SOURCES SOUGHT
99 -- BACTERIAL LAB ANALYSIS
- Notice Date
- 1/15/2020 9:01:56 AM
- Notice Type
- Sources Sought
- NAICS
- 541380
— Testing Laboratories
- Contracting Office
- OFC OF ACQUISITION GRANTS-DENVER DENVER CO 80225 USA
- ZIP Code
- 80225
- Solicitation Number
- 140G0220Q0041
- Response Due
- 1/22/2020 8:59:59 PM
- Archive Date
- 02/22/2020
- Point of Contact
- Theeke, Cheryl
- E-Mail Address
-
ctheeke@usgs.gov
(ctheeke@usgs.gov)
- Awardee
- null
- Description
- Special Notice of Intent to Award a Sole Source Procurement THIS IS NOT A REQUEST FOR QUOTE. THIS IS A NOTICE OF THE GOVERNMENT'S INTENT TO ISSUE A SOLE SOURCE AWARD. This Notice is to announce that the U.S. Department of the Interior (DOI), U.S. Geological Survey (USGS), is proposing to negotiate a contract with the University of Georgia, Georgia Genomics and Bioinformatics Core, on a sole source basis. The requirement is for 16S rRNA and 18S rRNA (amplicon) next generation sequencing targeting the Bacteria 16S rRNA/Archaea 16S rRNA gene and Eukaryote 18S rRNA gene. Work will include library preparation using a targeted amplicon sequencing protocol for Illumina-based sequencing platforms (Illumina MiSeq) and sequencing of amplicons on the Illumina MiSeq. The proposed action is for services for which the Government intends to solicit and negotiate with only one source under the authority FAR 13.106-1(b)(1). The reason justifying this sole source procurement is that the Government believes only one responsible source can provide the services that will satisfy the agency's requirement. The following services are provided: Services, non-personal, to provide all plant equipment, labor, travel, and materials including replacement parts (unless otherwise provided herein) necessary for the analysis of bacterial samples to produce high quality data as described in the following Work Requirements and Standards. Work Requirements and Standards: The technical requirements list current methods used by the project. The lab shall maintain those methods or equivalent in terms of sample processing, analysis, and data reporting. The laboratory shall also have the personnel and equipment necessary to process the estimated sample volume and tasks as outlined in the technical requirements. A. Technical Requirements. 1. Description. Genomic DNA will be sent frozen and on dry or wet ice to the laboratory for library prep, library pooling, pre-sequencing QC, and sequencing. Library prep will be a targeted amplicon sequencing protocol for Illumina MiSeq platform that includes two polymersase chain reaction (PCR) steps. The first step of PCR will use target universal Bacteria 16S rRNA and Archaea 16S rRNA specific primers (revised 515F/806R (V4 hypervariable region) revised by Parada et al. 2015 and Apprill et al. 2015) Eukaryote 18S rRNA (targeting 18S V4 region) with overhang sequences to amplify selected marker and enable barcoding. The second round of PCR will add Illumina compatible barcodes to each amplicon. Library pooling of up to 96 samples per plate by PCR will occur followed by pre-sequencing QC (via Qubit, FA, or Kapa system). Barcoded amplicons will be sequenced on the Illumina Miseq (500 cycles) (v2) flow cell for 250PE reads (maximum number of reads=24-30 million reads; 7.5-8.5 Gbases). Demultiplexed, raw sequencing data will be provided for all runs. Sequencing facility will notify researchers if samples do not pass quality control checks following library prep, prior to sequencing, or after sequencing analysis. 2. Criteria for acceptance of Product or Service. Data should be accompanied by a spreadsheet listing sample identifiers, sample barcodes, number of reads, read quality scores, % of read quality scores over a score of 30, and yield (Mbp). The overall % of quality scores over a score of 30 should be 75% per sequencing run. B. Deliverables. 1. Characteristics for work product described in II.A.1., identified by name and quantity. � Approximately 150-250 samples per year for Bacteria/Archaea 16S library prep and sequencing. � Approximately 100-150 samples per year for Eukaryotic 18S library prep and sequencing � Provide demultiplex and raw sequencing data for all data. � Spreadsheet listing sample identifiers, sample barcodes, number of reads, read quality scores, % of read quality scores over a score of 30, and yield (Mbp). � Written document describing methods used for all processes including library preparation through sequencing and provide all details on reagents, kits, and equipment used. 2. Delivery dates for work/product to be completed and point of delivery. � Data and accompany methods are to be delivered no later than 60 business days following receipt of samples for library prep. The contractor shall provide the USGS with access to and FTP server or other secure server for downloading sequencing data. � All corresponding quality control information including barcodes (tags), library prep kit information, and primers (as appropriate) should be accompanied with data delivery. � Provide access to data for downloading for at minimum 60 days following receipt of sequencing data.
- Web Link
-
SAM.gov Permalink
(https://beta.sam.gov/opp/1082fbf1eebd4ff3a75d194cd1d328d3/view)
- Record
- SN05536213-F 20200117/200115230201 (samdaily.us)
- Source
-
SAM.gov Link to This Notice
(may not be valid after Archive Date)
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