Whole Genome Bisulfide Sequencing (WGBS)

This is a combined synopsis/solicitation for commercial items prepared in accordance with the procedures contained in FAR Part 12.6, Acquisition of Commercial Items, and FAR Part 13, Simplified Acquisition Procedures, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotes are being requested and a written solicitation will not be issued.

This acquisition is for the selected contractor to provide Whole Genome Bisulfide Sequencing (WGBS) on 100 lettuce accessions for USDA-ARS 1636 E. Alisal St Salinas, Ca

(A) The solicitation number is 12905B21Q0075 and is issued as a Request for Quotation (RFQ).

(B) The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular (FAC) Number 2021-03.

(C) This solicitation is issued as unrestricted. The associated NAICS code is 541380.

(D) Contract Line Items:

            1. Qiagen DNeasy Plant Mini Kit (50 Samples) x 2 each

            2. Thermo Plant RNA Isolation Aid (10ml) x 1 each

            3. DNA Extraction, Library preparation, Illumina, Whole genome bisulfite; Illumina 2x150 bp sequencing, single index (~Gb/sample); whole genome bisulfite analysis x 100 each

(E) Description/Statement of Work/Specification:

Requesting Whole Genome Bisulfide Sequencing (WGBS) on 100 lettuce accessions. WGBS is needed to determine epigenetics differences among cultivars and between cultivated and wild lettuce. Methylation of DNA at cytosine nucleotides forms 5-methylcytosine (5mC), which impacts various cellular processes involving gene expression and chromatin remodeling. These processes can influence development through methylation of promoter regions, cell differentiation, remodeling of chromatin, and suppression of transposable elements. The requested service includes DNA extraction from lettuce seeds, WGBS, and bioinformatics analyses of methylation.

Seeds for the DNA extraction will be provided by the USDA-ARS Salinas, Ca lab immediately after an award is made. Seeds will be mailed to the company by FedEx or UPS. It is desirable to receive sequencing data and results of analyses within two months after the seeds are submitted to the company. Besides sequencing data, the bioinformatics results should include alignment of the sequencing data to the reference genome of lettuce, analyses of methylation for each individual cultivar (or accessions), description and comparison of methylation profiles, identification of CpG islands, and methylation proportional distribution within each genome and comparison between genomes. Data can be delivered on an external hard drive, send via e-mail, or to be available online for downloading.

Species: Lettuce spp.

Sample Type: Seeds

Sequencing Configuration: Illumina, 2x150 bp

Data Output: ~50 Gb per sample

Quality: ≥80% of bases ≥Q30

Deliverables: Raw data in FASTQ format, methylation report, differential methylation report

Turnaround time: 60 days after receipt of reagents

(F) Date(s) and place(s) of delivery and acceptance:

60 days after receipt of reagents

(G) FAR Provision 52.212-1, Instructions to Offerors-Commercial, is incorporated by reference and applies to this acquisition. Please see the attached RFQ terms and conditions for the submission requirements.

(H) Evaluation:

For the evaluation criteria, please see the attached RFQ terms and conditions.

(I) Offerors are required to complete in full FAR Provision 52.212-3, Offeror Representations and Certifications-Commercial Items, with their offer online at SAM: www.sam.gov.  An offeror must state in their offer if they completed FAR 52.212-3 online and that is it up-to-date and valid. See the attached RFQ terms and conditions for more requirements.

(J) FAR Clause 52.212-4, Contract Terms and Conditions-Commercial Items, applies to this acquisition. Please see the attached RFQ terms and conditions for its Addendum.

(K) FAR Clause 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders-Commercial Items, is incorporated and applies to this acquisition. Please see the attached RFQ terms and conditions that are applicable to the acquisition.

(L) A statement regarding any additional contract requirement(s) or terms and conditions (such as contract financing arrangements or warranty requirements) determined by the contracting officer to be necessary for this acquisition and consistent with customary commercial practices: N/A.

(M) The Defense Priorities and Allocations System (DPAS) and assigned ratings are not applicable to this solicitation.

(N) Date, time and place offers are due.

Offers are due by August 11th at 3:00pm Pacific Time

Submit offers to the following e-mail address(es), by the offer due date and time:

Derek.Celedon@USDA.Gov

(O) Any and all questions regarding this solicitation shall be submitted in writing to Derek Celedon no later than August 9th at 12:00 PM Pacific Time.