Samac SOW isoSeq FY23.pdf

Statement of Work (SOW)

Project: Alfalfa RNA sequencing for full length transcripts from 9 genotypes and 5 tissue types

GENERAL INFORMATION

1.0 Scope of Work:

The service provider will perform Hi-Fi PacBio RNA sequencing of alfalfa total RNA from plant samples provided by Plant Science Research Unit located at the University of Minnesota, St. Paul, MN. The goal of the ARS project is to identify the gene transcripts from nine different plants to aid in genome annotation (gene identification) and to identify gene expression differences 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 core set of genes in alfalfa and the genes that are specific to plants with specific characteristics such as fall dormancy, winter survival and disease resistance. For this reason, we are interested in performing long read RNA sequencing from unique plants. Currently, several core facilities are providing this service and we would like to utilize one of these cores to perform long read RNA sequencing of alfalfa.

CONTRACTOR REQUIREMENTS

2.0 Technical Requirements/Tasks:

A total of 45 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 Hi-Fi RNA sequencing.

3. Barcode samples to run five RNA libraries per SMRT cell.

4. Perform single-molecule real-time RNA sequencing using Pacific Biosciences

SMRT cell technology on the Sequel IIe.

5. Generate at least 500,000 reads of data for each tissue sample.

6. Provide all raw and analyzed DNA 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.

mailto:debby.samac@usda.gov