STATEMENT OF WORK.pdf
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- Solicitation number
- 12905B23Q0117
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This statement of work outlines RNA sequencing services required by the USDA Agricultural Research Service. The contractor will extract RNA from 77 animal tissue samples from two dietary intervention studies, prepare libraries for sequencing, and conduct Illumina PE150 sequencing. As part of bioinformatics analysis, the contractor will perform data quality control, read mapping, gene expression quantification, correlation analysis for replicates, differential expression analysis between sample groups, and gene ontology, pathway enrichment, and protein interaction analyses. Results will provide insight into transcriptional changes related to metabolic syndrome, cognitive function, and inflammation.
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Other files
| File | Type | Posted |
|---|---|---|
| RFI No. 01.pdf | ||
| Sol_12905B23Q0117_Amd_0002.pdf | ||
| RFI Form 2 QandA.docx | DOCX document | |
| RFI Form.pdf | ||
| TandCs with PandCs for 12905B23Q0117.docx | DOCX document |
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Text version
May 11, 2023
STATEMENT OF WORK
Purpose of the requested service is to analyze mRNA expression levels in animal tissues collected from the dietary intervention study, with a specific focus on biomarkers of metabolic syndrome, brain cognitive function, and inflammation. This analysis aims to gain a deeper understanding of transcriptional changes in adipose and brain tissues.
Previously, we have utilized the services of a vendor to analyze RNA expression in mouse tissues. It is important to note that different vendors employ distinct chemistry and methods for sample preparation, utilize different instruments from various manufacturers, and employ diverse software algorithms for data analysis. It is worth mentioning that the analysis of a single organ generates approximately 100 GB of data, highlighting the significance of post-chemical proprietary analysis methods.
The samples we plan to analyze are from 13 months dietary intervention study. Therefore, highly experienced vendor with long history of successful business is crucial.
We have 77 samples to analyze that consists of 4 different sample types and they are identified as:
• Project WY118, Adipose, n = 15
• Project WY118, Hippocampus, n = 15
• Project WY114, Adipose, n = 27
• Project WY114, Hippocampus, n = 20
A service that provides:
1. Vendor will extract RNA from samples and check RNA quality
2. Vendor will prepare RNA library including removing rRNA
3. Vendor will reverse transcribe to cDNA, fragment and sequence cDNA by Illumina PE150 technology
4. Vendor will perform bioinformatics analysis consisting of:
1) Data Quality Control: filtering reads containing adapter or with low quality.
2) Statistics Analysis of Data Production and Quality
3) Mapping Reads to Reference Genome
4) Gene Expression Quantification
5) Correlation analysis (For biological replicates only)
6) Differential Expression Analysis (two or more groups of samples)
7) GO Enrichment Analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples)
8) KEGG Pathway Enrichment Analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples)
9) GSEA Enrichment Analysis of Expressed Genes (two or more groups of samples)
10) Protein-Protein Interaction Analysis
11) Reactome Pathway Enrichment Analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples and only for mouse samples)
12) Oncogene Functional Annotation analysis of Differentially Expressed Genes (DEGs)
(two or more groups of samples and only for mouse samples)
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