Attachment 1 - RNA-Seq Performance Work Statement.doc

Performance Work Statement (PWS)

Project: RNA-Seq Service

GENERAL INFORMATION

1.0 Background and Purpose: The Fargo Small Grains Genotyping Lab investigates the genomics of small grains in the US. Our focus is to assist the community by providing genotyping service and performing primary research on the identification of gene regions that influence traits. Once found, this knowledge is used to accelerate breeding of better cultivars with high yield, excellent quality, and innate disease resistance. To do this high-throughput sequencing capacity is necessary to evaluate the genomes of populations to find these regions.

2.0 Definitions: QC – Quality Control; Gb – Gigabase; POC – Point of Contact; PE – Paired End; DNA - Deoxyribonucleic acid; RNA - Ribonucleic acid

CONTRACTOR REQUIREMENTS

3.0 Technical Requirements/Tasks:

mRNA-seq: Messenger RNA sequencing library generation – Preparation of sequencing library from submitted total RNA. Quality report submitted via email 4.0 Deliverable / Schedule:

· Every submitted RNA sample will be QC analyzed and converted into sequencing libraries and sequenced to the customers specifications as described in the contractor’s submission documentation.

· All reports will be delivered via email to the government POC.

· All final sequencing data (raw and assembled) will be provided via a download link.

· Timely submission of deliverables is essential to successful completing this requirement. Schedules for deliverables are specified in below.

Key Deliverables

5.0 Government Furnished: N/A 6.0 Travel: N/A 7.0 Contractor’s Key Personnel: Contractor must have laboratory staff experienced in assaying the quality of sequencing libraries and running the sequencing instruments.

8.0 Security Requirements: Data submission portal will be password protected.

9.0 Data Rights: The data will be solely owned by the government and the contractor will have no rights or obligations to the data once it is transferred.

10.0 Reserved 11.0 Performance Requirement Measures: {Indicate how the government will measure the contractor's performance for specific tasks or work critical to the mission essential items).

· Payment deduction is generally a remedy for non-performance, not as an incentive. Non-Monetary incentives may include award term contract arrangement (contractor is awarded periods of performance) or Past Performance for quality level of performance.

% for NOT meeting the Task

-1% of lane price every 1% decrease from 80% Q30 of the requested sequencing amount.

Attachment: N/A Background

Fusarium head blight is a very impactful disease for the US, causing loss of yield and quality in wheat and barley grain. This project is to investigate disease resistance mechanisms in spring and durum wheat. This project is important because even though we have spent 30 years developing “resistant lines”, actual resistance is variable. We just recently are investigating why certain major resistance genes do not always provide the support we expect. This will lead to better understanding of how these genetic players interact and how we can leverage this information to develop varieties that are naturally resistant to the disease all the time.

Objectives

The project involves artificially inoculating wheat spikes with fungal spores, then taking tissue samples after the fungus has started to grow. Total RNA is then extracted from these samples and messenger RNA (that is converted into protein) is sequenced. Analysis of this sequencing information will provide insights into biological pathways that are turned on and off in response to disease and will assist in identifying key genes that are needed to mount a success resistance response. The specific objective of this contract is to generate mRNA-Sequencing libraries and sequence.

Scope Generate mRNA-Sequencing libraries from total RNA and sequence

Tasks or Requirements 252 samples requiring the following requirement:

RNA sample QC

RNA-Seq Library construction

40 M PE 2x150 sequencing

Deliverables or Delivery Schedule

RNA QC Report – 3 business days after sample received

RNA-Seq Library construction – 5 business days after sample QC confirmation

40 M PE 2x150 required – 10 business days after Library construction

Sequencing QC Report – 3 business day after sequencing is completed

Sequencing Data – 2 business days after Sequencing QC report confirmation

Reporting Requirements All reports and correspondence will be delivered via email to the government POC.

All final sequencing data will be provided via a download link.

Travel

· N/A Place of Performance

· Perform at contractor site

Homeland Security Presidential Directive (HSPD)-12 (If applicable)

· When contract performance requires contractors to have routine physical access to a Federally-controlled facility and/or routine access to a Federally-controlled information system, indicate that all applicable contractor employees must go through the identity proofing and registration process, and must have been successfully identity proofed, and have a successfully adjudicated National Agency Check with (Written) Inquiries (NACI) or Office of Personnel Management (OPM)/National Security (NS) Background