# Revealing the transcriptional basis of corticothalamic projections using in situ sequence-based neuroanatomy

> **NIH NIH R01** · ALLEN INSTITUTE · 2024 · $672,827

## Abstract

Project Summary
In neuronal circuits, the relationship between gene expression and long-range neuronal projections
defines the structure of circuits and constrains computational models of their functions. In the past few
years, systematic studies on the gene expression and projections of cortical neurons across the whole
cortex have revealed tremendous diversity in cell types defined by gene expression, i.e. transcriptomic
types, and in long-range projections. These previous studies have laid the foundation for understanding
the complex relationship among gene expression, projections, and cortical areas at cellular resolution.
Unraveling this relationship, however, is challenging, because it requires associating gene expression and
projections across large areas of the cortex at cellular resolution. Furthermore, gene expression that are
associated with the development of projections may be transiently expressed in development. Here we
overcome these challenges by applying two high-throughput in situ sequencing-based neuroanatomical
approaches, BARseq and retro-BARseq, to comprehensively interrogate both gene expression and
projections in the cortex. These techniques rely on in situ sequencing of RNA barcodes to determine the
projections of thousands of neurons together at cellular resolution. Because these techniques use in situ
sequencing, they can also simultaneously interrogate the expression of hundreds of genes in the same
cells. Thus, the highly multiplexed nature and the ability to associate projections with gene expression in
the same cells make BARseq and retro-BARseq uniquely suited for unraveling how gene expression
associate with projections. We will combine these high-throughput techniques with robust meta-analysis to
take advantage of existing systematic single-cell RNAseq datasets in the cortex to identify association
between gene expression and projections with unprecedented details. We will focus on the corticothalamic
circuit because its projections are highly diverse and organized across both cortical areas and
transcriptomic types. We will start by building a whole-cortex to whole-thalamus projection map of
transcriptomic types. We will match transcriptomic types in our data to cell types in reference
transcriptomic datasets to broaden our impact. We will then focus on a portion of the cortex encompassing
multiple neighboring cortical areas to identify gene correlates of projections within the same transcriptomic
types across neighboring areas. Finally, we will apply the same approach to the developing brain to
assess the developmental association between gene expression and projections. The datasets generated
in this study will not only provide a foundational resource that enables future structural and functional
studies at the cell type resolution, but also provide a unique view of the relationship between cellular
programs encoded by gene expression and wiring diagrams encoded by projections.

## Key facts

- **NIH application ID:** 10804116
- **Project number:** 1R01MH133181-01A1
- **Recipient organization:** ALLEN INSTITUTE
- **Principal Investigator:** XIAOYIN CHEN
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $672,827
- **Award type:** 1
- **Project period:** 2023-11-15 → 2028-10-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10804116

## Citation

> US National Institutes of Health, RePORTER application 10804116, Revealing the transcriptional basis of corticothalamic projections using in situ sequence-based neuroanatomy (1R01MH133181-01A1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10804116. Licensed CC0.

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