Attachment 1 - Statement of Work.pdf

Statement of Work (SOW) Project: Purchase a system for high-resolution, single cell spatial transcriptomics

GENERAL INFORMATION

1.0 Background:

The objectives of our approved CRIS research project focus on the nutritional impact on dairy cattle and how the microbial communities in the gut contribute to host nutrient use efficiency and gut diseases, both of which are important to dairy producers who thrive to make the dairy operation profitable.

The insights into the interplay between gut microbes, host physiology and immune responses are critical for us to understand the beneficial or pathological role of the gut microbes, and to leverage their benefits to improve nutrient use and production efficiency in cattle. Such insights require granular information in spatial context, which is not achievable by traditional bulk RNA sequencing or metagenomics methods.

Thus, we will need a reliable, high-throughput system to capture both the cellular layout in spatial context and transcriptome expression profile of cattle gut tissues influenced by its surrounding, ever changing microbial environment.

2.0 Objectives:

• Purchase a system to perform high-quality, in-situ cell barcoding and subsequent single-cell level whole transcriptome sequencing of cattle gut tissues under different microbial environments

3.0 Scope: A high-throughput system for high-resolution, spatial transcriptomics analysis

4.0 Technical Requirements/Tasks:

• The system has the following performance requirement

a. Offers both probe-based and 3’ poly-A based capture, species agnostic labeling and profiling for non-model organism for non-model organism

b. Offers transfer of probe or transcripts of tissues mounted on glass slides to spatially barcoded slides. Before transfer, the glass slides are quality checked using H&E or staining to ensure high-quality capture of spatially defined cells.

c. Be compatible with a diverse range of tissue types, including fresh frozen, fixed frozen, formalin fixed and paraffin-embedded (FFPE) tissues.

d. Equipped with ultra-high density of probes on the spatially barcoded slides:

more than 10 million, 2x2 µm, barcoded squares. This high-density probe layout enables best-in-class, continuous coverage of tissues and single-cell level spatial resolution.

e. Combines whole transcriptome spatial analysis with high-plex protein detection in the same FFPE tissue section

5.0 Deliverables or Delivery Schedule

The contractor performs the delivery and installation of the new instrument without government supervision. The service will ensure the instrument operates at the original, factory level performance.

6.0 Government Furnished: Government will receive the instrument and review the installation work. The facility is located at: 1925 Linden Dr. Madison, WI.

It is open Monday-Friday, from 8-4PM.

7.0 Deliverables / Schedule:

Key Deliverables:

1. The system is capable to provide high-quality, in-situ cell barcoding and subsequent single-cell level whole transcriptome sequencing of frozen tissues

2. The system includes all the critical and nonstandard reagents and slides required for high-resolution, spatial transcriptome library preparation

3. The system offers both probe-based and 3’polyA capture based whole transcriptome library preparation of spatially labeled cells

4. The reagents and slides offer ultra-high-density probe layout (more than 10 million, 2x2 µm, barcoded squares) that enable continuous coverage of tissues

5. Prepared sequencing libraries are compatible with the QC and workflows established in our laboratory using pre-installed 10X Chromium system.

6. Provides certified training on operating the instrument and certified workflows

8.0 Travel: If travel is required for the service repair, the contractor will be responsible for all the travel expenses.

9.0 Place of performance: 1925 Linden Dr. Madison, WI.

10.0 Key Personnel Requirement: the key to successful performance of the contract will include the following: 1. Successful delivery of the instrument; 2. Complete installation of the instrument at the working site to ensure the instrument performs at its original, factory-level performance; and 3. The contractor provides certified training on operating the instrument and certified workflows

11.0 Security Requirements: NA

12.0 Data Rights: Any log data on the instrument belongs to the government and cannot be distributed without government permission.

10.0 Section 508 – Electronic and Information Technology Standards: NA

Attachment: NA