Statement of Work 10X Genomics.docx

Contract VA241-15-D-0148 Contract VA241-15-D-0148 10X Genomics Multiome Single-Cell Kits 689-26-3-7111-0024

1.0 Background & Introduction

The Clinical Neurosciences Division (CND) of the National Center for PTSD and the VA Brain Bank are studying the neurobiology of posttraumatic stress disorder (PTSD) and comorbid conditions with the goal of identifying novel targets for more effective therapeutic treatments. Specific purpose funding has been made available during fiscal year 2026 to procure 10X Genomics Multiome Single-Cell kits to facilitate these research efforts. Nearly all medical disease in need of new therapeutics results from complex interactions between gene expression and epigenetic triggers. To understand the pathological processes and find effective treatments, multimodal single-cell analysis is required. The dominant technology in this field is 10x Genomics’ Single Cell Multiome ATAC + Gene Expression solution (10x Multiome). 10x Multiome allows investigators to connect information on regulatory cell activity to gene expression in the same nucleus (i.e. direct one-to-one connection between gene expression and epigenetic elements not otherwise capturable). The technology also allows the identification of neural cell subpopulations and can separate the expression of cell types, which is particularly useful in complex brain and multicellular neurodegenerative diseases. These kits are required for ongoing research in single-cell genomics within the National PTSD Brain Bank to parse out intricate questions related to the neurobiological underpinnings of PTSD and associated comorbid conditions. Specific requirements of the research program necessitate the use of 10X Genomics’ kits due to their proprietary technology, unmatched performance, reliability, compatibility with existing experimental laboratory methods and compatibility with previously collected sample data using the same kits.

2.0 Objectives

The objective is to establish a follow-on contract to contract 36C24125P0565 with 10x Genomics, Inc. 6230 Stoneridge Mall Road Pleasanton, California, 94588-3260 to procure 10X Genomics Multiome Single-Cell Kits with the following components:

· Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 reactions

· Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 4 reactions

· Chromium Next GEM Chip J Single Cell Kit, 48 reactions

· Single Index Kit N Set A

· Dual Index Kit TT Set A, 96 reactions

· Xenium Decoding Reagents (1 run, 2 slides

· Xenium Decoding Consumables (1 run, 2 slides)

· Xenium Cell Segmentation Add-on Kit (2 rxns)

· Xenium Slides & Sample Prep Reagents (2 slides, 2 rxns)

3.0 Competition and Contract Type Selection

The request is for other than full and open competition with a single source.

4.0 Minimum Salient Requirements

The kits must be able to facilitate a variety of genomic research tasks related to single-cell analysis, including these main applications:

4.1). Single-Cell RNA Sequencing (scRNA-seq)

· Profiling gene expression at the single-cell level to understand cellular heterogeneity.

This research evaluates how individual cells in tissue express genes differently, which is crucial for understanding the developmental biology, disease mechanisms, and responses to treatments.

4.2). Single-Cell ATAC Sequencing (scATAC-seq)

· Investigating chromatin accessibility and regulatory elements.

This technique enables research into chromatin structure and accessibility change in different cell types and under various conditions. It’s useful for studying gene regulation, transcription factor binding sites, and epigenetic modifications.

4.3). Single-Cell Multiome (RNA + ATAC)

· Simultaneous profiling of gene expression and chromatin accessibility in single cells.

This is an advanced application where both RNA sequencing (scRNA-seq) and chromatin accessibility (scATAC-seq) are performed in parallel on the same cells. It allows for the study of gene expression regulation and the interaction between transcription and chromatin accessibility within individual cells.

4.4). Single-Cell DNA Sequencing (scDNA-seq)

· Profiling DNA content, mutations, and genomic alterations at the single-cell level.

This is especially important in research where cells may have unique mutations or genetic alterations. It can also be used for studying genetic diversity within a population of cells in development or disease.

4.5). Spatial Transcriptomics

· Mapping gene expression in tissue sections while preserving spatial context.

The spatial transcriptomics technology from 10X Genomics allows the profiling of gene expression in intact tissue sections with spatial context (i.e. gene expression can be mapped across a tissue sample without losing information about where specific genes are being expressed in relation to the tissue architecture). This is critical for understanding tissue development, organ function, and disease progression.

4.6). Cellular Barcoding (Cell Type Identification)

· Identifying cell types or tracking cells across experiments.

By incorporating unique molecular barcodes, researchers can tag and track individual cells across different conditions or over time. This is useful for studying dynamic processes like differentiation, migration, and response to therapy.

4.7). Single-Cell Epigenomics

· Investigating DNA methylation and histone modifications at the single-cell level.

This application provides insights into epigenetic changes that regulate gene expression.

4.8). Gene Expression Profiling of Rare Cell Populations

· Analyzing rare or low-abundance cell types.

Single-cell RNA sequencing can help identify and profile rare cell populations that are difficult to detect using traditional bulk methods. This is especially useful in studying stem cells, progenitor cells, or rare disease-associated cell types.

4.9). Saliant Features necessary for postmortem brain genomics work:

· Droplet-based microfluidics technology to enable highly efficient partitioning and barcoding of individual cells, allowing for accurate and scalable single-cell RNA-seq, immune profiling, and other multi-omic analyses.

· High Sensitivity and Resolution: Kits must be validated for their ability to achieve exceptional depth and coverage of gene expression, even with very low input RNA, making them ideal for high-resolution single-cell analysis.

· Comprehensive Applications: Kits must support a broad range of applications, including single-cell RNA sequencing, cell surface protein analysis, immune profiling, and spatial transcriptomics. These applications are critical for the success of current research.

· Proven Performance and Validation: Extensive track record of peer-reviewed literature demonstrating the successful application of the kits in a wide variety of research fields. This body of evidence assures reliability and reproducibility of experimental efforts.

5.0 Deliverables and Price Cost Schedule

Bundle, 16 rxns

Bundle, 4 rxns

6.0 Delivery

Deliverables should be received within 8 weeks post contract award. Shipments should be sent to VA National PTSD Brain Bank, Connecticut Mental Health Center S304, 899 Howard Avenue, New Haven, CT, 06519.

Any changes to this statement of work shall be authorized and approved only through written correspondence to the COR and approval from the CO. A copy of each change will be kept in a project folder. After delivery, invoices shall be submitted via the Tungsten portal for COR review, certification and payment by the Financial Service Center in Austin, Texas.

7.0 Government-furnished property, material, or equipment

None

8.0 Security

No security requirements are associated with this purchase.

9.0 Special Material Requirements

There are no other special requirements or considerations for this contract.

10.0 Other Unique Requirements

There are no other unique requirements or considerations for this contract.

11.0 Period of Performance

The period of performance is 8 weeks from the contract award date.

12.0 Records Management

12.1. Applicability

This clause applies to all Contractors whose employees create work with, or otherwise handle Federal records, as defined in Section B, regardless of the medium in which the record exists.

12.2. Definitions

“Federal record” as defined in 44 U.S.C. § 3301, includes all recorded information, regardless of form or characteristics, made or received by a Federal agency under Federal law or in connection with the transaction of public business and preserved or appropriate for preservation by that agency or its legitimate successor as evidence of the organization, functions, policies, decisions, procedures, operations, or other activities of the United States Government or because of the informational value of data in them. The term federal record:

· includes VHA records.

· does not include personal materials.

· applies to records created, received, or maintained by Contractors pursuant to the VHA contract.

· may include deliverables and documentation associated with deliverables.

12.3. Requirements

The following standard items relate to records generated in executing the contract and should be incorporated, including, citations to pertinent laws, codes, and regulations such as 44 U.S.C chapters 21, 29, 31 and 33; Freedom of Information Act (5 U.S.C. 552); Privacy Act (5 U.S.C. 552a); 36 CFR Part 1222 and Part 1228.

12.3.1. Contractor shall treat all deliverables under the contract as the property of the U.S Government for which the Government Agency shall have unlimited rights to use, dispose of, or disclose such data contained therein as it is determined to be in the public interest.

12.3.2. Contractor shall not create or maintain any records that are not specifically tied to or authorized by the contract using Government IT equipment and/or Government records.

12.3.3. Contractor shall not retain, use, sell, or disseminate copies of any deliverable that contains information covered by the Privacy Act of 1974 or that which is generally protected by the Freedom of Information Act.

12.3.4. Contractor shall not create or maintain any records containing any Government Agency records that are not specifically tied to or authorized by the contract.

12.3.5 The Government Agency owns the rights to all data/records produced as part of this contract.

12.3.6. The Government Agency owns the rights to all electronic information (electronic data, electronic information systems, electronic databases, etc.) and all supporting documentation created as part of this contract. Contractor must deliver sufficient technical documentation with all data deliverables to permit the agency to use the data.

12.3.7. Contractor agrees to comply with Federal and Agency records management policies, including those policies associated with the safeguarding of records covered by the Privacy Act of 1974. These policies include the preservation of all records created or received regardless of format [paper, electronic, etc.] or mode of transmission [e-mail, fax, etc.] or state of completion [draft, final, etc.].

12.3.8. No disposition of documents will be allowed without the prior written consent of the Contracting Officer. The Agency and its contractors are responsible for preventing the alienation or unauthorized destruction of records, including all forms of mutilation. Willful and unlawful destruction, damage or alienation of Federal records is subject to the fines and penalties imposed by 18 U.S.C. 2701. Records may not be removed from the legal custody of the Agency or destroyed without regard to the provisions of the agency records schedules.

12.3.9. Contractor is required to obtain the Contracting Officer's approval prior to engaging in any contractual relationship (sub-contractor) in support of this contract requiring the disclosure of information, documentary material and/or records generated under, or relating to, this contract. The Contractor (and any sub-contractor) is required to abide by Government and Agency guidance for protecting sensitive and proprietary information.

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