SOW - DNA single cell sequencing of mouse tissue specimens.doc

GENERAL INFORMATION

Title of Project:

DNA single cell sequencing of mouse tissue specimens

Statement of Need and Purpose:

Neurodegenerative diseases are common, debilitating, and often untreatable. The Laboratory of Neurogenetics (LNG) knows that mutations in ~50 genes cause the majority of inherited forms of Alzheimer’s disease and related dementias (ADRD). In addition, LNG knows that some ADRD genes function together to regulate key cellular processes, strongly suggesting the presence of converging disease mechanisms in ADRD. Genetically-defined patient cohorts now exist and are growing, setting the stage for future precision medicine trials. However, in order to develop effective targeted therapies for these defined cohorts, LNG needs a deeper mechanistic understanding of how individual gene mutations cause disease. In addition, LNG needs to systematically identify and characterize converging ADRD disease pathways, which may be ideal drug targets because single drugs could be effective in patients with mutations in different, but functionally related, genes. To aid in this effort, LNG requires the RNA and DNA sequencing analysis of mouse brain specimens harboring mutations associated with neurodegenerative diseases.

Background Information and Objective:

Laboratory of Neurogenetics (LNG) is working to create a national resource of isogenic sets of ADRD mutation iPSC lines, complimented by foundational phenotypic datasets from differentiated disease-relevant cells derived from these lines. LNG anticipates that this resource will substantially accelerate the pace of mechanistic discovery regarding how ADRD mutations cause disease. LNG requires the vendor to sequence mouse brain specimens for the purpose of creating a national cell repository as an open resource for the scientific community and as a tool to characterize how mutations change fundamental biological properties of disease-relevant cell types.

Period of Performance:

7/19/2021 to 12/1/2021

SCOPE OF WORK

General Requirements:

Independently and not as an agent of the Government, the Coractor shall furnish all the necessary services, qualified personnel, material, equipment, and facilities, not otherwise provided by the Government as needed to perform the Statement of Work below.

Specific Requirements:

Nuclei isolation, library preparation, and sequencing of 7 mouse samples, with 10x Genomics platform for each sample. Prior to the sequencing runs; nuclei isolation, washing, counting, and quality checking. Library QC and sequencing shall be at the level of 100 million read pairs per sample, ~5,000 read pairs per nucleus. Data analysis includes demultiplexing, quality control, sequence alignment, quantifying expression levels of each cell, clustering of single cells to identify subpopulations, aggregate analysis by pooling samples together for differential gene expression analysis under the given subpopulation.

Data can be transferred via cloud-based data transfer tool (if applicable) or in HDD format. The turnaround time should be approximately 4-6 weeks after samples have passed initial quality control.

LEVEL OF EFFORT:

Vendor staff shall provide the assay results via reporting transfer thru email.

GOVERNMENT RESPONSIBILITIES

A minimum of 100 mg snap-frozen mouse tissue per sample will be submitted as the starting material to the vendor.

DELIVERY OR DELIVERABLES

Raw data in fastq format delivered by 2TB external hard drive

REPORTING REQUIREMENTS

The vendor shall provide documentation regarding:

a. Single cell sequencing

OTHER CONSIDERATIONS

Travel:

The principal place of performance is the vendor’s work site. Travel for contractor employees will not be necessary.

Key Personnel:

Vendor shall provide a dedicated project manager to the government as a contact point for the services.

Information System Security Plan:

Not Applicable

Data Rights:

Section 508—Electronic and Information Technology Standards:

The contractor shall comply with Section 508 of the Rehabilitation Act (29 U.S.C. § 794d), as amended by the Workforce Investment Act of 1998 (P.L. 105-220), August 7, 1998.

Publications and Publicity:

Confidentiality of Information:

Version 11-30-2016-1

FAR Part 11—Describing Agency Needs