SOLICITATION NOTICE
B -- Sole Source - Focused Genome Sequencing of the Cattle Tick Genome using BAC Clones
- Notice Date
- 3/11/2011
- Notice Type
- Justification and Approval (J&A)
- NAICS
- 541380
— Testing Laboratories
- Contracting Office
- Department of Agriculture, Agricultural Research Service, Southern Plains Area, Area Office, 1001 Holleman Drive East, College Station, Texas, 77840, United States
- ZIP Code
- 77840
- Solicitation Number
- AG-7MN1-S-11-AA04
- Archive Date
- 4/13/2011
- Point of Contact
- Michael A. Douglas, Phone: (979) 260-9480
- E-Mail Address
-
michael.douglas@ars.usda.gov
(michael.douglas@ars.usda.gov)
- Small Business Set-Aside
- N/A
- Award Number
- AG-7MN1-P-11-0012
- Award Date
- 3/14/2011
- Description
- The USDA, ARS, Knipling-Bushland U.S. Livestick Insects Research Laboratory, Kerrville, Texas intends to solicit and negotiate with only one source under the authority of FAR 13.106-1 to Amplicon Express, 2345 NE Hopkins Court, Pullman, WA 99163. This procurement is being conducted under Simplified Acquisition Procedures (SAP) - a follow-on contract for the continued development or production of a major database that will have significant impact on our research goal of obtaining the genome sequence to the Boophilus microplus cattle tick. Amplicon Express synthesized and are storing our 2 current BAC libraries (which consist of 193,000 clones and 504-384 well plates). Amplicon Express also has in their possession, from their original library synthesis for us, the prepared genomic DNA from the Deutsch strain of Boophilus microplus ticks that is necessary for synthesizing new libraries, should these be required. The tick material from this strain is in low supply and the material is needed for several other purposes in our laboratory. By using the prepared material which Amplicon Express has saved from the previous library, we save precious Deutsch tick strain material for other research needs. The following is the minimum work required: We require focused genome sequencing with Illumina runs, bioinformatic assembly, and tech support for genome sequencing of BACs from a BAC library synthesized from Boophilus microplus genomic DNA from the Deutch strain of Boophilus microplus. Clones are to be systematically pooled using 18,432 BAC clones (9,216 from each of two preexisting BAC libraries), Illumina grade BAC DNA prepared from a series of 368 pooled BAC samples, 368 Illumina libraries prepared, ~30 Gbp of Illumina sequencing generated from the libraries, deconvolution analysis performed and a superpool of ALL 18,432 BAC clones and a ~3 Kb Mate Pair library made and one Illumina channel run. All of these data must be assembled and after evaluating initial results, 96 primers at gap frontiers will be designed and used to Sanger sequence the appropriate BAC clone(s) DNA directly for gap closure. We are requesting that Amplicon Express conduct this BAC library focused genome sequencing project because they were the company that synthesized and are storing our 2 current BAC libraries (which consist of 193,000 clones and 504-384 well plates). Amplicon Express also has in their possession, from their original library synthesis for us, the prepared genomic DNA from the Deutsch strain of Boophilus microplus ticks that is necessary for synthesizing new libraries, should these be required. The tick material from this strain is in low supply and the material is needed for several other purposes in our laboratory. By using the prepared material which Amplicon Express has saved from the previous library, we save precious Deutsch tick strain material for other research needs. This pooled BAC focused genome sequencing is proprietary technology developed by Amplicon Express, and only recently made available to the general scientific community. This technology will enable us to produce a draft physical map of the cattle tick genome, using the BACs as source material. The current BAC library clones which are the foundation of this project are stored at Amplicon Express and, by using Amplicon Express to do this genome sequence project, we prevent having to ship these unique and very expensive BAC libraries to a different location. These BAC libraries must remain frozen at -80 degrees C to maintain long term viability. Off-site shipment risks the libraries will thaw during shipment or the plastic library plates that hold the individual clones arrayed in a known pattern might be broken. The Government intends to acquire a commercial item using FAR Part 12. Interested organizations may submit their capabilities and qualifications to perform the effort in writing to the identified point of contact above not later than 3:00pm CST on March 25, 2011. Such capabilities/qualifications will be evaluated solely of determining whether or not to conduct this procurement on a competitive basis. A determination by the Government not to compete this proposed effort on a full and open competition basis, based upon responses to this notice, is solely within the discretion of the government. Oral communications are not acceptable in response to this notice. No RFQ will be issued based upon this Notice of Intent. Interested parties may submit any information for consideration by the Government to Michael Douglas, Contract Specialist at the email address listed above with the solicitation number referenced in the subject line.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/USDA/ARS/SPAO/AG-7MN1-S-11-AA04/listing.html)
- Place of Performance
- Address: USDA, ARS, SPA, Knipling-Bushland U.S. Livestoct Insects Research Laboratory, 2700 Fredericksburg Road, Kerrville, Texas, 78028-9184, United States
- Zip Code: 78028-9184
- Zip Code: 78028-9184
- Record
- SN02399165-W 20110313/110311234544-46534af2c89a9c0e3ca1f35c8f524d50 (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
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