DNR & RNA SEQUENCING

This is a combined synopsis/solicitation for services in which the government intends to acquire in accordance with FAR Part 13, Simplified Acquisitions Procedures. Department of Commerce (DOC), National Oceanic & Atmospheric Administration (NOAA), National Marine Fisheries Service (NMFS), Alaska Fisheries Science Center, Auke Bay Laboratories has a requirement for DNR and RNA Sequencing. Researchers at the Alaska Fisheries Science Center will use RNA and DNA sequencing in a variety of ways to better understand and manage fish and crab stocks. First, RNA transcriptomics will be used to understand effects of ocean acidification on commercially managed crab species. Understanding how crab adjust to changes in the pH of ocean water can help predict future abundance and therefore quotas of crab in Alaska (>$275M ex-vessel value). Preparation of RNA for sequencing is technically challenging, which is why this work will include the extraction of RNA from the larvae, preparing RNA for sequencing (RNA library building), and sequencing, which takes place on a next-generation sequencer. The sequencing platform (machine) needed is the Illumina HiSeq 4000 or the NovaSeq S4 flowcell. The services to be purchased are RNA extraction, RNAseq library building, and paired-end RNA sequencing of crab larvae using a low yield protocol for RNAseq. We require up to several hundred barcoded samples paired-end sequencing to 100bp, PE100 on an Illumina HiSeq 4000 next-generation sequencing platform. We also will need the laboratory to be willing to pool larvae into a single barcode if there is not sufficient RNA in a single larval sample and to use a low yield protocol. Second, DNA sequencing will be used for continuing assessment of genetic population structure of Alaska groundfish. This work will require two methods of DNA sequencing, RAD (restriction-site associated DNA) sequencing and whole genome sequencing, both of which can be used to obtain single nucleotide polymorphisms (SNPs). SNPs provide information that will be used to understand genetic population structure in commercially managed fish species. RAD sequencing can provide on the order of thousands of SNP markers and whole genome sequencing can provide millions of SNPs. Our DNA sequencing projects do not require any DNA extractions or library prep (those will be done in-house). RAD sequencing will require paired-end sequencing (DNA is bi-directional, and paired end sequencing provides sequence data from both directions), abbreviated PE 150. Single-end reads may be required as well. The sequencing platform (machine) needed for RAD sequencing is the Illumina HiSeq 4000 or the NovaSeq 6000 platform with an S4 flowcell. mRNA sequencing: We require RNA extraction, RNAseq library building, and paired-end RNA sequencing of crab larvae using a low yield protocol for RNAseq. We require 90 barcoded samples paired-end sequencing to 150bp, PE150 on an Illumina HiSeq 4000 next-generation sequencing platform or NovaSeq S4 flowcell. We anticipate that there will be >400ng RNA based on past experience (past extractions yielded >750ng RNA per larval sample). We require at least 50 million reads per individual, so around 7 individuals per lane, if there were 400 million reads per lane. We also will need the laboratory to be willing to pool larvae into a single barcode if there is not sufficient RNA in a single larval sample. We would like the option to repeat this experiment with up to 90 samples in the second year. DNA sequencing: We require sequencing for pre-prepared DNA libraries. We will need at least 4 NovaSeq 6000 lanes (PE150) in the base year and the option of up to 20 NovaSeq 6000 lanes (PE150) and up to 5 lanes of PE150 on a HiSeq4000 in each year, including the option year. TECHNICAL SPECIFICATIONS: RNAseq: The Illumina HiSeq 4000 sequencing platform or NovaSeq with S4 flowcell are required for paired-end (PE150) mRNA sequencing, averaging at least 150 base pairs each read and at least 50 million reads per sample. A low-yield kit for RNA library preparation is preferred for low yield samples, or pooling may be performed as well. We would like Poly-A enrichment/pulldown to remove ribosomal RNA (rRNA). We have 45 samples and require 6-7 lanes for paired-end sequencing (PE150). The Illumina HiSeq 4000 sequencing platform and NovaSeq 6000 platform are required for paired-end DNA sequencing. DELIVERABLE SCHEDULE: October 31, 2020 - October 30, 2021 See attached Statement of Work for more information. All interested concerns must submit a quotation and documentation demonstrating the qualifications to provide services as described above within fifteen (15) days of the publication date of this notice. This announcement constitutes the only solicitation, quotations are being requested and a written solicitation has been issued. A firm-fixed order is anticipated to be issued in within 24 hours of closing date and time. All responses must be in writing and delivery to fax number +1 (555) 000-0000 attention to Heather Mahle, email to contact@example.gov, or provide to address indicated in solicitation. Emailed Correspondence or Response to Solicitation should reference solicitation # ABL-20102, in the Subject line to ensure it is received successfully. Evaluation and resulting award anticipated to within 48 hours of due date. This is a simplified acquisition with an estimated value of less than $150,000.00. The following provisions and clauses shall apply to this solicitation and resultant award. The provisions and clauses may be downloaded at http://www.acqnet.gov/far *** All contractors doing business with this Acquisition Office must be registered and active in the System for Award Management (SAM). No Award can be made unless Cotnractor/Vendor is registered and active in SAM. For additional information visit www.sam.gov. In order to register with SAM and to be eligible to receive an award from this acquisition office, all offerors must have a Dun & Bradstreet Number. A Dun & Bradstreet number may be acquired free of charge by contacting Dun & Bradstreet on-line at www.dnb.com/eupdate or by phone at +1 (555) 000-0000.