Statement of Work - Microbiome-Sequencing Q0252.pdf
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- Attached to
- DNA Sequencing Federal contract opportunity
- Solicitation number
- 12505B23Q0252
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This statement of work outlines requirements for microbiome sequencing services for the Department of Agriculture Agricultural Research Service. The contractor will prepare amplicon libraries and perform Illumina PE250 high throughput sequencing for 312 greenbug insect samples, yielding a minimum of 50,000 reads per sample, to analyze the impact of host plant species, cultivar, biotype, and time on the insect gut microbiome. The contractor must provide fastq sequence files accessible via their FTP server and conduct sample quality control and library preparation. The government will provide PCR products for sequencing. The contractor's personnel must be highly trained in the required sequencing and bioinformatics tasks. The USDA retains rights to the sequence data.
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Other files for this federal contract opportunity
| File | Type | Posted |
|---|---|---|
| Revised SOW Q0252.pdf | ||
| RFQ Industry Questions and Government Responses Q0252.pdf | ||
| SF 1449 Q0252.pdf | ||
| Clauses and Provisions 31 July Q0252.pdf |
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Text version
Statement of Work RNA-Sequencing
GENERAL INFORMATION
1.0 Scope of Work: Contractor will prepare amplicon libraries and perform quality control for 312 samples and provide Illumina PE250 high throughput sequencing yielding 150k reads on average and 50k reads minimum per sample with data quality control. Contractor will make fastq files available via download from the contractor’s FTP server.
2.0 Background: Diet in general affects the gut microflora in animals, including insects. In addition, many insect species host bacterial endosymbionts, which potentially respond to diet and condition of the insect host. We want to understand how host plant species and cultivar affect the greenbug microbiome over time. To this end, we can amplify a region each of 16S and 18S rDNA with highly conserved primers for sequencing and enumeration of sequence variants in response to time, aphid biotype, and host taxon and cultivar. We expect the results to inform us about the effect on community composition from (1) moving to a new plant of the same genotype and growth stage; (2) passing 48, 96, and 192 hours after arrival on the new plant; (3) moving to each of five host plant species; (4) moving to six wheat cultivars; and (5) the genotype of two biotypes, K and E.
CONTRACTOR REQUIREMENTS
3.0 Technical Requirements/Tasks:
• Perform sample quality control
• Prepare amplicon libraries
• Perform Illumina PE250 high throughput sequencing
• Provide Illumina sequence files in fastq format and accessible for download from the contractor’s FTP server.
4.0 Government Furnished: PCR product amplified with 16S- and 18S-specific primers for
312 greenbug samples will be shipped to the contractor.
5.0 Deliverables / Schedule: Illumina PE 250 fastq files will be provided via download from the contractor’s FTP site.
6.0 Contractor’s Key Personnel: Contractor’s personnel will be highly trained and experienced in performing library preparation, library quality control, Illumina PE 250 sequencing, and sequence quality control.
7.0 Data Rights: USDA retains the rights to the Illumina fastq data files provided by the contractor.
| CONTRACTOR REQUIREMENTS |
| 3.0 Technical Requirements/Tasks: |
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