SOW_draft.pdf

US Department of Agriculture (USDA)

Statement of Work

Contents Project General Information

1.0 Scope of Work

2.0 Background

Contractor Requirements

3.0 Technical Requirements / Tasks

4.0 Government Furnished

5.0 Deliverables / Schedule

6.0 Travel

7.0 Contractor’s Key Personnel

8.0 Security Requirements

9.0 Data Rights

10.0 Section 508 – Electronic and Information Technology Standards Attachment

Project Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

General Information

1.0 Scope of Work

a. Tissue permeabilization optimization (maximum 4 permeabilization time points)

b. Tissue processing for 4 Stereo-seq transcriptomics chips (1cm x 1cm each)

c. cDNA generation and library construction

d. Sequencing of Stereo-seq library (sequencing quantity: ≥ 1 billion reads; actual data output depends on sample quality)

e. Primary and secondary bioinformatics analysis (FastQ files; chip and tissue specific gene count matrix in GEF or GEM formats)

2.0 Background

We successfully completed the first-ever single-cell RNA sequencing of rumen tissue with a high-impact publication. We established the procedures for the isolation and preparation of single cells. The project was finished by contracting outside resources for the single-cell RNA library preparation and sequencing. To extend the application of single-cell sequencing technology with the latest generation of genomics technologies, This work will capture the positional context of transcriptional activity within intact tissues for single cells.

Contractor Requirements

2.0 Technical Requirements / Tasks

The Contractor must be able to provide a service provide a service for accelerating genetic improvement of ruminants through enhanced genome assembly, annotation, and selection. The Contractor must be able to provide capability of spatial transcriptomics; specifically, the molecular profiling method to measure all the gene activity in a tissue sample (1cm X 1cm) and map where the activity is occurring with a resolution of 500 nanometers.

In fresh frozen tissues, the tissue is fixed and permeabilized to release RNA which binds to adjacent capture probes, allowing for the capture of gene expression information. cDNA is then synthesized from captured RNA and sequencing libraries prepared.

3.0 Government Furnished

Tissue samples (four fixed) will send to the contractor.

5.0 Deliverables / Schedule

The project will be completed within 5 months after the contract is established.

Primary and secondary bioinformatics analysis (FastQ files; chip and tissue-specific gene count matrix in GEF or GEM formats)

Contact: George.liu@usda.gov Dr. George Liu, 10300 Baltimore Ave. BARC EAST, Building 306 Room 111, Beltsville, MD, 20705.

6.0 Travel

N/A

7.0 Contractor’s Key Personnel

Craig Morley, Director North America Business Development, craigmorley@mirxes.com

8.0 Security Requirements

N/A

9.0 Data Rights

ARS, USDA

10.0 Section 508 – Electronic and Information Technology Standards When information technology is to be acquired, include language describing Section 508 requirements.

Insert Section 508 Here

Attachment If applicable, include an Attachment stating Evaluation Factors and significant Subfactors representing the key areas of importance and emphasis to be considered in the source selection decision.