Attachment 2_SOW_1232SA26Q0963.pdf
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- Genotyping
- Solicitation number
- 1232SA26Q0963
About this file
This is a Statement of Work for genotyping services required by the USDA Agricultural Research Service (ARS), U.S. Arid Land Agricultural Research Center, Plant Physiology and Genetics Unit in Maricopa, Arizona. The contractor must perform next-generation genotyping of 1,824 brassica carinata leaf DNA samples organized across 19 plates to support the ARS's research objectives under NP301 Plant Genetic Resources, Genomics, and Genetic Improvement.
The scope of work includes library preparation using ApeKI restriction enzyme digestion to prepare genotyping-by-sequencing (GBS) libraries, library quality assessment, and sequencing and genotyping using Illumina NovaSeq X or similar platform with a read length of 2 x 150bp. All samples must be processed in a single batch to maintain consistency and data quality. The contractor must perform bioinformatic data analysis and SNP calling, including trimming raw sequence data, analyzing preprocessed data using TASSEL v5.0 GBS v2 pipeline or alternative pipeline, aligning trimmed data to the Brassica carinata genome, filtering mapped SNPs, and converting data to HAPMAP format. The guaranteed turnaround time is 60 days from DNA sample receipt. The contractor must demonstrate specialized experience with all aspects of DNA sequencing. The single line item deliverable includes raw sequence reads and filtered SNP data in suitable formats for all 1,824 samples, with electronic data transfer required.
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| File | Type | Posted |
|---|---|---|
| Attachment 1_Solicitation Terms and Condition_1232SA26Q0963.pdf | ||
| 1449_1232SA26Q0963.pdf |
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Statement of Work Genotyping
Background The USDA, Agricultural Research Service (ARS), U.S. Arid Land Agricultural Research Center, Plant Physiology and Genetics Unit in Maricopa, AZ has a requirement for the next-generation genotyping of 1824 brassica carinata leaf DNA samples. The data generated will help us to understand the genome structure of an advanced population and identify sequence variants between the brassica carinata genotypes. This work will help to breed better brassica carinata varieties and advance our research objectives under NP301 Plant Genetic Resources, Genomics, and Genetic Improvement.
Statement of Work Sequencing 1824 DNAs extracted from brassica carinata leaf tissues (19 plates). This will include library preparation, library quality assessment, sequencing and genotyping using high throughput genotyping by sequencing technology, and bioinformatic data analysis and SNP calling.
Specifically, provided DNA extracted from young brassica carinata leaf tissues will be used to generate sequencing libraries Using ApeKI restriction enzyme digestion to prepare GBS libraries.
Genotyping by sequencing technology must be completed using the Illumina NovaSeq X or similar platform with a read length of 2 x 150bp. All samples must be run together in a single batch to maintain consistency and ensure optimal data quality.
Sequencing and genotyping analyses must be done according to vendor’s pipelines to trim raw sequence data, analyze the preprocessed data using the TASSEL v5.0 GBS v2 pipeline or other pipeline. The trimmed GBS sequencing data must be aligned to the Brassica carinata genome to call and identify SNP. Mapped SNP must be filtered, and data must be converted to HAPMAP format. The guaranteed turnaround time from the date of receiving DNA samples must be 60 days. The vendor must have specialized experience with all aspects of DNA sequencing.
Schedule of Line Items Line Item – quality assessment, PCR free library preparation, and sequencing of 1824 DNAs extracted from brassica carinata Deliverable will include raw sequence reads and filtered SNP data in suitable formats for each of 1824 brassica carinata DNA samples, data must be transferred electronically.
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