Transcription Factor Chip Sequence

THIS IS A NOTICE OF INTENT TO AWARD A SOLE SOURCE CONTRACT AND IS NOT A REQUEST FOR COMPETITIVE QUOTES. 

The USDA/ARS intends to award a Firm fixed price sole source contract under the authority of FAR 13.106-1(b)(1), single source for purchase not exceeding the simplified acquisition threshold, to:

Diagenode

400 Morris Ave.

Suite 101

Denville, NJ 07834

Contractor’s personnel must have knowledge in ChIP Sequencing and analysis from frozen plant (barley) tissue, not fixed tissue. The contractor should offer expertise in isolating chromatin from plant (barley) tissue. The chromatin isolation and immunoprecipitation are key steps in the success of the project and require demonstrated expertise. Required ChIP-Seq service requirements include a full service starting with frozen barley leaves from which chromatin will be isolated and immunoprecipitated.

To preserve the binding sites at the specified timepoints, it is also imperative that the analysis is from frozen plant (barley) tissue, not fixed tissue. The contractor should also offer expertise in isolating chromatin from plant (barley) tissue. The chromatin isolation and immunoprecipitation are key steps in the success of the project and require demonstrated expertise. We have conducted ChIP-seq research with the vendor Diagenode, who based on their expertise and track record in the field of epigenomics, was awarded a previous contract in FY21 to proceed with one transcription-factor antibody and an infection time-course for this purpose.  There were multiple steps to that contract, and the initial chromatin isolation from cryo-preserved barley tissue, parameters for chromatin shearing, massively parallel sequencing, and follow-up bioinformatics were successfully established.

The work is still ongoing. The initial project was thought to be a one level project.  However, based on the results so far, we plan to take this project to the next level, to answer critical questions related to transcriptional reprogramming and the regulation of crop disease resistance.  

Diagenode has already optimized the highly technical sample preparation, sequencing, and bioinformatic data analysis during the first project, so to transfer to another vendor for phase 2 would be a loss of one-year’s time that we have already invested, as well as the funds for the FY21 award.  A new vendor will need to redo all these initial steps.  In addition, we would need to generate new experimental material, which is a complex and labor-intensive task here in Ames, IA.  Diagenode already has this material in their -80 C Freezers from our work with them in the past year, and thus the continuity of the project would remain as we move forward. 

Part 2 of the project would then involve the complete protocol we have done in the past year, only with four additional antibodies

The NAICS code for the expected acquisition is 541380, with a Size Standard $16.5 million and the PSC Code is 6640.

NO solicitation or solicitation package will be issued.  This notice of intent is not a request for competitive quotes; however, interested persons may identify their interest and capability to respond to this requirement.  All information received by 2:00 PM Central Time on September 8, 2022 will be considered by the Government.  Responses shall be submitted to Melissa Grice at melissa.grice@usda.gov.  The e-mail subject line shall state:  Transcription Factor Chip Sequence - Notice of Intent to Sole Source.  A determination by the Government not to compete this proposed contract based on responses to this notice is solely within the discretion of the Government. 

NO TELEPHONE REQUESTS WILL BE HONORED.