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B -- Prokaryotic Genome Shotgun Sequencing to 5X Coverage

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Reference-Number-PSM-512-03Federal

Contract Overview

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AI Contract Overview

The contract from the USDA Agricultural Research Service in Albany, California, involves sequencing a prokaryotic genome of approximately 2.2 megabases using whole genome shotgun sequencing to achieve 5X coverage. The work requires the preparation of two genomic libraries from supplied DNA: a high copy plasmid library with inserts ranging from 1.5 to 3.0 kb and a Fosmid library with 40 kb inserts, both derived from mechanically sheared DNA. The sequencing process will encompass key activities such as transformation and plating of clones, automated colony picking and arraying into 384-well glycerol stocks, culturing, and purification of clones. Sequencing will be conducted through dye-terminator fluorescent reactions on both ends of the plasmid clones, followed by purification, detection of fragments, and generation of data files including chromatograms, PHRED quality scores, and FASTA sequences. Deliverables will be transmitted to the USDA via FTP. A successful sequencing read is defined by a minimum yield of 200 high-quality bases with a PHRED score above 20, and average read lengths are expected to fall between 600 and 650 bases. The contract specialist listed for this requirement is Clarice E. Dixson.

General Info

USDA contract for 2.2 Mb prokaryotic genome sequencing using plasmid and Fosmid libraries.

Agency

N/A

NAICS

541715 - Research and Development in the Physical, Engineering, and Life Sciences (except Nanotechnology and Biotechnology)

Place of Performance

USDA, Agricultural Research ServiceWestern Regional Research Center 800 Buchanan Street Albany, CA 94710

Set-Aside

NONE

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Timeline

PhasePresolicitation

PostedJun 20

Presolicitation

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Organization & Contact Information

AgencyN/A

Contacts1 person available

OfficeN/A

Organization / Agency

N/A

Office AddressN/A

Contacts

Clarice E. DixsonContract Specialist

contact@example.gov

+1 (555) 000-0000

Full Description

The USDA, Agricultural Research Service in Albany, California has a requirement for a prokaryotic genome of approximately 2.2 megabases sequenced by shotgun sequencing to 5X coverage. Whole genome shotgun libraries must be prepared from the genomic DNA provided by the USDA. Two libraries shall be constructed from mechanically sheared DNA and will be used for paired-end sequencing. The libraries should include a 1.5 - 3.0 kb insert high copy plasmid library and a 40 kb Fosmid library. The shotgun sequencing services should include (1) Transformation and agar plating of genomic library clones, (2) automated colony picking and arraying of clones into 384 well format glycerol stocks, (3) culturing and purification of library clones, (4) dye-terminator fluorescent sequencing reactions from each vector end of plasmid clones, (5) purification of sequencing reactions, (6) detection of sequencing fragments, and (7) creation of chromatograms, PHRED quality scores, and FASTA sequence files that will be delivered to the USDA via FTP. A passing sequencing read will be defined as an attempt that yields greater than 200 high quality bases (>PHRED 20). Average high quality read lengths should be approximately 600 - 650 bp.

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