DNA isolation and Whole Genome Sequencing (WGS) of mango germplasm

Agency: AGRICULTURE, DEPARTMENT OF
State: Florida
Type of Government: Federal
Category:
  • B - Special Studies and Analyses - Not R&D
Posted: Jun 24, 2022
Due: Jun 30, 2022
Solicitation No: 12405B22Q0167
Publication URL: To access bid details, please log in.
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DNA isolation and Whole Genome Sequencing (WGS) of mango germplasm
Active
Contract Opportunity
Notice ID
12405B22Q0167
Related Notice
12405B22Q0167
Department/Ind. Agency
AGRICULTURE, DEPARTMENT OF
Sub-tier
AGRICULTURAL RESEARCH SERVICE
Office
USDA ARS SEA AAO ACQ/PER PROP
General Information
  • Contract Opportunity Type: Combined Synopsis/Solicitation (Original)
  • All Dates/Times are: (UTC-05:00) CENTRAL STANDARD TIME, CHICAGO, USA
  • Original Published Date: Jun 24, 2022 09:59 am CDT
  • Original Date Offers Due: Jun 30, 2022 02:00 pm CDT
  • Inactive Policy: 15 days after date offers due
  • Original Inactive Date: Jul 15, 2022
  • Initiative:
    • None
Classification
  • Original Set Aside:
  • Product Service Code: B529 - SPECIAL STUDIES/ANALYSIS- SCIENTIFIC DATA
  • NAICS Code:
    • 541380 - Testing Laboratories
  • Place of Performance:
    Miami , FL
    USA
Description

This is a combined synopsis/solicitation for commercial goods and commercial services prepared in accordance with the format in FAR subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotes are being requested, and a written solicitation will not be issued. The solicitation number is 12405B22Q0167 and is issued as a request for quotation (RFQ). The NAICS code is 541380 - Testing Laboratories. This solicitation document incorporates those provisions and clauses in effect through Federal Acquisition Circular 2022-06.





The USDA-SHRS, Miami, FL maintains a large collection of mango germplasm with several accessions displaying different horticultural characteristics. The overall objective of this project is to sequence mango germplasm using whole genome sequencing approach. This project requires isolation and quality check of DNA from 288 mango samples followed by sequencing and bioinformatics. The project will generate approximately 6000 Gbp DNA sequence data. This project will be completed by an outside vendor. Following are the tasks that will be performed in this project:




  1. Mango leaf sample collection: Freshly growing new leaves and flowers will be collected from 288 mango trees in the field using a leaf sampling kit. This task will be performed by the staff at USDA-ARS, Subtropical Horticulture Research Station, Miami, Fl. Sampling kits with the tissues will be send out to an outside vendor who will perform the following tasks.

  2. DNA isolation: DNA will be isolated by the vendor from all samples using standardized DNA isolation protocol from mangos leaves and flowers.

  3. DNA quality check: DNA quality and quantity will be checked using standard procedures usually employing bioanalyzer and/or other procedures.

  4. DNA library preparation: DNA samples will be sheared to approximately 300 bp and indexed with unique adapters, quality checked (QC), and sequencing libraries prepared and quality checked.

  5. DNA library sequencing: All libraries will be sequenced using 2 X 150 PE reads on 2.1 NovaSeq 6000 S4 Cells to achieve 50X coverage of the approximately 439 Mbp mango genome. This will generate approximately 6000 Gbp in approximately 40 Billion 150X Paired End reads.

  6. Bioinformatics: Reads will be demultiplex, quality checked (QC), and adapters trimmed. Bam mapping files will be generated and along with raw data from sequencing facility provided by the vendor.

  7. DNA storage and return: DNA will be stored at -80 oC and provided by the vendor.



Any quotes not meeting the minimum specifications will not be considered.





DOCUMENTS TO BE INCLUDED IN QUOTE: In order to be considered for award Offerors shall provide 1) a Quote on company letterhead detailing the item description, unit price per item, discounts for trade-ins, total price and valid for at least 60 days after receipt of quote; and 2) FAR 52.212-3, OFFEROR REPRESENTATIONS AND CERTIFICATION-COMMERCIAL GOODS AND COMMERCIAL SERVICES; The Representation and Certification section must be completed electronically in the System for Award Management (SAM) website at www.sam.gov.





REJECTION OF QUOTATION: Failure to demonstrate compliance will be caused to reject the quote without further discussions. All responsible sources may submit an offer and will be considered.





The following clauses and provisions apply to this acquisition. 52.252-2 Clauses Incorporated by Reference; 52.212-4 CONTRACT TERMS AND CONDITIONS - COMMERCIAL GOODS AND COMMERCIAL SERVICES; 52.212-5 CONTRACT TERMS AND CONDITIONS REQUIRED TO IMPLEMENT STATUTES OR EXECUTIVE ORDERS - COMMERCIAL GOODS AND COMMERCIAL SERVICES applies,; 52.222-3, Convict Labor; 52.233-3, Protest after award; 52.222-26, Equal Opportunity; 52.222-35, Equal Opportunity for Special Disabled Veterans, Veterans of the Vietnam Era, and Other Eligible Veterans; 52.222-36, Affirmative Action for Workers with Disabilities; 52.222-37, Employment Reports on Special Disabled Veterans, Veterans of the Vietnam Era, and Other Eligible Veterans; 52.222-19, Child Labor - Cooperation with Authorities and Remedies; 52.223-2 Affirmative Procurement of Biobased Products Under Service and Construction Contracts; 52.223-15 Energy Efficiency in Energy-Consuming Products; 52.223-17 Affirmative Procurement of EPA-designated Items in Service and Construction Contracts; 52.225-13, Restrictions on Certain Foreign Purchases; 52.232-33, Payment by Electronic Funds Transfer - System for Award Management; applicable to this acquisition; 52.252-1 Solicitation Provisions Incorporated by Reference; 52.212-1 INSTRUCTIONS TO OFFERORS - COMMERCIAL GOODS AND COMMERCIAL SERVICES; 52.223-1 Biobased Product Certification; 52.223-4 Recovered Materials Certification; 52.212-2 Evaluation-Commercial goods and commercial services ; 52.212-3 OFFEROR REPRESENTATIONS AND CERTIFICATIONS - COMMERCIAL GOODS AND COMMERCIAL SERVICES; 52.217-8 Option to Extend Services.





DELIVERY: FOB Destination. USDA -ARS, 13601 Old Cutler Rd, Miami, FL 33158.





QUOTED PRICE MUST INCLUDE: any delivery costs as well as any applicable duties, brokerage, or customs fees.





DELIVERY DUE DATE: The Government requires delivery on or before 30 ARO, however, each offeror shall include their proposed delivery schedule as part of their quotation.





PAYMENT: Any award made under this solicitation is subject to 31 CFR Part 208 which requires all payments made by the government to be made by electronic funds transfer.



Contractors intending to conduct business with the Federal Government MUST register with the System for Award Management (SAM) database prior to submitting quotation. You may register online at www.sam.gov. Any amendment and documents related to this procurement will be available electronically at the Internet site: http://www.beta.SAM.gov.



FAR 52.212-2, Evaluation-Commercial Item, the significant evaluation factors, in the relative order of importance, are (i) technical capability of the item offered to meet the Government requirement including delivery date; (ii) past performance; and (iii) price (based on F.O.B. Destination), technical and past performance are more important than price. Award will be made based on overall BEST VALUE to the Government.





The government anticipates award of a firm fixed priced contract resulting from this solicitation to the responsible offeror whose offer conforms to the specifications that will be the most advantageous to the government in accordance with FAR 13.106-2. Responses shall include technical specifications, descriptive material and capabilities of the offeror’s equipment. Offerors shall identity where the offered item meets or does not meet each of the Government's functional and performance minimum specifications listed herein. All sources wishing to furnish a quotation must respond by 2:00 p.m. central time, June 30th, 2022. Quotations are to be addressed to Richard Hawthorne, Purchasing Agent, at richard.hawthorne@usda.gov. Additional information may be obtained by contacting the Purchasing Agent by email.





Place of Performance:



USDA-ARS

13601 Old Cutler Rd



Miami, FL, 33158





Primary Point of Contact:



Richard “Brad” Hawthorne



Purchasing Agent



richard.hawthorne@usda.gov.




Attachments/Links
Contact Information
Contracting Office Address
  • 141 EXPERIMENT STATION ROAD
  • STONEVILLE , MS 38776
  • USA
Primary Point of Contact
Secondary Point of Contact


History

Related Document

Jun 14, 2022[Sources Sought (Original)] DNA isolation and Whole Genome Sequencing (WGS) of mango germplasm
Jul 22, 2022[Award Notice (Original)] DNA isolation and Whole Genome Sequencing (WGS) of mango germplasm
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