# ShEEP Request for MERSCOPE Instrument

> **NIH VA IS1** · VETERANS AFFAIRS MED CTR SAN FRANCISCO · 2023 · —

## Abstract

Technological advances have now greatly expanded the frontier of single cell
transcriptomics. We can now measure individual cells within their spatial context and
directly observe cell-cell interactions. A leading technology in this area, named
MERFISH, uses digital barcoding of mRNAs in the cell to measure gene expression at
sub-cellular resolution. We propose to request the MERSCOPE instrument, which
allows for MERFISH processing of hundreds of genes on tumor and tissue sections to
advance our studies of cancer and other diseases that affect Veterans’ health.
In situ hybridization (ISH)-based methods entail a process whereby a target sequence is
detected by hybridization of a complementary fluorescent probe. The addition of
sequential rounds of hybridization and imaging combined with barcoding have enabled
substantial multiplexing.
In multiplexed error-robust fluorescence ISH (MERFISH), successive rounds of
hybridizations are imaged to detect the presence or absence of fluorescently labelled
probes. The serial images are then decoded, using the error-robust barcode associated
with each transcript identity. MERFISH has been used over a wide range of scales, from
transcript location within individual cells to tissue-level spatial transcriptomics.
Research projects advancing studies of diseases highly relevant to the Veterans’
community that will be supported by this instrument include studies focusing on cancers
such as prostate and lung cancer, brain diseases, such as traumatic brain injury (TBI),
frontotemporal dementia (FTD), and lung diseases.
Spatial transcriptomics is required to simultaneously image multiple cells in affected
tissues to determine cellular localization and gene expression. Lung transplant and
pulmonary fibrosis studies will be served by this equipment to image specific cell types
in lung transplant and fibrotic tissues. Infectious disease research projects related to
HIV and SARS-CoV-2 will be able to utilize this instrument to better understand the
pathogenic mechanisms of infection and persistence in tissues. Studies of prostate,
hepatocellular, and lung cancer will also utilize this equipment to characterize
prognostic biomarkers and understand the tumor microenvironment.
We are excited to request the MERSCOPE, a state-of-the-art spatial transcriptomics
instrument that will provide innovative and outstanding images for research studies to
advance Veterans’ health.
We anticipate the MERSCOPE to provide services essential towards accomplishing
VA’s research goals to understand and treat diseases of high importance to the Veteran
population.

## Key facts

- **NIH application ID:** 10741700
- **Project number:** 1IS1BX006324-01
- **Recipient organization:** VETERANS AFFAIRS MED CTR SAN FRANCISCO
- **Principal Investigator:** Franklin W Huang
- **Activity code:** IS1 (R01, R21, SBIR, etc.)
- **Funding institute:** VA
- **Fiscal year:** 2023
- **Award amount:** —
- **Award type:** 1
- **Project period:** 2023-03-01 → 2023-09-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10741700

## Citation

> US National Institutes of Health, RePORTER application 10741700, ShEEP Request for MERSCOPE Instrument (1IS1BX006324-01). Retrieved via AI Analytics 2026-06-12 from https://api.ai-analytics.org/grant/nih/10741700. Licensed CC0.

---

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