SOLICITATION NOTICE
A -- Custom BAC Libraries
- Notice Date
- 9/9/2008
- Notice Type
- Combined Synopsis/Solicitation
- NAICS
- 621511
— Medical Laboratories
- Contracting Office
- Department of Agriculture, Agricultural Research Service, Pacific West Area Office, 800 Buchanan Street, Albany, California, 94710-1105
- ZIP Code
- 94710-1105
- Solicitation Number
- AG95CVS08a153
- Response Due
- 9/15/2008
- Archive Date
- 9/30/2008
- Point of Contact
- Frederick O. Gifford,, Phone: 510-559-6017
- E-Mail Address
-
fred.gifford@ars.usda.gov
- Small Business Set-Aside
- N/A
- Description
- The US Department of Agriculture, Agricultural Research Service in Hilo, Hi has a requirement for Custom BAC Library from Ananas comosus pineapple with 10x coverage and 2 sets of filters from screening. Custom BAC library from Dimocarpus Iongan with 10x coverage and two sets of filters for screening. Custom BAC library from Bactrocera Dorsalis oriental fruit fly with 10.7x coverage and two sets of filters for screening. Creation of three BAC libraries One of an insect with a genome between 419 and 619 Mbp and the second and third from two different Plants; one with a genome estimated at -600 Mbp and the other at -690 Mbp. Each BAC library will consist of positive BAC clones arrayed in plates (384 well format). Vendor shall provide library screening tool description as follows; Nylon Filter w/18,432 colonies (in duplicate) filter should be 22cm X 22 cm. Entire resource for the individual BAC libraries should be on 3 filters. Vendor to hold duplicate BAC library for a period of not less than 2 years for each of the three BAC libraries (4 years in the case of the Oriental fruit fly BAC library). Amplicon Express company specializes in genomic DNA library construction including BAC and Fosmid libraries. Amplicon Express (AEX) has constructed one of the largest number (+975) of high quality BAC libraries, hundreds of Cosmid libraries and Fosmid libraries in the past. Plus thousands of randomly sheared shotgun libraries for DNA sequencing. They have constructed hundreds of genomic libraries and because of their deep knowledge and experience, they have succeeded in making libraries from difficult to work with species; cases where other companies have failed. Also because of their expertise, they have one of the fastest turnaround times (2-4 weeks). They have developed an in house, unique, and patent pending polymerase chain reaction (PCR) amplification technique to screen genomic libraries by so-called "pools" and "superpools" for target genes. We have the option not only of requesting the superpools be made in the future, but we can also request that they actually screen the library for a target gene of our choosing with this method or by non-radioactive, DIG-labeled DNA probes, collectively services that are not even offered by other genomic construction companies. In addition to shipping us a copy of the library, they keep a copy of the BAC library at their own facilities; this service is not offered by most other companies. It is important that we have a separate copy of the BAC library at the company facilities because the library needs to be kept at -80°C to retain good integrity/viability, thus we will not lose the entire BAC library in case our freezer breaks down. More importantly, housing a copy of the BAC library at the company facilities is necessary so that they have the ability to make more screening filters from the library should we need it. We do not have the ability to make screening filters from the BAC libraries since we have no robotic colony pickers at our USDA facility. Since the main activity and function of the BAC libraries for the various purposes are to screen filters of the BAC libraries for certain target genes, the housing of the library at the company is an essential continued customer service. The option of creation of PCR superpools, creations of new filters, requires that the company has access to the entire library which they will, since they will keep at copy on company premises. The samples in the arrays are not 100% due to limitations of the picking robot (something that occurs with all companies), so they track the missing colonies (<3%) and include the documentation along with the library - this information is important with regards to knowing the true genome coverage of the library. Amplicon Express is the only one of four companies investigated with a proprietary method to reduce organelle DNA (specifically chloroplast DNA) contamination in the BAC genomic (nuclear) DNA library. As an example of the importance of this is demonstrated in the whole genome shotgun sequencing of papaya (Ming et al, 2008, Nature 452: 991-996), the reported organelle DNA (chloroplast and mitochondrial) represented sequence contamination of 19% of the total sequence information. This contamination can vastly change genome coverage based on number of clones alone. A RFQ is not available for this requirement the USDA intends on negotiating with the Amplicon Express on a sole source basis. See numbered note 22
- Web Link
-
FedBizOpps Complete View
(https://www.fbo.gov/?s=opportunity&mode=form&id=9893e018a791a4ebfa2ca5735b012488&tab=core&_cview=1)
- Place of Performance
- Address: Hilo, HI, Hilo, Hawaii, United States
- Record
- SN01664992-W 20080911/080909223158-9893e018a791a4ebfa2ca5735b012488 (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
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