SOW - Spatial Assay.pdf

Statement of Work

Project: In situ molecular spatial assay to assess porcine gene expression using formalin-fixed, paraffin-embedded pig tissues

GENERAL INFORMATION

1.0 Scope of Work: Acquire service for bioinformatics analysis to develop a porcine specific gene assay (up to 300 gene targets) for use in an in situ spatial molecular assay, and provide reagents, instrument, service, and final data analysis to use designed probes to assess spatial gene expression in formalin-fixed, paraffin-embedded porcine tissues.

2.0 Background: Our preliminary research data suggests we have identified spatially distinct regions of tissues correlating with different biological states, including pathogenic infection. However, we cannot readily detect expression of multiple gene markers at the cellular level in tissues without implementation of in situ spatial gene expression technology. We have a critical need to identify and characterize gene expression in spatial regions of tissues at cellular and subcellular resolution (spatial transcriptomics technology).

CONTRACTOR REQUIREMENTS

3.0 Technical Requirements/Tasks:

• Contractor must provide assay capable of multi-analyte analysis to obtain

RNA, protein (immunofluorescence) and morphology (through H&E staining) on the same formalin-fixed, paraffin-embedded (FFPE) tissue section using a custom probe-based assay (not whole transcriptome) at cellular and subcellular resolution.

• Contractor must be able to provide required reagent kits capable of characterizing spatially-resolved gene expression at cellular and subcellular resolution.

• Contractor must be able to provide reagent kits compatible with the Xenium imaging system for spatial transcriptomics assay analysis.

• Contractor must meet with researchers prior to development of porcine probes for custom assay including discussion of sample type, genes of interest, and sample processing.

• Contractor must have a panel designer tool with technical experts for the development a 300 gene probe assay specific to pig.

• Contractor must meet with researchers prior to execution of porcine specific in situ spatial custom assay to discuss sample type, sample prep, and sample processing.

• Contractor must provide slides to lab for sectioning tissues onto with 12x24mm imagable region per slide with 4 slides total. Each 12x24 region can include a single tissue or multiple tissues within the allotted area.

• Contractor will perform in situ spatial assay using custom porcine probes and provided ancillary reagents, instrument run time, and generation of data. Post assay the contractor will perform H&E staining of the tissue.

• Contractor will provide data within two weeks of in situ spatial assay completion and be able to be analyzed using open-source file formats.

Software should be free and accessible on any desktop or laptop.

• Contractor will provide bioinformatics support for data analysis.

• Contractor will provide image files that must be of unified tissue, not only a single field of view. The entire tissue sample should be explorable with transcript distribution and density viewed at any scale.

4.0 Government Furnished: USDA will provide list of up to 300 genes with accession numbers within 15 days of date of award for development of the porcine probes for the custom assay. USDA will provide synthesized porcine probes and porcine tissues sectioned onto contractor-provided slides within 90 days of date of award.

5.0 Deliverables/Schedule: Contractor shall complete all testing and provide final data, within 6 weeks of date of receipt of testing material (tissue sections and probe mix) from USDA.

6.0 Technical Point of Contact: To be determined at time of award.

7.0 Place of Delivery: USDA, 1920 Dayton Avenue, Bldg 24, Ames, IA 50010