challenges and succeed at generating
a comprehensive molecular and anatomical atlas of the mouse br...

## Key facts

- **NIH application ID:** 10168626
- **Project number:** 5U19MH114821-05
- **Recipient organization:** COLD SPRING HARBOR LABORATORY
- **Principal Investigator:** Paola Arlotta
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $6,278,950
- **Award type:** 5
- **Project period:** 2017-09-21 → 2023-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10168626

## Citation

> US National Institutes of Health, RePORTER application 10168626, Project-001 (5U19MH114821-05). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10168626. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*