Questions_WGSTranscriptomics_0002.pdf
PDF 83 KB Posted
- Attached to
- METAGENOMICS & TRANSCRIPTOMIC SERVICES
- Solicitation number
- 140G0226Q0145
About this file
This document is a Questions and Answers (Q&A) clarification regarding sequencing service requirements for a federal contract opportunity focused on analyzing mixed microbial communities from freshwater and soil environments.
The buyer requires two primary sequencing services: Whole Genome Sequencing (WGS) and RNA-seq. For WGS, sample batch sizes will range between 15-65 samples, with potential replicates of 2-10 samples per run as needed. WGS requirements specify a minimum of 150-300 million paired-end reads for PE150 reads, adjustable based on target genome size and read length, with depth sufficient for species/strain identification and antimicrobial resistance gene detection. The buyer will consider both PE150 and PE250 read lengths but does not typically use single-end sequencing for WGS. For RNA-seq, the buyer anticipates 10-20 million informative reads from 30-50 million raw reads per sample, with requirements varying based on project focus (gene expression profiling versus metatranscriptomics). Historically, the buyer has used PE100 reads for RNA-seq and will consider single-end sequencing for gene expression profiling and both single- and paired-end options for gene expression and transcriptome analysis. The buyer's primary research interests include species/strain identification, antimicrobial resistance and virulence gene pathways, nutrient cycling, and biodegradation within mixed microbial communities. Vendors should use these specifications as baseline assumptions for pricing proposals, recognizing that specific requirements may vary by individual project.
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Other files
| File | Type | Posted |
|---|---|---|
| Sol_140G0226Q0145_Amd_0002.pdf | ||
| B08_Attachment_A_-_Statement_of_Work_0001.pdf | ||
| B08_Attachment_B_Pricing_Schedule_transcriptomic_services_0001.xlsx | XLSX spreadsheet | |
| Sol_140G0226Q0145_Amd_0001.pdf | ||
| Sol_140G0226Q0145.pdf |
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1. Sample Quantities and Library Preparation
Could you please clarify the anticipated sample batch sizes? Specifically, should vendors expect to receive batches of approximately 65 individual samples, or will the samples require multiple replicate library preparations? If replicates are required, how many library preparations should be anticipated per sample?
Sample batch sizes will vary based on project needs and will likely range between 15-65 samples. Depending on project need, we may decide to sequence replicates for a select group of samples per run (i.e. 2-10 samples)
2. WGS and RNA-seq Sequencing Depth
Could you please clarify the expected sequencing depth for each service?
• Whole Genome Sequencing (WGS): How many sequencing reads or read pairs are required per sample?
At minimum, we would aim for 150-300 M paired-end reads for PE150 reads. That number would adjust depending on target genome size and paired-end read length.
Depth must be sufficient for species/strain identification and antimicrobial resistance gene detection.
• RNA Sequencing (RNA-seq): How many sequencing reads or read pairs are required per sample?
For RNA-seq, our requirements will vary based on projects and whether they are focused on gene expression profiling or metatranscriptomics. We would likely aim for 10-20 M informative reads from 30-50 M raw reads/sample for transcriptomics.
In the past, we have sequenced PE100.
Additionally, are there specific requirements for read length and single-end versus paired-end sequencing?
For WGS, we will consider both PE150 and PE250. We do not typically use single-end sequencing.
For RNA-seq, we will consider single-end (for gene expression profiling) and both single-and paired-end (for gene expression and transcriptome analysis).
If these requirements vary by project, could you please advise what assumptions vendors should use when preparing their pricing?
Most of our sequencing needs stem from assessing potential metabolic function and/or gene expression of mixed microbial communities from freshwater and soil environments.
We are typically most interested in species/strain identification, antimicrobial resistance and virulence gene pathways, nutrient cycling, and biodegradation.
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