23QNFFM0054_STATEMENT OF WORK-REVISED.pdf

STATEMENT OF WORK (SOW)

for

NF-FM7820-23-01925

3’poly A library preparation and pooled sequencing of libraries using Next Generation sequencing

May 5, 2023

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. The requirement will support research to understand the transgenerational plasticity and ability to acclimate to ocean acidification. This contract aims to support two major projects investigating the response of bivalves to ocean acidification. 1.) Three separate experiments will be conducted on second and third generation bay scallops raised under 3 different ocean acidification conditions (n= 18, n=27, and n= 36) to characterize gene expression profiling under reciprocal ocean acidification exposures and identify genes of interest that could be responsible for increased resiliency. 2.) Field samples collected from surf clam transplant studies (n=16) to understand how the interaction of ocean acidification and temperature affect surf clam survival and identify genes of interest that could be responsible for increased resiliency. Additionally, we request an option year for 2024-2025 to include juvenile bay scallops exposed to ocean acidification under a laboratory setting (n= 36). Extracted RNA from individuals collected during each study will be shipped on dry ice to the facility for 3’poly A library preparation and pooled genomic sequencing using Next Generation sequencing. Pooled samples are a requirement to achieve a greater number of individuals within a lane of sequencing, similar to methods and outcomes achieved in TagSeq library preparation described Lohman et al., 2016. 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 up or down-regulated under each treatment condition in the experiments listed above. Pooled sequencing allows for an affordable alternative to RNASeq for gene expression profiling while providing sufficient data to interpret molecular response to environmental stress. Using bioinformatics pipelines, the FASTQ files for each sample containing the nucleotide sequences can then be aligned to the published genome and genes that are up- or down-regulated among treatments can be compared using differential gene expression analysis. Quantifying changes in gene regulation through differential gene expression analysis among treatments will help to understand the molecular response to rapidly changing environmental conditions.

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’ poly A RNA library preparation, for pooled sequencing using of prepared libraries Next Generation Sequencing, 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 16 - 36 individuals per batch) may therefore be shipped at different times.

The sequencing facility must provide essential salient features:

● Must be able to receive samples on dry ice

● 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’poly A RNA library preparation capabilities

● Must have the capability to pool multiple individuals on a single lane of sequencing (eg. using indexes)

● 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 (e.g. BaseSpace)

● Must have peer reviewed publications using the venders services for differential gene expression analysis. Minimum of three (3) is required over the last five (5) year period.

2.1.1 Contractor shall be a fully trained authorized service provider of Next Generation Sequencing and library preparation from purified RNA samples for pooled sequencing 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 libraries from purified RNA for pooled sequencing, sequence libraries using Generation Sequencing platforms, and deliver back to NEFSC all FASTQ files electronically within 60 days after receiving samples.

Period of Performance

BASE YEAR:

CLIN 0001 – CLIN 0004

15 September 2023 – 15 September 2024

OPTION YEAR 1:

CLIN 005

15 September 2024 – 14 September 2025

3.0 Security Requirements. Security Clearances are not required.

3.1 Contractor employees and associated subcontractors performing under this contract MUST be U.S. citizens or MUST have established and maintain legal residence in the U.S., and be authorized by the US Government to work in the United States (i.e. Green card, worker authorization, etc.).

4.0 Safety, Security, Fire Protection, Environmental Controls, Conservation of Utilities, and Compliance with Laws and Regulations.

4.1 Safety Requirements. Contractor shall take all necessary precautions to meet proper safety standards, and regulations of all local, state and federal codes and regulations.

4.2 Security. There are no specific security requirements for performance under this contract.

5.0 Government Roles.

5.1 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.

5.2 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. TPOC information is identified as:

Katherine McFarland 440-567-7335, katherine.m.mcfarland@noaa.gov

6.0 Government Responsibilities:

6.1 Government shall inspect the Work performed under this contract. Any corrective action required as a result of the inspection will be accomplished prior to final monthly billing. Government will document instances of deficiencies.

6.2 Contractor may be notified of deficiencies in performance in writing by the CO. Oral deficiency notifications will be confirmed in writing by the CO. Contractor shall take prompt corrective action upon notice of deficiency.

Prompt is defined as within 24 hours of notification.

6.3 Government Furnished Property, Materials, Equipment and Services (GFP/M/E/S). GOVERNMENT

FURNISHED PROPERTY IS NOT APPLICABLE.

7.0 Contractor Responsibilities.

7.1 Contractor Furnished Property, Materials, Equipment and Services (GFP/M/E/S). Contractor shall provide all plant, trained labor, equipment, materials, supervision, transportation, permits, insurance, and quality control necessary to achieve the quality performance standards of the Work in this contract.

7.1.1 Contractor shall immediately notify the CO if discrepancies are discovered between the existing property conditions and those noted on the SOW.

7.1.2. Contractor shall notify the CO immediately when it is discovered that the deliverable schedule will not be met to work together to revise the schedule as necessary. Contractor shall communicate with the CO and revise the schedule as necessary. Contractor shall not deviate from schedule without prior approval from the CO.

7.1.3 Contractor shall be fully knowledgeable of all requirements of the contract documents and shall make themselves aware of all job site conditions that will affect their performance.

7.1.4 Contractor shall maintain an adequate workforce trained to safely and satisfactorily perform under this contract.

7.1.5 Contractor shall ensure all employees and subcontractors are fully trained and have a full understanding of the statement of work task requirements; government will not provide instruction or oversight.

7.1.6 Contractor shall ensure all Contractor employees, and all associated subcontractor(s) are experienced in the type of work involved and familiar with the specifications of this contract. Contractor is responsible for damage to any Government equipment and supplies caused by Contractor personnel.

7.1.7 Contractor shall comply with all applicable interstate, local, state, and federal codes and laws.

7.1.8 Contractor shall perform in accordance with professional industry standards.

7.1.9 Contractor shall accomplish all tasks to meet the requirements of the SOW.

8.0 Specific Tasks. Contractor and subcontractors working under this contract shall be a fully knowledgeable and skilled in the scientific disciplines required to successfully fulfill this requirement. Contractor 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. Contractor shall perform the following tasks:

CLIN 0001: 3’poly A RNA library preparation, for pooled sequencing of prepared libraries using Next Generation Sequencing, and delivery of sequence data for eighteen (18) purified RNA samples extracted from bay scallop tissue.

CLIN 0002: 3’poly A RNA library preparation, for pooled sequencing of prepared libraries using Next

Generation Sequencing, and delivery of sequence data for twenty-seven (27) purified RNA samples extracted from bay scallop tissue.

CLIN 0003: 3’Tag-Seq poly A RNA library preparation, for pooled sequencing of prepared libraries using Next Generation Sequencing, and delivery of sequence data for thirty-six (36) purified RNA samples extracted from bay scallop tissue.

CLIN 0004: 3’Tag-Seq poly A RNA library preparation, for pooled sequencing of prepared libraries using Next Generation Sequencing, and delivery of sequence data for sixteen (16) purified RNA samples extracted from surf clam tissue.

CLIN 0005 (option year 1): 3’Tag-Seq poly A RNA library preparation, for pooled sequencing of prepared libraries using Next Generation Sequencing, and delivery of sequence data for thirty-six (36) purified RNA samples extracted from bay scallop tissue.

9.0 Deliverables. Contractor shall provide the identified deliverables in the manner and time frame identified.

DELIVERABLE DUE NO LATER THAN

CLIN 0001 electronic delivery of FASTQ files 60 days after receiving samples CLIN 0002 electronic delivery of FASTQ files 60 days after receiving samples CLIN 0003 electronic delivery of FASTQ files 60 days after receiving samples CLIN 0004 electronic delivery of FASTQ files 60 days after receiving samples CLIN 0005 (option year 1) electronic delivery of FASTQ files 60 days after receiving samples

10.0 IT Security. Not applicable. Requirements of 48 CFR 1352.239-73 do not apply and a Security Accreditation Package is not required.

11.0 Section 508. Not applicable. Section 508 of the Rehabilitation Act of 1973 (29 U.S.C. 794d) as amended by P.L.

105-220 under Title IV (Rehabilitation Act Amendments of 1998) is not required.

12.0 Invoicing. Contractor shall provide “proper” invoices in arrears of tasks performed (and expensed) with last invoice being submitted within 30 days of contract completion. Invoices shall be submitted (via electronic copy) no later than by the 10th day of the billing month.

Invoicing Instructions for Standard Form 1449

EFFECTIVE 1 OCTOBER 2023 – NEW INVOICING PLATFORM IS

MANDATORY

Reference: NOAA Acquisition Manual (NAM) 1330-52.232-72

Contractor shall prepare and submit a “proper” invoice to the TPOC for approval [with a copy to the contracting officer for information]. All invoices shall be submitted by the 10th day of the subsequent month the Work was performed in accordance with the Prompt Payment Act. Proper invoices must include as a minimum:

a) Name and address of the Contractor.

b) Name (where applicable), title, phone number, and mailing address of person to notify in the event of a defective invoice.

c) Invoice date and invoice number (Contractors should date invoices as close as possible to the date of mailing or transmission). Electronic submission of invoices is preferred.

d) Contract Number

e) Contract Line Item Number being billed, with description, quantity, unit of measure, unit price, and extended price of supplies delivered or services performed

The Government will return improper invoices to the Contractor and payment will not be made until receipt of a proper invoice. Contractor shall send invoices in accordance with the terms and conditions of this contract to the following email; address: https://www.ipp.gov

NOAA Transition to the Invoice Processing Platform Electronic Invoicing System (Feb 2023) Beginning October 1, 2023, when NOAA implements the Department of Commerce Business Applications Solution, the Contractor must submit payment requests electronically through the U.S. Department of the Treasury's Invoice Processing Platform (the IPP) System. The Contractor must use the IPP website to register, access, and submit payment requests. The IPP website address is https://www.ipp.gov.

"Payment request" means any request for contract financing payment or invoice payment to the Contractor. To be considered proper, invoices must be prepared in accordance with, and contain all elements specified in, the contract payment clause (e.g., FAR 52.212-4(g), FAR 52.23225(a)(3), FAR 52.232-26(a)(2), FAR 52.23227(a)(2)). All supporting documents required by the Contracting Officer must be included as attachments to payment requests submitted through the IPP.

If the Contractor is unable to comply with the requirement to submit payment requests through the IPP due to a threat to national security; a matter of unusual or compelling urgency; or because the political, financial, or communications infrastructure of a foreign country does not support access to the IPP, the Contractor must request an exception in writing.

Contact the Contracting Officer for more information about requesting an exception.

FREIGHT/SHIPPING COSTS: If freight costs exceed $100.00, a copy of the waybill must accompany the invoice to support the freight charges.