SOLICITATION NOTICE
A -- SEQUENCING OF METAGENOME CLONES
- Notice Date
- 6/14/2005
- Notice Type
- Solicitation Notice
- Contracting Office
- Environmental Protection Agency, Ow Service Center, 26 West Martin Luther King Drive, Cincinnati, OH 45268
- ZIP Code
- 45268
- Solicitation Number
- RFQ-OH-05-00107
- Response Due
- 6/29/2005
- Archive Date
- 7/29/2005
- Description
- NAICS Code: 621511 THE GOVERNMENT INTENDS TO CONDUCT A FULL AND OPEN COMPETITION FOR THIS REQUIREMENT. THE TEXT OF THE ANNOUNCEMENT IS BELOW: The National Risk Management Laboratory (NRMRL), located in Cincinnati, OH intends to negotiate using full and open competition for a project entitled "Sequencing of Metagenome Clones". The objective of this project is for the contractor to conduct sequencing of fecal clone libraries developed by EPA personnel and provide sequencing date in electronic form. The contractor shall perform sequencing reactions on PCR products provided by the EPA PO and provide sequence electropherograms to the project officer. Task 1 is as follows: Sequencing of PCR Products?The primary task of this project is to generate sequence information from partial genes (PCR products) obtained from fecal clone libraries. The genes that will be sequenced for this project will be enriched using genomic subtraction methods and total microbial community DNA. After the enrichment step, the genes will be amplified using PCR and directly cloned into TOPO A vectors (Invitrogen Corp). EPA personnel will screen the transformants for presence of inserts (i.e., clones) using PCR. The contractor shall comply with the QA/QC requirements as delineated in Appendix A and consult with the Project Officer prior to performing Task 1 to revise standard operating procedures pertinent to this project, including data delivery and pertinent positive and negative controls. Those PCR reactions that show the presence of inserts will then be sent to the contractor for sequencing. The contractor will perform the following steps: clean all PCR products, sequencing reaction of PCR products, cleaning of sequencing reactions, sequencing electrophoresis, submit electrophorograms to the project officer. The length of the clones will normally be between 400 and 800 bp. Unless otherwise specified, the contractor will perform sequencing in both directions with M13F or M13R primers which will be provided by the sequencing company. Sequencing reactions involving other primers will not exceed 10% of the total sequencing reactions. The project officer will provide the sequences for any new primers. The latter primer will be synthesized by the contractor. It is estimated that 135 96 well plates of PCR products will be processed as part of this task. DELIVERABLES and DELIVERABLES SCHEDULE The primary output of this purchase order will consist of electropherogram with a minimum of 700 bases per reaction with Phred 20 value per single base pair. Preferentially, the data will be accessed by the Project Officer via internet. Alternatively, the contractor will send the data on a CD via airmail. The data will not be shared with a third party unless authorized by the Project Officer. The contractor should maintain a backup of this data for the entire duration of the project. It is expected that the data will be compatible with sequencing analysis software like Sequencer or DNA Star. Due to the number of clones that will be sequenced in this project, the contractor must have high throughput capabilities and must be capable of producing high quality sequence data (i.e. clean readouts). In the cases that the PCR do not exceed 800 bp, it is expected that sequencing in both directions will produce contigs overlapping at least 85%. Microbial Contaminant Control Branch (MCCB) personnel will provide uncleaned PCR products and if necessary will provide copies of agarose gels to show the quality of the PCR. As most genes to be sequenced in this project are less that 800 bases pairs in length, the contractor shall provide a minimum of 700 bases per reaction of high quality Phred 20. Failure to accomplish this would require additional reactions. If EPA personnel provide good quality cultures (as evidenced by gel agarose pictures on PCR reactions), the additional reactions needed to complete the minimum number of bases will be performed by the contractor at no extra charge. The contractor shall complete the work within 12 months of purchase order award. The contractor shall deliver at least 25% of the total analytical services herein requested every (3) three months or 30-35 plates per quarter period. The NAICS code is 621511. The acquisition will be processed under FAR Part 13, Simplified Acquisition Procedures. It is anticipated that a Request for Quote (RFQ) will be issued on or about July 8, 2005. To receive a copy of the RFQ, interested firms must submit a written request to Yvonne Harris, harris.yvonne@epa.gov by Thursday July 7, 2005. Requests via email are preferred or fax is acceptable. The fax number is 513-487-2107. Requests must include company name, mailing address, fax number and email address. Reference RFQ-OH-05-000107. Appendix A Summary of Steps Involved in Task 1 DNA amplification products will be visualized by EPA personnel with agarose gel electrophoresis. PCR products and sequencing products clean up will be performed using the commercially available kits. PCR products will be inserted into pCR2.1 TOPO vectors (Invitrogen, Carlsbad, CS) therefore, M13F and M13R primers should be used in sequencing reactions. However, whenever necessary the sequencing reactions could be performed with other primers that align to sections of the linkers included in this type of vector. Sequences will be compared to public databases for identification and to determine phylogenetic affiliation. Quality Objectives and Criteria Data should be collected under standard procedures and conditions for molecular biology and PCR based analysis. Special Training Requirements The person conducting these experiments must have training and experience in molecular biology techniques in order to obtain quality data. Person must be experienced in sample handling: DNA extraction, purification and qualification; polymerase chain reaction methodologies; polyacrylamide gel methods; cloning and sequencing methods.
- Record
- SN00829766-W 20050616/050614212605 (fbodaily.com)
- Source
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