SINGLE CELL RNA SEQUENCING SYSTEM

Sources Sought (SS) Notice

Title: Single cell RNA Sequencing System

ID: NIAID-SS-25-2265393

Post Date: 07/18/2025

Response Date: 08/04/2025

Classification Code: 6640 – Laboratory Equipment and Supplies

NAICS: 334516 Analytical Laboratory Instrument Manufacturing

Introduction

This is a Sources Sought notice. This is NOT a solicitation for proposals, proposal abstracts, or quotations. The purpose of this notice is to obtain information regarding the availability and capability of all qualified sources to perform a potential requirement.

Project Summary

The Viral Pathogenesis and Evolution Section (VPES) and The Clinical Studies Unit (CSU) within Laboratory of Infectious Diseases (LID) conducts research directed toward defining the causes and epidemiology of influenza and SARS-CoV-2 viral disease and developing means for their control, including universal influenza and SARS-CoV-2 vaccine development. VPES and CSU engages in a wide range of research activities that extends from clinical virology to molecular characterization of highly virulent influenza and SARS-CoV-2 viruses that cause severe, acute disease of the respiratory tracts in animal models to the development of novel vaccines and antiviral drugs. We also study immune responses and disease following human influenza viral challenge at the NIH Clinical Center. Scientists in the VPES employ high-throughput genomic, proteomic and machine learning computational approaches to elucidate pathogenesis of influenza disease, understand the response to infection, contagiousness, development of severe illness, as well as identify the molecular correlates of vaccine protection in animals and humans.

This acquisition is for the H5N1 Countermeasures Research Project, to identify novel molecular structures with antiviral properties that can be utilized to help combat the ongoing avian influenza pandemic in poultry and wild birds (and prevent future spread to humans). The Chromium X single-cell sequencer will be used to understand cellular diversity and intracellular mechanisms of in-vitro and in-vivo samples. We will utilize the associated Chromium kits to perform scRNA-seq of cell suspensions isolated from infected animal tissues and dissociated primary human airway cultures.

Specifically, NIAID, is seeking one Single cell RNA Sequencing System capable of the following:

The Single cell RNA Sequencing System enables a broad range of applications and study sizes through sequencing by synthesis and sample multiplexing.

The minimal salient characteristics for the system are as follows:

• Size: The system shall have a small footprint of less than 12in height x 12in width x 20in depth, allowing for benchtop or BSC use. The machine shall weigh no more than 45lbs. 

• Capability: The high-throughput system shall efficiently partition and barcode up to 2.5 million fresh, frozen, or fixed cells in a single run. Runs shall be completed in 6 minutes or under, enhancing workflow efficiency. In addition to fresh and frozen samples, it shall also support a broad range of sample types including FFPE samples. The system shall support on-chip multiplexing without additional upstream tagging, and must provide efficient and reproducible cell recovery of up to 80% (reducing multiplet rates as compared to methods like combinatorial barcoding). An in-built microfluidics system shall enable large-scale analysis at less than 1 cent per cell, and input shall be flexible from 500 to 20k cells per sample. Custom probes shall accommodate analysis of sample types from both mice and humans. 

• Streamlined Workflow: The workflow should be able to be completed in a single day, half the time of manual methods. The platform shall include intuitive processing and visualization software with integrated analysis workflows, allowing rapid export of data and deep technical expertise.  

• Kit Integration and Cost: The system shall offer at least three integrated kits, which shall include a range of multi-omic assays for multiplex or customizable analysis. Assays shall provide whole transcriptome coverage and include gene expression, immune clonotype, chromatin accessibility, and cell surface and other protein detection platforms. Kits will include internal controls and normalization and be designed to minimize handling and user errors via automated cell partitioning and barcoding. 

• Flexibility and Connectivity: The system shall provide wireless connectivity and integration with a cloud backup for real-time support and software updates. The system should provide various connectivity options including ethernet, Wi-fi, USB, and cloud access with no limit to the number of runs or scale of studies.  

• Maintenance and Training: The system shall include a 12-month warranty and a 12-month service insurance plan, with technicians and specialist available for any questions or resources. The system should have the capability of providing training kits to allow for inexpensive instrument validation and practice, and tailored training sessions must be available to the user if needed. The vendor shall provide comprehensive resources for assistance, including user guides, protocols, how-to videos, and analysis guides. The system should provide continuous software development and free upgrades to allow for access to different assays and up-to-date performance.  

• Continuity: The laboratory section uses existing instrumentation from 10x Genomics. The system must be seamlessly compatible with 10x Genomic Kits, 10x Genomics GEM-X Universal Expression and Next GEM Single Cell Kits. To ensure the continuity of laboratory studies, the system must feature the same connections and capabilities.

Anticipated Period of Performance

It is anticipated that an award will be made on or about August 29, 2025. Estimated lead time for delivery of Equipment is 45-90 days upon Vendor’s receipt of the purchase order.

Capability Statement/Information Sought

If your organization has the potential capacity to meet the minimum requirements and performance capabilities listed above, please provide the following information:

1. Organization name, address, point of contact, email address, website address, telephone number, UEI number.
2. Company location(s) and number of years company has been in business.
3. Type of business (e.g., 8(a), HUBZone, Other than Small, etc.) pursuant to the applicable NAICS code.
4. Type of ownership for the organization.
5. Identification of any Best-In-Class contract vehicles including Government Wide Acquisition Contracts (GWAC) (e.g., GSA schedule) they may possess or are aware of that would support this possible requirement. If your organization does not provide the products/services under a GWAC, please identify availability as OPEN MARKET ONLY.
6. Tailored capability statement addressing the capability of the sequencing instrument to meet NIAID’s minimum requirements. Capability document shall be no more than six pages.
7. Place of manufacture for the Single cell RNA Sequencing System.
8. Evidence that the organization is an authorized reseller or manufacturer of the instrument. Only Original Equipment Manufacturer (OEM) products are acceptable.

Submission Instructions

Interested businesses who consider themselves qualified to provide the above specification for the Single cell RNA Sequencing System, are invited to submit a response to this Sources Sought Notice by August 4, 2025, at 1:00 PM EST. All responses under this Sources Sought Notice shall be emailed to Shaun Rostad at shaun.rostad@nih.gov

Disclaimer and Important Notes

This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization’s qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a pre-solicitation synopsis and solicitation may be published on SAM.gov. However, responses to this notice will not be considered adequate responses to a solicitation.

Confidentiality

No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s).