Questions and Answers 16 June.pdf

Questions and Answers from 6/16/2026:

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: We will not send tissue samples from any animal other than fish (specifically, Florida pompano), and these samples will not contain parasites.

Question: What is the biosafety level (BSL) associated with these tissue samples?

Answer: BSL1

Question: What specific type(s) of tissue will you be sending?

Answer: We will send fin clips collected from wild-caught and captive-bred Florida pompano.

Question: What is the expected amount or volume of tissue per sample?

Answer: The fin clips will be approximately 1-2 cm long, yielding >30 mg of tissue.

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: We do not require diƯerential gene expression analysis, as this is a WGS project focused on genome-wide SNP analysis for a high-density genomic selection tool.

Question: Will your project require strand-specific information?

Answer: No, we do not require strand-specific information.

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: The samples will be shipped together in a single batch.

Question: What type of RNA pre-processing is required for your project (e.g., poly-A selection or rRNA depletion)?

Answer: We do not require RNA pre-processing, as we intend to ship tissue samples for DNA extraction, whole-genome sequencing, and SNP panel development.

Questions and Answers from 6/15/2026:

Question: Will the fin clips be sent in any specific solution or in any specific condition (e.g. flash frozen, in RNAlater, etc.)?

Answer: Fin clips will be shipped in RNAlater cryovials on dry ice.

Question: Is each sample 1 fin clip? If not, please clarify.

Answer: Yes, each sample is one fin clip from an individual fish.

Question: What are the average sizes of the fin clips?

Answer: The fin clips are typically ~2 cm long.

Question: Do you need 20X coverage for each pool (5) or for each sample (5 x 10)?

Answer: We need 20X coverage for each sample.

Question: Will you ship your pools all in one batch? If not, please specify the number of batches and the number of pools per batch.

Answer: Yes, the samples will be shipped in a single batch.

Question: If known, is PCR-free library prep required?

Answer: Yes, we require PCR-free library preparation.

Question: When you mention that "scientists will assess the performance of SNP panels and determine the effectiveness before paying" does this mean scientists on your end will validate the panel performance, and we only need to perform WGS and panel development?

Answer: No, we will need you to perform WGS, panel development, and in-lab panel optimization + validation. We require a fully validated SNP panel ready for application in a selective breeding program.

Question: We noticed you mentioned the "SNP panel needs to be delivered 8 months after award and delivered to USDA Facility at 2001 South Rock Road, Fort Pierce, FL, 34945, USA." Can you confirm that you want a physical SNP panel (not just the design) delivered to this specific address?"

Answer: No, we will need the SNP panel design. This should include the raw and filtered data files (e.g., FASTQ, variant/genotype calls, FASTA sequences), detailed descriptions of the methods (for reproducible data analysis), and an interpretive report of the SNP results.