SOLICITATION NOTICE
A -- DETERMINATION OF GENE EXPRESSION PATTERNS FROM TOTAL RNA EXTRACTS OF MOUSE INTESTINAL TISSUE
- Notice Date
- 1/14/2004
- Notice Type
- Solicitation Notice
- Contracting Office
- Environmental Protection Agency, Ord Service Center/Nerl, Rtp Procurement Operations Division, Research Triangle Park, NC 27711
- ZIP Code
- 27711
- Solicitation Number
- RFQ-RT-04-00113
- Response Due
- 2/2/2004
- Archive Date
- 3/2/2004
- Point of Contact
- Point of Contact, Matt Ake, Purchasing Agent, Phone (919) 541-4826
- E-Mail Address
-
Email your questions to U.S. Environmental Protection Agency
(ake.matt@epa.gov)
- Description
- NAICS Code: 541380 THIS IS A SYNOPSIS FOR COMMERCIAL ITEMS PREPARED IN ACCORDANCE WITH THE FORMAT IN SUBPART 12.6, AS SUPPLEMENTED WITH ADDITIONAL INFORMATION INCLUDED IN THIS NOTICE. QUOTES ARE BEING REQUESTED. Additional specifications/information and a copy of the RFQ are available at the following website: http://www.epa.gov/oam/rtp_cmd. The solicitation number is U4RD05, and the solicitation is being issued as a Request for Quotation (RFQ). The associated North American Industry Classification System (NAICS) Code 541380, which has a size standard of $6 million to qualify as a small business, is applicable. This solicitation is 100 percent set aside for small business. A firm, fixed-price purchase order is anticipated to result from the award of this solicitation. Under the project titled DETERMINATION OF GENE EXPRESSION PATTERNS FROM TOTAL RNA EXTRACTS OF MOUSE INTESTINAL TISSUE, the contractor shall use an animal model (i.e., mouse) and/or tissue culture, tissues or cells of mice to prepare total RNA extracts for microarray processing. These extracts will be processed for evaluating changes in mRNA response to virulent versus avirulent strains. Use of the Affymetrix? protocol and scanner for all phases of the preparation and analysis of these samples is required, since it must be compatible with the Affymetrix equipment the US EPA possesses. Mouse genome chips 430A and 430B or the human genome chips U133A and U133B from Affymetrix are used in the testing. The expectation is to be able to differentiate virulence pattens of host mRNA response to waterborne microorganism exposure. The contractor shall perform the standard Affymetrix procedure for labeling and detecting gene expression profiles, as described in the Affymetrix Manual. It is expected that up to 100 samples will be provided for analysis. The samples will be shipped in sets of 10 samples, approximately every 4 to 5 weeks. The contractor shall provide the USEPA Project Officer with raw data files from the above testing. Specific experimental information shall be defined using Affymetrix Microarray Suite on a PC-compatible workstation with a Windows NT operating system. The probe array type, sample description and comments shall be entered in Microarray Suite and saved with a unique experiment name. Data from the Affymetrix system shall be saved, stored and delivered to USEPA on CDs. The following file types are generates by the Affymetrix system and shall be provided by the contractor: .dat, .exp and cel. The contractor shall critically assess output files for the following QC checks: 1. Probe Array Image (.dat) Inspection. Inspect for the presence of image artifacts (i.e., high/low intensity spots, scratches, high regional, or overall background, etc.) on the array, 2. GeneChip Analysis. The contractor shall confirm the alignment of the grid by zooming in on each of the four corners and on the center of the image. If the grid is not aligned correctly, the contractor shall adjust the alignment. 3. Average Background and Noise Values Although there are no official guidelines regarding background, Affymetrix has found that typical Average Background values range from 20 to 100 for arrays scanned with GeneArray Scanners calibrated to the new PMT setting (10% of maximum). Arrays being compared should ideally have comparable background values. 4. Noise (Q) is a measure of the pixel-to-pixel variation of probe cells on a GeneChip. Since a significant portion of Q is based on electrical noise, absolute Q values among scanners will vary. Arrays being compared that were scanned on the same scanner should ideally have comparable Q values. 5. B2 Oligo Performance The boundaries of the probe area shall be identified by the hybridization of B2 oligo, which must be spiked into each hybridization cocktail. Hybridization of B2 shall be highlighted on the image by the following: the alternating pattern of intensities on the border; the checkerboard pattern at each corner; and the array name, located in the upper-left or upper-middle of the array. 6. Poly-A Controls: The controls dap, lys, phe, thr, trp must be run and must be present. 7. Hybridization Controls: bioB, bioC, bioD, and cre. BioB is at the level of assay sensitivity (1:100,000 complexity ratio) and shall be called "Present" at least 50% of the time. BioC, bioD, and cre shall always be called "Present" with increasing Signal values, reflecting their relative concentrations. 8. Internal Control Genes For GeneChip expression arrays, actin and GAPDH shall be used to assess RNA sample and assay quality. Specifically, the Signal values of the 3' probe sets for actin and GAPDH shall be compared to the Signal values of the corresponding 5' probe sets. The ratio of the 3' probe set to the 5' probe set shall be no more than 3. There will be three deliverables: 1.a work plan which describes the intended approach and/or protocol regarding how the work will generate quality data, 2. Ten CD(s) containing the analytical results of each sample for each set of 10 RNA extract samples, 3. a final report. Evaluation criteria to be included (with your quotation) in paragraph (a) of provision 52.212-2 are as follows: 1. Price, 2. Past Performance, 3. Qualification of Key Personnel 4. Adequacy of Facilities. Award will be made to the offeror whose offer is the lowest priced offer meeting all of the technical requirements. Offerors must satisfactorily meet all of the technical requirements to be considered "technically acceptable". All offerors are to include with their offers a completed copy of provision 52.212-3, Offeror Representations and Certifications--Commercial Items. The following FAR clauses apply to this acquisition: 52.212-4, Contract Terms and Conditions--Commercial Items; 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders--Commercial Items and the following additional FAR clauses which are cited in Clause 52.212-5: 52.222-21, Prohibition of Segregated Facilities; 52.222-26, Equal Opportunity, 52.222-35, Affirmative Action for Special Disabled and Vietnam Era Veterans; 52.222-36 Affirmative Action for Handicapped Workers; 52.222-37, Employment Reports on Special Disabled Veterans and Veterans of the Vietnam Era; 52.222-41. The completed Representations and Certifications should be included with the price proposal. All technical questions are to be forwarded via email to the Contract Specialist at the following email address: ake.matt@epa.gov. Offerors should review the Statement of Work and other information posted with this Request for Quotation on EPA's website at the following address: http://www.epa.gov/oam/rtp_cmd. Arrow down to the REQUEST FOR QUOTATION section and click on the solicitation. Arrow down below that section to COMMERCIAL BUY CLAUSES AND FORMS which are provided for your convenience. Please submit two copies of the technical proposal and price proposal. For delivery via the US Postal Service: US Environmental Protection Agency Attention MATT AKE RTP Procurement Operations Division (D143-01) Research Triangle Park, NC 27711. For delivery via courier and hand carried: US Environmental Protection Agency Attention MATT AKE RTP Procurement Operations Division (D143-01) 4930 Page Road Durham NC, 27703. The date for submission of offers has been revised and extended. All offers are now due by 2 February, 2004, 5:00 P.M. EST. No telephonic or faxed requests will be honored.
- Record
- SN00503963-W 20040116/040114212514 (fbodaily.com)
- Source
-
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