Multiomics Profiling

This federal solicitation (No. 1232SA26Q0558) is issued by the United States Department of Agriculture (USDA) Agricultural Research Service (ARS) for the acquisition of specialized genetic sequencing and analysis services. The contract will support the NEA Animal Genomics and Improvement facility in Beltsville, Maryland. The scope of work is categorized into seven line items, which include nuclei isolation and sample quality control, 10X Genomics Chromium Multiome and GEX sequencing, meta-transcriptome short-read processing, and Illumina 2x150bp standard sequencing. The USDA intends to award a single, firm-fixed-price contract with a period of performance running from July 16, 2026, through June 30, 2027. Proposals will be evaluated using the Lowest Price Technically Acceptable (LPTA) source selection process. To be considered responsive, quoters must submit pricing for all seven line items and provide a detailed technical approach demonstrating their capability to fulfill the Statement of Work. Past performance will also be assessed on an acceptable, neutral, or unacceptable scale. Key administrative terms include mandatory vendor registration in the System for Award Management (SAM) and electronic invoice submission via the Invoice Processing Platform (IPP). The solicitation incorporates standard Federal Acquisition Regulation (FAR) provisions, specialized AGAR clauses regarding anti-discrimination and civil rights compliance, and guidelines for filing agency-level protests through the USDA Ombudsman Program. Offers are due by July 27, 2026.

This Statement of Work outlines a requirement by the USDA-ARS Animal Genomics and Improvement Laboratory (AGIL) for integrated multi-omics sequencing services. The initiative aims to support national livestock improvement programs and germplasm conservation efforts by analyzing 97 cattle samples to characterize gene expression, microbiome function, and immune diversity. The selected service provider will deliver full-service library construction and sequencing across three primary tasks: 1. **Chromium Multiome Profiling (n=25):** Targeting approximately 10,000 cells and 50,000 reads per cell per assay to jointly assess chromatin accessibility and gene expression. 2. **5' Gene Expression Profiling (n=12):** Featuring T-cell and B-cell receptor (TCR/BCR) enrichment targeting 10,000 cells and 50,000 reads per cell to evaluate adaptive immune diversity. 3. **Metatranscriptomics Sequencing (n=60):** Including RNA extraction, dual ribosomal RNA (rRNA) depletion, library preparation, and sequencing (approximately 50 million short reads per sample) to analyze rumen host-microbiome interactions. All library preparation, sequencing, and initial quality control must be performed at the contractor's facility. The period of performance runs from July 29, 2026, through June 30, 2027, which is also the final deadline for all data delivery. No government-furnished property, travel, or specialized security clearances are required for this contract.

This document outlines the United States Department of Agriculture's (USDA) decision to restrict competition under the Simplified Acquisition Threshold for requisition number 1169246. The USDA Agricultural Research Service (ARS) Northeast Area (NEA) Beltsville Agricultural Research Center (BARC) Animal Genomics and Improvement Laboratory (AGIL) requires a specialized provider to perform integrated multi-omics sequencing and data processing. This work, which supports livestock improvement and germplasm conservation, includes snMultiome profiling, metatranscriptomics sequencing, and 5’ gene expression with BCR/TCR repertoire enrichment for 97 cattle samples. The USDA has designated Azenta US, Inc. as the sole technically acceptable source for this acquisition. This restriction of competition is justified by the need to maintain strict consistency with AGIL's substantial body of existing genomic and transcriptomic datasets, which were generated using Azenta's proprietary pipelines. Using a different vendor would introduce data variability, increase integration risks, and potentially require data reprocessing. Additionally, Azenta offers a local operational presence that provides routine sample pickup at the BARC campus, rapid regional processing in Rockville, Maryland, and established secure data delivery. Market research—including queries of AbilityOne, GSA Advantage, and consultations with peer institutions—confirmed that while other sequencing vendors exist, none can satisfy the combined requirements for technical consistency, data compatibility, and logistical efficiency. Consequently, the USDA has authorized the sole-source procurement to avoid analysis delays, increased costs, and compromised data continuity.

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