Attachment_1_-_Statement_of_Work_dated_04_09_2026.pdf

STATEMENT OF WORK (SOW)

for 3’Tag-Seq poly A library preparation and Next Generation sequencing

1.0 Background.

The National Oceanic and Atmospheric Administration (NOAA), National Marine Fisheries Service (NMFS), Northeast Fisheries Science Center (NEFSC) is the research arm of NOAA Fisheries in the region. The Center plans, develops, and manages a multidisciplinary program of basic and applied research. Wild harvest of Atlantic sea scallops Placopecten magellanicus is the most lucrative commercial bivalve fishery in the US ($488 million USD annually), however sea scallop landings are projected to decline by 50% at the end of the century in part from ocean acidification (OA; elevated ρCO2). Adaptive genetic change can occur rapidly and offset consequences of environmental change yet depend on variation maintained within an existing population.

The requirement will support research to understand differences in how sea scallop populations respond to ocean acidification and temperature challenges. Extracted RNA from 40 individuals collected during this study will be shipped on dry ice to the facility for 3’Tag-Seq poly A library preparation (Lohman et al., 2016) and genomic sequencing using Next Generation sequencing. FASTQ files for each sample, which include the nucleotide sequences and sample quality scores of the prepared cDNA library from RNA samples, will be used to determine which genes are activated or suppressed under each treatment condition in the experiments listed above. TagSeq allows for an affordable alternative to RNASeq for gene expression profiling of many individuals while providing sufficient data to interpret molecular response. Using bioinformatics, the FASTQ files containing raw nucleotide sequence data can then be aligned to the sea scallop genome and genes that differ in abundance can be compared using differential expression and correlation network analysis. Identifying responsive genes for a given population in response to stimuli will help to understand population sensitivity to environmental challenges.

2.0 General Requirements

2.1 Scope of Work. Non-Personal Service. Contractor shall provide all plant, trained labor, equipment, materials, supervision, transportation, permits, insurance, and quality control necessary to provide for 3’Tag- Seq poly A RNA library preparation, Next Generation Sequencing of prepared libraries, and delivery of sequence data for the NMFS/NEFSC Milford Laboratory (212 Rogers Ave., Milford, CT 06460).

Performance under this contract known as “Work”. Contractor shall be fully knowledgeable of all contract requirements and shall ensure Work is accomplished in accordance with the terms and conditions of the contract in a manner that will promote and maintain a safe environment.

We require this work for four (4) unique experiments and batches of samples (purified RNA for 40 individuals).

The sequencing facility must provide essential salient features:

● Must be able to receive samples on dry ice

● Must be able to extract RNA from tissue in fixative (RNAlater or DNA/RNA shield)

● Must be able to ascertain quantity and quality of extracted RNA

● Must be able to process samples at concentrations between 10-100 ng/uL of purified RNA

● Must have quality control steps on final library

● Must have 3’Tag-Seq poly A RNA library preparation capabilities

● Must be able to ascertain to quantity and quality of 3’ Tag-Seq libraries

● Must have Next Generation Sequencing of the prepared libraries

● Must have a minimum standard coverage 3-4 Million single end reads per sample

● Must have electronic delivery of FASTQ files for all samples through web based repository

● Must have peer reviewed publications using the vendors services for transcriptomics

2.1.1 Contractor shall be a fully trained authorized service provider of Next Generation Sequencing and TagSeq library preparation from purified RNA samples and shall be fully knowledgeable of all contract requirements. Contractor shall at all times ensure Work is accomplished in accordance with the terms and conditions of the contract in a safe and professional manner.

2.1.2 Special Qualifications and Permits. None

2.1.3 Quality Control. Quality Control is the responsibility of the Contractor

2.2 Place of Performance. The vendor's laboratory and sequencing facility.

2.3 Period of Performance/Delivery: Contractor shall prepare TagSeq libraries from purified RNA, sequence libraries using Generation Sequencing platforms, and deliver back to NEFSC all FASTQ files electronically to the technical point of contact by direct download link, cloud transfer, or through a repository accession within 60 days after receiving samples.

3.0 Government Roles.

3.1 The Contracting Officer (CO) is the only individual with the authority to authorize changes within this contract that will have an effect on the scope, and monetary values (increase or decrease) of contract.

3.2 The Technical Point of Contact (TPOC) is the individual designated by the CO at contract award to perform administrative functions on the contract. The key role of the TPOC is to monitor the performance of the contract. The TPOC will observe, document, and communicate Contractor performance to the CO.

TPOC and alternate TPOC (if applicable) will be responsible for the inspection and acceptance of performance and any deliverables under the contract. The TPOC does NOT have authority to change the terms and conditions of the contract. When in the opinion of the Contractor, the TPOC requests efforts outside the existing scope of the contract, the Contractor shall promptly notify the CO in writing. Contractor under such direction shall take no action until the CO has resolved the issue or has otherwise issued a modification to the contract.