Revised SOW Q0252.pdf
PDF 136 KB Posted
- Attached to
- DNA Sequencing Federal contract opportunity
- Solicitation number
- 12505B23Q0252
About this file
This statement of work outlines requirements for a contractor to perform RNA sequencing services for the US Department of Agriculture Agricultural Research Service. The contractor will prepare amplicon libraries from 312 greenbug insect samples provided by the government, and conduct Illumina PE250 sequencing to obtain a minimum of 50,000 reads and average of 150,000 reads per sample. The contractor must perform quality control on the samples and sequencing runs, and deliver the resulting fastq files to the government via FTP. The goal is to understand how host plant species and cultivars affect the greenbug microbiome over time. The contractor's personnel must be highly trained and experienced in library preparation, sequencing, and associated quality control. The government will retain rights to the sequencing data delivered by the contractor.
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Other files for this federal contract opportunity
| File | Type | Posted |
|---|---|---|
| RFQ Industry Questions and Government Responses Q0252.pdf | ||
| SF 1449 Q0252.pdf | ||
| Clauses and Provisions 31 July Q0252.pdf | ||
| Statement of Work - Microbiome-Sequencing 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 624 (312 Individuals x2) 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.
• A mean of 150000 read pairs for each of the 624 sequencing runs
4.0 Government Furnished: PCR product amplified with 16S- and 18S-specific primers for
312 greenbug samples will be shipped to the contractor to be amplified separately with both the 16S and 18S rDNA primers (provided by the customer).
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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