SOW redacted 143041240264.docx

STATEMENT OF WORK FOR SERVICE

PURPOSE: The purpose of this solicitation is to procure mRNA extraction, library preparation and whole transcriptome sequencing services for fish tissue samples.

SCOPE OR MISSION: The scope of this solicitation is to have Next Generation sequencing of RNA (RNA-Seq) from salmon tissues, with the sample quality scores and final sequences, as fastq files, returned in order for NWFSC scientists to conduct subsequent gene expression analyses. A total of 120 tissue samples will be submitted to the vendor.

BACKGROUND: The Northwest Fisheries Science Center (NWFSC), of the National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), Department of Commerce (DOC) is a government agency charged with the mission of stewardship for living marine resources. The NWFSC is conducting experiments to determine if juvenile Chinook salmon and sablefish are affected by exposures to elevated CO2 condition reflective of current and near future ocean acidification (OA) conditions. Chinook salmon and sablefish were exposed to ambient, medium, and high levels of CO2 and tissues (olfactory bulbs, kidney, gill) hypothesized to be impacted by OA were isolated. Fish tissue samples were collected in order to analyze the response of individual fish to CO2 exposures at the transcriptome level. Using whole transcriptome Next Generation sequencing (RNA-Seq) we will evaluate gene expression differences in salmon and sablefish in response to CO2 exposures, and map those differences to phenotypic responses where possible. RNA-Seq is a high throughput method to create gene expression profiles FASTQ files for each sample, which include the nucleotide sequences and sample quality scores of the prepared library from RNA samples, will be used to determine which genes are up or down-regulated in salmon and sablefish within the different treatments. Quantifying changes in gene regulation through differential gene expression analysis among treatments will help to understand the molecular response to different environmental conditions.

TECHNICAL SPECIFICATIONS: 120 tissue samples will be provided by NWFSC personnel. The samples are frozen at -80 °C at the NWFSC, and will be shipped to the Vendor’s United States address on dry ice.

Vendor shall be a fully trained authorized service provider of Next Generation Sequencing of RNA-extracted tissue samples on the Illumina platforms, i.e. HiSeq or NextSeq. Vendor shall at all times ensure Work is accomplished in accordance with the terms and conditions of the contract in a safe and professional manner.

The sequencing facility must provide essential salient features:

1. Must have a United States address that is able to receive samples on dry ice

2. Must be able to process tissue samples with minimum sample size of 2 mg

3. Must be able to determine RNA quantity and quality, and consult with the NOAA Technical Point of Contact before proceeding with library preparation and sequencing.

4. Must have quality control steps on final library

5. Must have polyA enrichment for RNA library preparation

6. Must be able to assess library quantification

7. Must have Next Generation Sequencing of the prepared libraries with Illumina MiSeq, HiSeq or NovaSeq platforms.

8. Must generate ~50 million paired-end reads per sample.

9. Must provide electronic delivery of a quality report and FASTQ file containing nucleotide sequences for each sample through sFTP or Google Drive

10. Must have had peer reviewed publications using the vendor’s services for differential gene expression analysis

11. Must have a sample turnaround time of 12 weeks

12. RNA samples must be stored for up to 3 months and FASTQ data stored for up to 6 months following project completion.

RNA isolation, library preparation and sequencing Quality Control is the responsibility of the Vendor

PERIOD OF PERFORMANCE: Date of award plus nine months

DELIVERABLE SCHEDULE: Vendor shall electronically deliver the RNA-Seq final product, which will be FASTQ files and quality score reports for each sample, to NWFSC within 90 days of sample submission.

SECURITY

· Personnel performing work will work primarily off-site.

· Personnel performing work will not require access to NOAA facilities.

· Personnel performing work will not require a PIV or CAC.

· Personnel performing work will not require a NOAA email address.

· Personnel performing work will not require use of DOC owned IT Equipment (Laptop, Desktop Computer).

· Personnel performing work will not require Non-Government IT equipment to interconnect to a DOC network.

· Personnel performing work will not require access to non-public DOC/NOAA data.

DATA PRIVACY

Should work on this agreement require that personnel have access to Privacy information, personnel shall adhere to the Privacy Act, Title 5 of the U.S. Code, Section 552a and applicable agency rules and regulations.

Data created, obtained and collected during the performance of this agreement is the property of NMFS. Data may not be released by any party without written consent from the NMFS POC. Data must be protected from unauthorized disclosure. Personnel must comply with all Federal, DOC, NOAA, and NMFS policies relating to IT and data security.

NON-PERSONAL SERVICE

Personnel performing services under this order will be controlled, directed and supervised at all times by management personnel of the contractor. Personnel will perform independent of and without the supervision of any Government official. Actions of contractor employees may not be interpreted or implemented in any manner that results in any employee creating or modifying Federal policy, obligating the appropriated funds of the U.S. Government, overseeing the work of Federal employees, providing direct personal services to any Federal employee or otherwise violating the prohibitions set forth in Parts 7.5 and 37.1 of the Federal Acquisition Regulations. The NMFS will perform the inspection and acceptance of the completed work.