Statement of Work.pdf
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- Solicitation number
- 12505B24Q0084
About this file
This document is a Statement of Work (SOW) for a federal contract opportunity to provide bioinformatic analysis services to the USDA-ARS to analyze intron splicing variation in potato.
The key objectives are to identify differentially spliced genes in potato in the presence or absence of a specific protein from the late blight pathogen Phytophthora infestans. The contractor will be required to perform pre-processing of sequencing data, align and quantify gene and transcript abundances, and conduct differential analyses at the gene, transcript, and splice junction levels. Deliverables include a quality control report, alignment files, count matrices, a list of novel annotations, and results of the differential analyses. The contract has a period of performance ending on 4/30/2024 and will be awarded on a firm-fixed price basis. The associated federal contract opportunity is Solicitation Number 12505B24Q0084, which is a total small business set-aside with a lowest price technically acceptable (LPTA) source selection criteria.
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Statement of Work (SOW) Project: 5090-21220-005-00D
GENERAL INFORMATION
1.0 Scope of Work: The UDSA-ARS is requesting purchase of bioinformatic analysis service to analyze intron splicing variation in potato.
2.0 Background: The USDA-ARS is interested in analyzing intron splicing changes that occur in potato during infection with the late blight pathogen Phytophthora infestans. A specific protein from the pathogen called IPI-O1 is known to modulate intron splicing of specific genes in the plant. However, there are more unknown genes in potato that are also targeted. The purpose of this analysis is to identify differentially spliced genes in the presence or absence of IPI-O1.
CONTRACTOR REQUIREMENTS
3.0 Technical Requirements/Tasks:
• Pre-Processing:
o With FastQC/MultiQC: Assess quality of sequencing reads.
o With Trimmomatic: Pre-process reads (trim adapters, trim poor-quality bases)
– as necessary.
o Build appropriate STAR alignment indexes for potato / fungi (with guidance from USDA on o FASTA/annotation selection).
• Data Processing:
o Using STAR: align bulk RNA-sequencing reads to index from above.
o Using StringTie: Assemble transcripts / identify novel transcripts.
o Using RSeQC: Re-assess quality based on alignments.
o Using RSEM (and maybe feature counts): quantify gene / transcript abundances.
o Custom Script: Extract SJ counts from STAR output.
o Using DESeq2: Perform differential analysis at three levels
Differential gene expression (gene-level) using output from RSEM.
Differential transcript utilization (transcript-level) using output from
RSEM.
Differential splice junction utilization (junction-level) using output from STAR’s SJ counts.
Brand name or equal:
ViaScientific Foundry software platform
Deliverables must include:
• QC report
• Alignment files
• Count matrix o Gene-level o Transcript-level o Splice-junction level
• List of novel annotations
• Differential expression/utilization:
o Gene-level o Transcript-level o Splice-junction level
4.0 Government Furnished: N/A
5.0 Deliverables / Schedule:
Delivery is via electronic communication and data access by 4/30/2024 or as negotiated. Delivery will not include any physical items.
Patrick Maldonado, Administrative Office, USDA-Agricultural Research Service, Madison, WI
53706. Phone: 608-603-6749; email: patrick.maldonado@usda.gov; fax 608-807-5994.
6.0 Data Rights: Access to Foundry: Upon completion of the project, the USDA will have access to all data, metadata, analytical pipelines, and visualized results associated with this project within the Foundry platform for a period of three months.
mailto:patrick.maldonado@usda.gov
| CONTRACTOR REQUIREMENTS |
| 3.0 Technical Requirements/Tasks: |
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