D Attachment 5-SOW_single nuclei multiome.pdf

Version 11-30-2016-1 FAR Part 11—Describing Agency Needs

STATEMENT OF WORK (SERVICES)

(SOW)

GENERAL INFORMATION

Title of Project:

Single-nuclei multiome analysis of human brain tissue, iPSC-derived cells and human dorsal root ganglion.

Statement of Need and Purpose:

Single-nuclei multiome: This is an end-to-end service that allows both the transcriptome analysis and genome-wide detection of open chromatin at the single cell level. This assay will help provide insight into gene expression profile and the chromatin state at single-cell resolution.

This service will be utilized by the SCTL to obtain data to study the gene expression and chromatin profiles in human brain tissue, iPSC-derived cells and dorsal root ganglion. The data obtained from this study will be used to construct a high-resolution “map” of the genomic and epigenomic landscape of the above mentioned human derived cells and tissue.

Background Information and Objective:

The National Institutes of Health (NIH) is the nation’s leading medical research agency and the primary Federal agency whose mission is to seek fundamental knowledge about the nature and behavior of living systems and the application of that knowledge to enhance health, lengthen life, and reduce illness and disability, conducting, supporting and making medical discoveries that improve people’s health and save lives.

The National Center for Advancing Translational Sciences (NCATS) is a part of the National Institutes of Health (NIH), with the mission to catalyze the generation of innovative methods and technologies that will enhance the development, testing and implementation of diagnostics and therapeutics across a wide range of human diseases and conditions. The Stem Cell Translation Laboratory (SCTL) is a state-of-the-art research facility within NCATS’ Division of Pre-Clinical Innovation dedicated to addressing the scientific and technological challenges in the iPSC field.

The SCTL uses an integrated technological approach to better understand pluripotent stem cell biology and thereby leverage drug discovery and regenerative medicine.

The opioid crisis highlights the urgent need for novel non-addictive pain medications, as well as improved treatments, for opioid addiction and overdose. There is a need for pharmacological agents directed at novel targets to test new therapeutic hypotheses, new clinic-ready drugs directed at those targets, and new testing systems with the potential to be more predictive of human clinical response than traditionally used models. Through the Helping to End Addiction Long-term (HEAL) Initiative, NCATS will focus on the development of human cell-based models of opioid misuse, addiction, and pain. Specifically, the SCTL aims to develop a renewable supply of human cell-based models focusing on new patient-derived induced pluripotent stem cell (iPSC) lines that give rise to specialized, functional nerve cells that are relevant for opioid misuse, addiction, and pain.

To this end, SCTL has acquired human brain tissue, dorsal root ganglion and generated relevant iPSC-derived cell types. The single-cell multiome service is an integral part of the suite of analysis methods that will be carried out to construct a high-resolution “map” of the genomic and epigenomic landscape of neural cell types and human derived tissues. The streamline integration of all these analyses through will allow us to generate foundational datasets that will be shared with the scientific community.

Period of Performance:

The period of performance will commence within 30 days after receipt of order (ARO) and last 4-8 weeks from receipt of the samples intended for sequencing.

SCOPE OF WORK

General Requirements:

Independently and not as an agent of the Government, the Contractor 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:

The SCTL will obtain human tissues or culture the biological material and harvest the cells. The tissues or cell pellets will be flash frozen on dry ice and will be shipped to the vendor on dry ice.

Then, the vendor will extract the nuclei from the tissue or cell pellets, perform quality analysis, construct sequencing libraries, perform sequencing on an Illumina platform, perform data analysis, and biological interpretation. Finally, the vendor will make the data available to the SCTL via FTP or HTML download.

Specific Requirements:

Single-cell multiome

Single-cell multiome allow for both transcriptome analysis and genome-wide detection of open chromatin at the single cell level. Understanding both the gene expression profile and the chromatin state at single-cell resolution can help identify how epigenetic changes instruct gene expression in distinct cell populations. This technique can be used to identify cell subpopulations with different transcriptome and epigenetic profiles withing complex samples.

The SCTL will provide frozen cell pellets, then the vendor will:

For Single-nuclei multiome:

• Prepare nuclei

• Tn5 tagmentation of open chromatin regions

• Nuclei loaded onto 10X Genomics Chromium Controller

• Barcoding of mRNA and in the same nucleus

• Library generation

• Sequencing

• Bioinformatic analysis

LEVEL OF EFFORT:

The vendor will be responsible for carrying out nuclear extraction, QC of the of the nucleic acid samples, sequencing, and data analysis.

GOVERNMENT RESPONSIBILITIES

The SCTL will derive a total of 50 samples, and ship them to the vendor for analysis.

DELIVERY OR DELIVERABLES

Deliverables:

• Raw data (FASTQ) output files.

• Aligned data (BAM) files.

• Differential methylation analysis tables.

• Figures & graphs – Includes coverage depth analysis, heatmaps & pie charts.

REPORTING REQUIREMENTS

All reports will be provided by the vendor in electronic form – PDF, MS Excel sheets, MS Word, TXT files, PNG, TIFF figures, or other format based on the type of report. Raw sequencing data will be provided in the form of FASTQ files and will be furnished using as an FTP or HTML server download.

OTHER CONSIDERATIONS

Travel:

N/A

Key Personnel:

N/A

Information System Security Plan:

N/A

Data Rights:

Data generated as a result of ALL services will be the properties of NIH, NCATS, SCTL.

Section 508—Electronic and Information Technology Standards:

N/A

Publications and Publicity:

The datasets derived by the SCTL from these experiments will be part of scientific publications and they will be made available to the public on the SCTL public-facing internet website. The contractor will not publish any result of the work.

Confidentiality of Information:

The Contractor will keep the results of the contract confidential. An MTA with NCATS OSA is in progress.