Statement of Work Q0286 .pdf

Statement of Work Single-Cell Chromatin Accessibility Profiling Preparation Kit

GENERAL INFORMATION

1.0 Scope of Work. Several research programs at the US Dairy Forage Research Center are presently or evolving to perform single-cell RNA-sequencing. The objectives of our CRIS project plan focus on the impact of nutrition on dairy cattle physiology and the associated microenvironment in the gastrointestinal (GI) tract. Specifically, we are interested in investigating the role of rumen microbial community in host feed fermentation and methane production.

2.0 Background. Cattle rumen microbial community plays a critical role of converting nondigestible feed into absorbable nutrients to the host. A comprehensive knowledge of metabolic function of the ruminal microbes is critical for the host health, production and well-being. Conventional method for the investigation of rumen microbial community is through 16s ribosomal RNA sequencing. However, this method is only capable to provide the taxonomy presence/absence of the microbial community at phylum or genus level. It lacks the ability to provide any insights into the metabolic or physiological roles of the resident microbes.

To address this deficit, we will employ recently developed single-cell RNA sequencing technology to interrogate the transcriptome profile and its regulatory mechanisms through chromatin accessibility analysis of the ruminal microbes at the single cell level. Different from bulk RNA sequencing, which only This method will provide the gene content, their expression profile and regulatory networks for individual microbes. Most importantly, this method will enable the identification of heterogeneity in cell types and subpopulations within a given microbial strain. To fulfill the research needs, we wish to purchase a single-cell library preparation kit that allows us to perform rumen bacterial single cell sequencing.

CONTRACTOR REQUIREMENTS

3.0 Technical Requirements. Successful performance of the contract will include the following: Successful delivery of the library preparation kit; the kit is packaged and delivered at the required temperature indicated by the manufacturer; and the contractor provides a complete list of all the items included in the kit and ready for inspection upon delivery.

The library preparaton kit has the following performance requirement

• Capability to provide assays for Transposase Accessible Chromatin

• Analyze open chromatin regions at single cell resolution

• Perform epigenetic profiling for hundreds to tens of thousands of nuclei

• Resolve cell types and states using genome-wide, epigenetic profile

• A ready-to-follow workflow that can applied to various sample types, including cell lines, primary cells, fresh and frozen tissues.

The kit should include the following:

• Reagents sufficient for processing 16 sample preparations

• Index needed for 96 reactions

• Chip need for gel beads-in-emulsion, sufficient for 48 reactions

4.0 Deliverables / Schedule. Government will receive the kit and review the included components. The facility is located at 1925 Linden Dr. Madison, WI. It is open Monday-Friday, from 8-4PM.

3.0 Technical Requirements. Successful performance of the contract will include the following: Successful delivery of the library preparation kit; the kit is packaged and delivered at the required temperature indicated by the manufacturer; and the con...