A04_Statement of Work - 1232SA26Q1291.pdf
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- Solicitation number
- 1232SA26Q1291
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This is a Statement of Work for RNA extraction and sequencing services for the USDA ARS National Cold Water Aquaculture Center (NCCCWA). The contractor must perform total RNA extraction on 90 frozen rainbow trout whole-body tissue samples homogenized in Trizol and conduct RNA-seq library preparation with poly-A selection and mRNA sequencing on all 216 samples, which include the 90 extracted samples plus 90 samples of extracted spleen tissue and 36 samples of extracted primary muscle cell cultures.
The work is divided into three line items: (1) RNA extraction of 90 samples; (2) RNA-seq library preparation and mRNA sequencing of 216 samples; and (3) return of all remaining total RNA samples. All 216 samples will be provided frozen on dry ice within 90 days of contract award. Extracted RNA samples must meet strict quality standards with minimum concentration >50ng/µL, minimum volume >100µL, A260/A280 ratio between 1.8 and 2.0, and RIN value greater than 7 as verified by BioAnalyzer or similar analysis. The contractor must perform standard Illumina RNA-seq library preparation (or similar), using Illumina technology with PE 150 cycles, generating paired-end reads of 2 x 150 nucleotides with a minimum of 40 million paired-end reads per sample (20M in each direction), where greater than 85% of bases have QC≥30 in fastq format. The contractor must implement quality control procedures throughout RNA extraction, library preparation, and sequencing and return remaining RNA samples in clearly labeled microcentrifuge tubes shipped overnight with dry ice. All deliverables, including sequencing data and a Final Project Report describing extraction, library preparation, QC procedures, and sequencing methods, must be completed and delivered within 60 days of receipt of all 216 samples via secure portal download or external hard drives to the USDA-ARS-NCCCWA facility in Kearneysville, WV.
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Other files
| File | Type | Posted |
|---|---|---|
| Attachment 2 - Vendor Questions and Answers.pdf | ||
| 1232SA26Q1291-0001.pdf | ||
| 1232SA26Q1291.pdf |
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RNA extraction and Sequencing of 216 Rainbow Trout Samples
Statement of Work: The USDA ARS NCCCWA requires total RNA extraction and total RNA-seq library preparation (poly-A selection) and mRNA sequencing of 90 frozen samples of rainbow trout whole-body tissue homogenized in Trizol, and total RNA-seq library preparation (poly-A selection) and mRNA sequencing of 90 samples of extracted rainbow trout spleen tissue total RNA and 36 samples of extracted rainbow trout primary muscle cell cultures total RNA.
Contractor shall provide all services, supplies, equipment and facilities necessary for total RNA extraction and mRNA sequencing of 90 frozen samples of rainbow trout whole-body tissue homogenized in Trizol and mRNA sequencing of additional 126 frozen RNA samples. Contractor shall fully meet the required performance elements and benchmarks described below.
Schedule of Line Items:
Line Item 01 RNA extraction of 90 Samples.
Line Item 02 RNA-seq library preparation and mRNA sequencing of 216 samples.
Line Item 03 Return of all remaining total RNA samples.
All samples will be provided frozen on dry ice within 90 days after the contract is awarded. RNA samples will be provided in nuclease free water with a minimum concentration >50ng/uL and a minimum volume >100uL. The A260/A280 value of each RNA sample shall be within a range from 1.8 to 2.0. The RNA quality shall also be evaluated with BioAnalyer RNA chip or similar, and RIN value for each sample shall be greater than 7.
Required performance elements and benchmarks:
1. Total RNA shall be extracted by the contractor from 90 of the 216 samples. The total RNA should be stored in nuclease free water with a minimum concentration >50ng/uL and a minimum volume >100uL.
2. Contractor shall re-extract total RNA until RNA quality for each sample meets the following quality requirements. The A260/A280 value of each RNA sample shall be within a range from 1.8 to 2.0. The RNA quality shall also be evaluated with BioAnalyer RNA chip or similar, and RIN value for each sample shall be greater than 7.
3. Standard Illumina RNA-seq library preparation or similar shall be performed by the vendor.
4. Platform and configuration: Illumina technology, PE 150 cycles, or similar.
5. Read Length: 2 x 150 nucleotides (paired-end)
6. Data Output: A minimum of 40 million paired-end reads per sample (20M reads in each direction). For each read, greater than 85% of bases shall have QC≥30.
The output data files are in standard fastq format.
7. Contractor shall have in place a series of quality control (QC) steps during RNA extraction, library preparation and mRNA sequencing.
8. The remaining total RNA samples shall be returned in clearly labeled microcentrifuge tubes and shipped overnight with dry ice.
9. Deliverables shall include the RNA sequencing data for all samples, and a Final Project Report describing RNA extraction, library preparation, QC procedures and sequencing methods. All data must be provided via secure portal download OR in external hard drives to the USDA-ARS-NCCCWA, 11861 Leetown Road, Kearneysville, WV 25430.
Completion and return of all deliverables is required within 60 days from receipt of all 216 samples. The order number shall be included on all documentation and shipments.
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