66 -- CONSTRUCT, PLATE, PICK AND GRID A BACTERIAL ARTIFICIAL CHROMOSOME (BAC) LIBRARY USING MALE RAINBOW TROUT GENOME

Notice Date

March 26, 2001

Contracting Office

USDA, ARS, North Atlantic Area, Contracting Office, 600 East Mermaid Lane, Wyndmoor, PA 19038

ZIP Code

19038

Solicitation Number

03-3615-01

Response Due

March 29, 2001

Point of Contact

Lisa Botella, Point of Contact, (215) 233-6551, fax (215) 233-6558, Eileen LeGates, Contracting Officer

Description

Correction: The requirement was initially synopsized on March 7, 2001. Amendment No. 01 was issued on March 14, 2001. This amendment provides: 1) Answers to questions received in response to the subject solicitation: QUESTION: Just to be clear- you will want ONE BAC library, but you want three quotes (6X coverage, 8X coverage and 10X coverage). Right? ANSWER: Refer to Amendment No. 01, Item A.2 NOTE. QUESTION: Do you agree with our math- in order to get the various levels of genome coverage for the ~2.5x10E9 base haploid genome trout in the three respective clone totals, the average insert size must be ~135,000 bases (not 130,000 bases as page 6 indicates)? ANSWER: Revises Item A.5(3) from average size of 130,000 base pairs to average size of 135,000 base pairs 135,000. Replaces Page 6 in its entirety. QUESTION: Regarding the nylon filters: the total number of BAC clones does not fit evenly onto filters (for the 6X, 8X or 10X libraries there is one plate too many). I assume you want the whole library to fit on evenly on 22.5cm x 22.5 cm filters (for example with 481 plates on the 10X library you would have 10 filters with 36,864 and one filter with only 384). Note 184,704 / 18,432 = 10.02 filters). If you decrease the total number of plates of each set by ONE PLATE the complete library will fit perfectly on 6, 8 or 10 filters respectively. ANSWER: The number of clones required was calculated based on the genome coverage, not how many can fit on a membrane. The Contractor is required to provide the appropriate number of filters (an odd number of filters is acceptable) in accordance with our specifications in Item A.5(8). QUESTION: Are you sure that you want the filters to be 36,854 total clones? Many researchers are reporting problems in identifying a single clone responsible for a positive hit at this density (so they have to make an additional experiment with several putative positive clones to resolve the hit). We can do 36,854 but we think you would be happier with 18,432 total per filter (however, it doubles the number of filters). ANSWER: Yes, refer to Section A.5(8) in the Technical Specifications. QUESTION: Is it OK to have BAC clones greater than 150,000 bases? (page #6 indicates that 150,000 bases is the maximum size). ANSWER: No, refer to Section A.5(3) in the Technical Specifications. QUESTION: Will the contractor be the "commercial distributor" of the library to interested researchers? ANSWER: No, USDA/ARS/NCCCWA will be the sole owner of the library; 2) Revises A.7, Deliverables within 120 calendar days after receipt of the samples; and 3)THE HOUR AND DATE SPECIFIED FOR RECEIPT OF OFFERS REMAINS AT 4:00 P.M. (LOCAL TIME) ON MARCH 29, 2001. All other information in the initial synopsis is correct. A Copy of this amendment can be faxed to the contractor after receipt of your written request to the Contact Point above.

Record

Loren Data Corp. 20010328/66SOL007.HTM (W-085 SN50H2Y5)