Questions and Answers 18 June.pdf
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- Transcriptome Services of RNA samples Federal contract opportunity
- Solicitation number
- 1232SA26Q0705
About this file
This document is a Questions and Answers (Q&A) file addressing technical specifications for a USDA research contract involving RNA sequencing of animal tissue samples.
The project involves 110 intestinal tissue samples from two species: approximately 40 lambs (sheep) and 70 rodents. Samples will be stored in TRIzol and are classified as Biosafety Level 2 (BSL2) due to potential parasite content. Each sample must contain sufficient tissue for more than 100 micrograms of total RNA, approximately 2 centimeters in length of intestine. Samples will be delivered in up to two batches with variable batch sizes. Required preprocessing includes rRNA depletion, and strand-specific sequencing information is mandatory. Deliverables must include standard differential gene expression analysis with software versions and parameters documented, raw count tables, FPKM tables, DEG results and annotation, and raw sequence data deposited to NCBI SRA with the principal investigator's permission.
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Other files for this federal contract opportunity
| File | Type | Posted |
|---|---|---|
| Questions and Answers 23 June.pdf | ||
| Questions and Answers 17 June.pdf | ||
| Solicitation_1232SA26Q0705.pdf |
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Question: Can USDA confirm the species represented in the 110 tissue samples? The Statement of Work references research involving goats, sheep, and rodents, but the species for the samples to be sequenced are not explicitly stated. If multiple species are anticipated during the contract period, please provide an estimated breakdown.
Answer: We do not know the number or ratios, because the animal experiments have not started yet. Tentatively 40 lambs (sheep) and 70 rodents.
Question: Regarding the tissue samples from goats, sheep, and rodents: Will any of these contain parasites? If so, what specific protocols have been implemented to ensure the tissues are safe for handling?
Answer: Yes. The tissues are stored in TRIzol
Question: What is the biosafety level (BSL) associated with these tissue samples?
Answer: BSL2
Question: What specific type(s) of tissue will you be sending?
Answer: Intestine
Question: What is the expected amount or volume of tissue per sample?
Answer: SuƯicient for >100 ug of total RNA (or ~ 2 cm in length of the intestine)
Question: You mentioned "providing digital gene expression signature profiles with full data analysis." Could you clarify if standard diƯerential gene expression analysis is suƯicient, or if you require any specific downstream analysis beyond that?
Answer: Standard gene expression analysis is suƯicient (must include software version and parameters used, raw count table, FPKM table, DEG results and annotation), but the raw sequence data will need to be deposited to NCBI SRA wit PI’s permission.
Question: Will your project require strand-specific information?
Answer: Yes
Question: Do you plan to send the samples altogether in one batch? If they will be split up, how many batches should we expect, and how many samples will be in each?
Answer: Up to two batches. The number of samples in each batch may vary.
Question: What type of RNA pre-processing is required for your project (e.g., poly-A selection or rRNA depletion)?
Answer: rRNA depletion is required.
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