7-22-2025 Contractor RFIs and Government Responses.pdf
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- Attached to
- 1232SA25Q0103 - RFI Responses Solicitation Sequencing of DNA Samples USDA-ARS-NEA Wyndmoor PA
- Solicitation number
- 1232SA25Q0103
About this file
This document is a Contractor Request for Information (RFI) with detailed government responses regarding a DNA sequencing project. The RFI covers technical specifications for a shotgun sequencing project involving 131 microbial samples, with specific requirements including Illumina sequencing platform, PE 2 X 150 flow cell, TruSeq or Nextera library prep kit, and PCR-free library preparation. The government seeks a minimum of 3M total reads (1.5M reads each direction) per sample, with all samples to be delivered in a single batch and raw data files as the final deliverable.
The solicitation is a 100% Small Business Set-Aside under NAICS code 541380 with a $19M size standard, issued by the USDA Agricultural Research Service. The contract involves metagenomic analysis of gut microbial communities, with offers due by August 7, 2025, and all questions to be submitted by July 29, 2025, to Theodore Blume. Deliverables are required within 60 days after order receipt, to be provided via secure portal download, with the solicitation number 1232SA25Q0103.
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Other files
| File | Type | Posted |
|---|---|---|
| Contractor RFIs and Responses.pdf | ||
| Attachment IV - Past Performance Questionnaire (PPQ).doc | DOC document | |
| Attachment III - Contractor RFI FORM.pdf | ||
| 1232SA25Q0103 with T-n-Cs and Attach I - II.pdf |
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Contractor RFIs and Government Responses
7-21-2025
1. The SOW states shotgun sequencing for hundreds of complex microbial samples. However to calculate the pricing and offer for this tender we would please require a bit more precise number of estimated total number of samples to be sequenced. Do you have an estimate on:
(a) how many samples will be sequenced in total ?
Response: There are 131 samples.
(b) Will all samples be delivered I one batch or will there be multiple batches and if yes, what would be the sample batch size? If there are multiple batches over which time period would they be delivered?
Response: They would be delivered in one batch for this requirement.
(c) Does the work (i.e.) the tender involve also bioinformatics work? The SOW states:
“Scientists from the ERRC are interested in evaluation of the structural change in the gut microbial ecosystem in response to food, nutrition, and environmental stimuli, using next generation DNA sequencing technology and bioinformatics analysis.". Could you please confirm that the bioinformatics work will be performed by the ERRC/DFFRU scientist or is this part of the tender service work. We understand that only raw data files have to be delivered, correct?
Response: That is correct.
(d) Are transport cvosts covered by the customer ERRC/DFFRU or should they be part of the offer for the tender?
Response: Shipping should be included in the quote.
(e) Which sequencing output do you need? 3M total reads (1.5M reads each direction ) per sample or is it 6M (3M reads each direction)?
Response: We are requesting a minimum of 3M total reads (1.5M reads each direction).
(f) Is there a preference (or requirement) for a specific sequencing platform, i.e. Illumina?
Response: Yes. There is a requirement for Illumina.
(g) Is there a preference for flow cell size and type, i.e. PE2X150bp?
Response: Yes. PE 2 X 150
(h) Is there a preference for choice of library prep kit, i.e. Illumina?
Response: Preference is for TruSeq of Nextera.
(i) Is PCR free library prep required?
Response: Yes, PCR-free library prep is required.
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