PWS RNA_Seq FY23.pdf

Performance Work Statement (PWS)

Project: Alfalfa RNA sequencing from nine genotypes

GENERAL INFORMATION

1.0 Scope of Work:

The service provider will perform Illumina RNA sequencing of alfalfa total RNA from samples provided by Plant Science Research Unit located at the University of Minnesota, St. Paul, MN. The goal of the ARS project is to sequence gene transcripts from nine different plants to aid in differential gene expression patterns among the different plants.

2.0 Background:

Developing genomic resources for alfalfa has lagged behind other crop species. One goal of this project is to identify the differentially expressed genes are specific to plants with specific characteristics such as fall dormancy, winter survival, and disease resistance. For this reason, we are interested in performing RNA-Seq from unique plants using Illumina technology. Currently, several core facilities are providing this service and we would like to utilize one of these cores to perform RNA sequencing of alfalfa.

CONTRACTOR REQUIREMENTS

2.0 Technical Requirements/Tasks:

A total of 135 RNA samples from nodules, roots, leaves, stems, and flowers plus seed pods from nine plants will be shipped to the service provider on dry ice. The service provider will perform these specific tasks:

1. Perform qualitative analysis to ensure that RNA meets standard sequencing center QC standards for size, quality, and quantity.

2. Prepare RNA libraries for sequencing from the above samples as per the manufacturer’s procedure for Illumina RNA sequencing.

3. Conduct sequencing, 2 x 150 bp, ~350 million paired end reads (~105 GB), single index, per lane

4. Conduct standard RNA-seq analysis: quality report, FASTQ files, data QC, trimming, mapping, differential gene expression, alternative splicing, and gene ontology analysis.

5. Provide all raw and analyzed sequence data via secure HTTP download.

Delivery schedule: 90 calendar day from the time of contract award.

3.0 Government Furnished:

The service provider is solely responsible for the entire service. There will be no support or use of federal facility by the service provider. The service provider will submit a report to end user at the end of the completion of the service.

4.0 Deliverables / Schedule:

All data generated by the vendor will be submitted to Deborah Samac at debby.samac@usda.gov within 90 calendar days from date of contract award.

5.0 Travel:

No Travel requirements

6.0 Contractor’s Key Personnel:

Not applicable

7.0 Security Requirements:

Not applicable

8.0 Data Rights:

All the data generated by the vendor belongs to the government.

9.0 Section 508 – Electronic and Information Technology Standards:

Not applicable.