MODIFICATION
B -- Sequence ChIP-Seq, MeDIP-Seq and RNA-Seq experiments followed by quantitative informatic analysis
- Notice Date
- 1/14/2011
- Notice Type
- Modification/Amendment
- NAICS
- 541712
— Research and Development in the Physical, Engineering, and Life Sciences (except Biotechnology)
- Contracting Office
- Other Defense Agencies, Uniformed Services University of the Health Sciences, Directorate of Contracting, 4301 Jones Bridge Road, Bethesda, Maryland, 20814-4799
- ZIP Code
- 20814-4799
- Solicitation Number
- HU00011366
- Point of Contact
- Christina Johnson, Phone: 3012953069, Zamora Olin, Phone: 301-295-3922
- E-Mail Address
-
cjohnson@usuhs.mil, Zamora.Olin@usuhs.mil
(cjohnson@usuhs.mil, Zamora.Olin@usuhs.mil)
- Small Business Set-Aside
- N/A
- Description
- The purpose of this amendment is to change the response date. 1. The required response date/time has changed from January 18, 2011 at 12:00 pm to January 25, 2011 at 12.00 p.m. This requirement is full and open. The Uniformed Services University of the Health Sciences (USUHS) located on the National Naval Medical Center (NNMC) in Bethesda, MD intends to solicit offers to sequence ChIP-Seq, MeDIP-Seq and RNA-Seq experiments followed by quantitative informatic analysis. This is a combined synopsis/solicitation for a commercial items prepared in accordance with the format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; offers are being requested and a written solicitation will not be issued. The solicitation number is HU00011366, and it is being issued as a Request for Quotation (RFQ). The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2005-47, effective 13 DEC 2010. NAICS code 541712, Research and Development in the Physical, Engineering, and Life Sciences (except Biotechnology) applies. This is a firm-fixed price requirement. The expected period of performance is 15 February 2011 - 15 December 2011. All analysis and requested data shall be completed and delivered during this time. Price: The contractor should provide pricing as set up below: Contract Line Number (CLIN), description, and unit of issue. Your offer is based on the services outlined in the enclosed statement of work. CLIN 0001 Sequencing Chip-Seq, MeDIP-Seq, and 1.00 JB tiny_mce_marker________ RNA-Seq Experiments Statement of Work (SOW) The Department of Anatomy, Physiology and Genetics at the Uniformed Services University of the Health Sciences (USUHS) has a requirement to: 1) To identify alterations in gene-specific chromatin modifications, DNA methylation and gene expression changes in mice brain tissues impacted by long-term exposure to embedded pellets of tungsten alloy and its constituent metals including tungsten, nickel & cobalt as well as tantalum (negative control inert metal); and 2) To identify alterations in gene-specific chromatin modifications, DNA methylation and gene expression changes in mice brain tissues impacted by traumatic brain injury. To achieve these specific aims, USUHS will perform whole-genome ChIP-Seq (for chromatin modifications), MeDIP-Seq (for DNA methylation changes) and RNA-Seq (for alterations in gene expression). USUHS will be responsible for performing Chromatin immunoprecipitation (ChIP), methylated DNA immunoprecipitation (MeDIP) and RNA isolation assays with brain tissue derived from mice subjected to traumatic brain injury or mice with implanted metal pellets of tungsten alloy and its constituent metals including tungsten, nickel, cobalt, tantalum (negative control inert metal) as well as naïve controls (with no injury or pellet). These high quality DNA (from ChIP & MeDIP protocols) and RNA samples with be sent to the contractor for performing next generation sequencing ChIP-Seq, MeDIP-Seq and RNA-Seq experiments followed by quantitative informatic analysis to normalize the raw sequencing data and align the data with mice genome sequence. DELIVERABLES: 1. DNA and RNA samples will be sent to the contractor to: a. Perform quality control and quality assurance experiments on the DNA and RNA samples provided by USUHS. b. Perform the ChIP-Seq, MeDIP-Seq and RNA-Seq experiments for the samples from pilot study. The completion of this task shall establish the quality of samples and generate the quality of the final data. 2. The Contractor shall process thirty (30) samples for whole-genome ChIPSeq or MeDIP or RNASeq, as provided by USUHS. - The samples provided shall be processed within sixty (60) days (upon mutual agreement) of receipt by the contractor. The samples shall be processed and bar-coded using indexing which enables the pooling of many samples into a single sequencing experiment. - The total number of samples for whole-genome ChIPSeq or MeDIP or RNASeq that will be provided to the Contractor by USUHS is: • Five (5) mice per group for ChIPSeq (3 antibodies and Input); • Five (5) mice per group for MeDIP; and • Five (5) mice per group for RNASeq - Each for aforementioned groups of animals shall be tested for the following: a. Tungsten-alloy b. Tungsten c. Nickel d. Cobalt e. Tantalum f. Naïve control g. Single TBI (Traumatic brain injury) h. Repetitive TBI i. Sham Single TBI j. Sham Repetitive TBI A total of 300 samples shall be provided by the Contractor (200 ChIPSeq samples, 50 MeDIP samples, and 50 RNASeq samples). 3. The Contractor shall perform the ChIP-Seq, MeDIP-Seq and RNA-Seq experiments with the samples provided within sixty (60) days (upon mutual agreement). 4. The Contractor shall perform informatic analysis to quantify and normalize the raw sequencing data and align the data with mice genome sequence. 5. The Contractor shall provide the data generated within sixty (60) days (upon mutual agreement) of receipt of the samples from USUHS. 6. USUHS will perform the final data storage/management, followed by statistical evaluation/data-analysis. USUHS will also validate the CHIPSeq, MeDIP and RNA-Seq results by conducting quantitative real time PCR analysis of the top hits identified from the data analysis of CHIPSeq, MeDIP and RNA-Seq experiments. USUHS will then publish the findings of the results. Upon completion of the processing of each sample batch, as provided by the USUHS, the Contractor shall provide a briefing or report synopsis to the designated USUHS point of contact along with the results of each sample batch. The Contractor shall also provide all necessary research support to ensure the successful completion of the project. GOVERNMENT'S RESPONSIBILITIES: The Government will deliver the following to the Contractor: 1) Chromatin immunoprecipitated DNA samples 2) DNA samples enriched for methylated fragments 3) RNA samples PERFORMANCE PERIOD: The period of performance is 15 February 2011 - 15 December 2011. All analysis and requested data shall be completed and delivered during this time. This requirement as being set forth by the USUHS shall be driven by results and the scientific requirements related to the quality of the results received and the direction taken by the achieved results. All available access to data analyzed and submitted by the Contractor will be restricted until their finalized publication. EVALUATION FACTORS: The successful awardee shall be able to analyze and process samples, and provide high quality data from ChIP-Seq, MeDIP-Seq and RNA-Seq experiments conducted at the USUHS. Contractors shall address all evaluation factors within fifteen (15) pages in length. Offers that exceed the page limit will be evaluated using only the first fifteen (15) pages. The following criteria will be used to evaluate all offers submitted: A. Delivery 1. The Contractors shall posses the resources and equipment required to perform these services in the designated period of performance. 2. The Contractor shall be available, if required, to provide scientific collaborative to the Government after the contract has expired. If additional collaboration is needed, a separate requirement will be issued at a later date. 3. The Contactor shall possess access to and knowledge of unpublished protocols that would assure us that the results will be of the highest quality. 4. The Contractor shall guarantee the transfer of all finalized results using one common platform that will be accessible to USUHS personnel and designated users. B. Past Performance 1. The Contractor shall posses satisfactory past performance which highlights: - An established scientific track record documented by PubMed. - Significant research achievements documented by publications in professional and academic journals. - Recognized by NIH Epigenome RoadMap Program. - Recognized by epigenetic research community. C. Price BASIS FOR AWARD: Award will be made to the responsible, technically acceptable offeror, whose quote, conforming to the combined Synopsis/Solicitation, offers the lowest evaluated price. PROVISIONS AND CLAUSES The following FAR and DFAR provisions and clauses apply to this solicitation and are incorporated by reference: 52.204-7 Central Contractor Registration; 52.212-1 Instructions to Offerors-Commercial Items; 52.212-2 Evaluation-Commercial Items; 52.212-3 Alt I Offeror Representations and Certifications - Commercial Items (Offerors are advised to include a completed copy of this provision with their quote or a statement stating that it is available via the ORCA website, http://orca.bpn.gov.); 52.212-4 Contract Terms and Conditions-Commercial Items; 52.212-5 Contract Terms and Conditions Required to Implement Statutes or Executive Orders - Commercial Items 52.219-28 Post-Award Small Business Program Representation. 52.222-3 Convict Labor, 52.222-19 Child Labor - Cooperation with Authorities and Remedies, 52.222-21 Prohibition of Segregated Facilities, 52.222-26 Equal Opportunity, 52.222-35 Equal Opportunity for Disabled Veterans (over 100K) 52.222-36 Affirmative Action for Workers with Disabilities, (Over 15K) 52.222-37 Employment Reports on Special Disabled Veterans (When 52.222-35 Applies) 52.223-18 Contractor Policy to Ban Text Messaging While Driving 52.225-13 Restrictions on Certain Foreign Purchases, and 52.232-33 Payment by Electronic Funds Transfer --Central Contractor Registration 52.222-41 Service Contract Act 252.204-7004 Required Central Contractor Registration. Alternate A; 252.212-7001 Contract Terms and Conditions Required to Implement Statutes or Executive Orders Application to Defense Acquisition of Commercial Items 252.225-7000 Buy American Act--Balance of Payments Program Certificate, 252.232-7003 Electronic Submission of Payment Requests; and 252.247-7023 Transportation of Supplies by Sea Alternate III. 52.252-2 Clauses Incorporated by Reference This contract incorporates one or more clauses by reference with the same force and effect as if they were given in full text. Upon request, the Contracting Officer will make their full text available. Also, the full text of a clause may be accessed electronically at this/these address(es): http://www.arnet.gov/far To be eligible for contract award, all contractors must be registered in the Central Contractors Register (CCR), http://www.ccr.gov, and be registered with the Online Representations and Certifications Application (ORCA), http://orca.bpn.gov. For instructions on registering, please visit the individual web sites. Responsible sources shall provide the following: 1. Price quote which identifies the requested item(s) 2. Total price 3. Address all evaluation factors. It is essential for the offerors to provide sufficient documentation, etc., in order for the Government evaluation team to make an adequate technical assessment of the offer as meeting technical acceptability. The evaluation package should be no more than fifteen (15) pages in length. 4. Prompt Payment Terms 5. Remittance address, Tax Identification Number, DUNS number and Cage Code Direct any questions or inquiries in writing by January 7, 2011 to Christina Johnson, Contract Specialist, via e-mail: cjohnson@usuhs.mil, ATTN: HU00011366. Responses to this solicitation are due 18 January 2011 at 12:00 p.m. eastern local time. LATE QUOTES MAY NOT BE CONSIDERED FOR EVALUATION. Quotes may be emailed to Christina Johnson at cjohnson@usuhs.mil, ATTN: HU00011366. Please reference the solicitation number on your quote.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/ODA/USUHS/BethesdaMD/HU00011366/listing.html)
- Place of Performance
- Address: Bethesda, Maryland, 20814, United States
- Zip Code: 20814
- Zip Code: 20814
- Record
- SN02360894-W 20110116/110114234355-4dd8e1f5aaf6189bbe3c0a519328f78f (fbodaily.com)
- Source
-
FedBizOpps Link to This Notice
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