68 -- Construction of a normalized plasmid cDNA library and the subsequent sequencing of 15,000 ESTs

THIS MODIFICATION IS TO ALERT VENDORS THIS COMBINED SYNPOPSIS/SOLICITATION FOR COMMERCIAL ITEMS WILL NOT BE AWARDED. IT IS BEING RE-ADVERTISED UNDER SOLICITATION NUMBER AG-64PP-S-06-0002. This announcement constitutes the only solicitation; quotes are being requested and a written solicitation will not be issued. Solicitation No. 64PP-6-0001 is being issued as a Request for Quotes (RFQ). This solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2005-09. The NAICS code applicable to this acquisition is 325414. For a company to qualify as a small business, the small business standard is 500 employees. The USDA, ARS, MWA, Plant Genetics Research Unit, Columbia, MO has a requirement/need for the construction of a normalized plasmid cDNA library and the subsequent sequencing of 15,000 ESTs, from Sprorobolus stapfianus leaves. The starting material will be provided by Plant Genetics Research Unit, Columbia, MO. CLIN No. 1 - Construction of a normalized plasmid cDNA library. CLIN No. 2 - EST Sequencing. CLIN No. 3 - Delivery of a glycerol stock of the transformed cDNA library. THE SALIENT CHARACTERISTICS: the construction of a normalized plasmid cDNA library and the subsequent sequencing of 15,000 ESTs, from Sprorobolus stapfianus leaves must meet or exceed these minimum requirements (1) Must construct a normalized cDNA library from total Sprorobolus stapfianus RNA derived directly from material or provided by PGRU researchers. cDNA synthesis should be of high efficiency and quality and utilize a rare restriction enzyme site contained in Primer Adapter sequence to increase cloning efficiency and ensure directionality. cDNAs must be subjected to size selection. No adapter ligation is to be used to construct the library (this can be achieved if an appropriate rare cutter restriction site is contained in the primer adapter used for cDNA synthesis). A positive control should be used to monitor each step of library construction including overall efficiency. A high copy number plasmid containing a suitable multiple cloning site must be used to generate the library. The vector containing T7 promoter and SP6 promoter sites, an F1 phage origin of replication and an ampicillin resistance gene will be used. The manufacturer must deliver a minimum of 3 x 106 primary clones (cfu) with an average inserted cDNA of greater than 1.0 kb in size and a minimum of at least 87% of the clones containing inserts. (2) EST Sequencing (sequencing of inserts). Manufacturer will provide colony picking of 15,000 clones from the library for DNA purification and subsequent sequencing. Sample genealogy and quality parameters should be tracked on a well-by-well basis to ensure accurate sample tracking and data quality, to give confidence in the integrity of the sequence data. The tracking system should allow real-time assessment of pipeline success rates, quality scores, overall signal strengths and read lengths to maintain optimum performance and maximize sequence quality. A passing sequence read should match the National Human Genome Research Institute's standard definition; that is an attempt that yields a minimum of 100 PHRED 20 bases. The expected quality should have pass rates for high copy plasmids of 85-90% with average Phred 20 read-lengths of 550-650 bp standard read type. Manufacturer will deliver sequence data as trace files (.scf or .ab1). A standard nomenclature system will be utilized: - CustomerAssignedPlateName'_Well ID'_F or R. FileType. In addition, sequence files (.seq) and quality files (.qual) in FASTA format will be made available. Preferably all information can be transferred via FTP. (3) Manufacturer will deliver a glycerol stock of the transformed cDNA library. The customer will receive glycerol stocks of normalized library in addition to the primary library if remaining after the normalization process. Manufacturer will also deliver any arrayed library plates that were generated for downstream sequencing by the Manufacturer. REJECTION OF QUOTATION: Failure to demonstrate compliance will be cause to reject the quote without further discussions. All responsible sources may submit an offer which will be considered. The following provisions and clauses apply to this acquisition and can be found in full text at http://www.acquisition.gov/comp/far/index.html. FAR 52.252-1, Solicitation Provisions Incorporated by Reference are as follows: FAR 52.212-1, Instructions to Offerors Commercial Items; FAR 52.212-2, Evaluation - Commercial Items; FAR 52.212-3, Offeror Representations and Certifications Commercial Items (Provide with Quote); FAR 52.204-7, Central Contractor Registration (All Offerors must be registered in the Central Contractor Registration (CCR) Database in order to receive an award. The website address for registration is: http://www.ccr.gov; and FAR 52.222-22, Previous Compliance Report. FAR 52.252-2, Clauses Incorporated by Reference, FAR 52.212-4, Contract Terms and Conditions Commercial Items; FAR 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders - Commercial Items apply to this acquisition. The following FAR clauses cited in 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders - Commercial Items are applicable to this acquisition: FAR 52.222-3, Convict Labor (E.O. 11755); FAR 52.222-19, Child Labor; 52.222-21, Prohibition of Segregated Facilities; 52.222-26, Equal Opportunity; 52.222-35, Equal Opportunity for Special Disabled Veterans; 52.222-36, Affirmative Action for Workers with Disabilities; 52.222-37, Employment Reports on Special Disabled Veterans; 52.225-13, Restriction on Certain Foreign Purchases; 52.232-33, Payment by Electronic Funds Transfer - Central Contractor Registration (31 U.S.C. 3332); 52.232-36, Payment by Third Party (31 U.S.C. 3332) and FAR 52.233, Protest After Award. The above FAR clauses may be viewed at http://www.acquisition.gov/comp/far/loadmainre.html. SHIPPING: FOB Destination. 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, and unit price per CLIN and total price; 2) at least 3 to 5 references for the proposed service. References must have received the proposed services within the last three (3) calendar years (Government references preferred but will accept commercial references). References shall be provided for the service proposed and if possible include the email address of the person to be contacted; and 4) Offerors shall include a completed copy of the provisions FAR 52.212-3, OFFEROR REPRESENTATIONS AND CERTIFICATIONS - COMMERCIAL ITEMS, with this offer; a copy of this provision may be obtained at http://www.acquisition.gov/comp/far/loadmainre.html. DELIVERY TO: USDA-ARS, Columbia, MO. QUOTE PRICE MUST INCLUDE any freight or shipping, as well as any applicable duties, brokerage, or customs fees. DELIVERY DATE DUE: The Government requires delivery on or before 8 weeks after receipt of government furnished material, however, each offeror shall include their proposed delivery schedule as part of their quotation. 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. EVALUATION & AWARD FACTORS - The contract resulting from this solicitation will be awarded to the responsible party whose offer, conforming to the solicitation, is determined most advantageous to the government, cost, and other factors considered. Each Quote shall respond to each of the evaluation factors identified below. With the exception of past performance, a technical evaluation will be performed on each quote based solely on the information furnished and not on previous knowledge or associations. The evaluation factors are as follows: (1) Technical Evaluation Factors: A) All quotes will be rated against the salient characteristics and minimum requirements. B) Delivery. C) Warranty. The Offeror shall extend to the Government the full coverage of any standard commercial warranty normally offered in a similar commercial sale, provided such warranty is available at no additional cost to the Government. Acceptance of the standard commercial warranty does not waive the Government's rights under the Inspection clause nor does it limit the Government's right with regard to the other terms and conditions of this contract. In the event of a conflict, the terms and conditions of the contract shall take precedence over the standard commercial warranty. The contractor shall provide a copy of its standard commercial warranty (if applicable) with this response. Any amendment and documents related to this procurement will be available electronically at the Internet site: http://www.fbo.gov. Potential offerors will be responsible for downloading their own copy of those documents related to this procurement, if any. Furnish Quotes to Karen L. Reddick, Contracting Officer, USDA, ARS, MWA, 493 Vandiver Drive, Suite D, Columbia, MO 65202, no later than 2:00 p.m., July 24, 2006. Quotes and other requested documents may be provided by facsimile to (573) 449-6148 if desired. Additional information may be obtained by contacting the Contracting Officer at (573) 875-5291 or email below.