Specifications.pdf
PDF 196 KB Posted
- Attached to
- Promethion 2 Solo Pack Federal contract opportunity
- Solicitation number
- 1232SA25Q0879
About this file
This document is a Specifications file for a USDA Agricultural Research Service (USDA-ARS) project to validate causative mutations in agriculturally important vertebrates. The project will utilize Nanopore sequencing technology from Oxford Nanopore Technologies to phenotype gene-edited cells in pigs and poultry, with the goal of identifying improved traits that enhance production, animal welfare, and farm profitability. Specifically, the project requires two Nanopore sequencing device packs: a PromethION 2 Solo Pack for high-coverage sequencing (including 4 flow cell packs, 2 ligation sequencing kits, a rapid barcoding kit, and 3-year standard support) and a MinION Mk1D Pack for lower-coverage targeted sequencing (including 5 flow cells, a native barcoding kit, and support).
The equipment must be delivered within 60 days of award to the USDA ARS at the University of Missouri, located at 163 ASRC, 920 East Campus Dr, Columbia, MO 65211. The project objectives include developing poultry and livestock genotypes with improved disease resistance to viral/bacterial pathogens and other performance-related traits by systematically altering DNA sequences. The Nanopore sequencing platform will enable comprehensive molecular characterization of wildtype and gene-edited cell lines through whole genome, transcriptomic, metagenomic, and targeted sequencing. No travel, security requirements, or specific data rights are associated with this procurement.
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Other files for this federal contract opportunity
| File | Type | Posted |
|---|---|---|
| 1232SA25Q0879 LPTA - RFQ - TCs -.pdf | ||
| 1232SA25Q0879 - Combined Syn-SOL -.pdf | ||
| SF 1449 (11_2021) SOL.pdf |
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Text version
Specifications Project: Validate Causative Mutations in Agriculturally Important Vertebrates
GENERAL INFORMATION
1.0 Scope of Work: The overall goal is to phenotype gene-edited cells to identify improved traits in pigs and poultry leading to increased production, improved animal welfare, enhancing farm profitability and sustainability. Gene editing to produce changes in DNA thought to enhance production agriculture traits will be analyzed by culturing edited cells in vitro to determine if there is a positive effect on cell phenotype. The objective of this work is to develop poultry and livestock genotypes that provide improved disease resistance to viral/bacterial pathogens and/or other performance related traits.
2.0 Background: A new Research Geneticist position at USDA-ARS was recently filled. The scientist will use gene editing and other technologies to systematically alter DNA sequences predicted to cause beneficial changes in livestock production and test these changes in vitro and in vivo where warranted. The scientist will contribute towards identifying and establishing poultry and porcine cell lines that can be used to phenotype agriculturally important traits in vitro and evaluate the effects of natural genetic variation or novel mutation on corresponding cellular phenotypes. The Nanopore sequencing platform will provide rapid whole genome, transcriptomic, metagenomic, and targeted sequencing of raw or pre-amplified DNA and RNA samples enabling comprehensive molecular characterization of wildtype and gene-edited cell lines or animals.
CONTRACTOR REQUIREMENTS
3.0 Technical Requirements/Tasks: The Nanopore sequencing platform is only manufactured by Oxford Nanopore Technologies; thus, a Sole Source Justification has also been drafted. There are multiple Nanopore sequencing devices or packs that can be utilized independently or in-combination depending on project type. For our work, we will need the PromethION 2 Solo Pack for high-coverage or multi-plexed/metagenomic sequencing and the MinION Mk1D Pack to provide a cost-effective option for routine lower-coverage or targeted sequencing of samples. Both packs include the sequencing device, consumables, and standard support services.
Specifications for the customizable components of each pack are indicated below.
• PromethION 2 Solo Pack Selections:
o 4x PromethION Flow Cell packs for DNA sequencing based on latest nanopore chemistry (R10.4.1) o 2x Ligation Sequencing Kit using latest chemistry (V14) o 1x Rapid Barcoding Kit with 24 distinct barcodes using latest chemistry (V14) o P2 Solo Standard Support for 3 years
• MinION Mk1D Pack Selections:
o 5x Flow Cells for DNA sequencing based on latest nanopore chemistry (R10.4.1) o 1x Native Barcoding Kit with 24 distinct barcodes using latest chemistry
(V14)
4.0 Government Furnished: NA
5.0 Deliverables / Schedule:
Must be delivered within 60 days of award. The equipment must be delivered to:
USDA ARS
University of Missouri
163 ASRC
920 East Campus Dr Columbia, MO 65211
6.0 Travel: Travel is not required.
7.0 Contractor’s Key Personnel: NA
8.0 Security Requirements: There are no security requirements.
9.0 Data Rights: There are no data rights to be acquired.
10.0 Section 508 – Electronic and Information Technology Standards: NA
| CONTRACTOR REQUIREMENTS |
| 3.0 Technical Requirements/Tasks: The Nanopore sequencing platform is only manufactured by Oxford Nanopore Technologies; thus, a Sole Source Justification has also been drafted. There are multiple Nanopore sequencing devices or packs that can be utili... |
| PromethION 2 Solo Pack Selections: |
| 6.0 Travel: Travel is not required. |
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