Sol_12905B23Q0036_Amd_0001.pdf

(x)

12905B23Q0036 x x copies of the amendment; (b) By acknowledging receipt of this amendment on each copy of the offer submitted ; or (c) By separate letter or electronic communication which includes a reference to the solicitation and amendment numbers. FAILURE OF YOUR ACKNOWLEDGEMENT TO BE

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OFFER. If by virtue of this amendment you desire to change an offer already submitted , such change may be made by letter or electronic communication, provided each letter or electronic communication makes reference to the solicitation and this amendment, and is received prior to the opening hour and date specified.

x

ARS-12905B

ALBANY CA 94710

800 BUCHANAN STREET

USDA ARS PWA AAO ACQ/PER PROP

03/31/20230001

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03/31/2023

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14. DESCRIPTION OF AMENDMENT/MODIFICATION (Organized by UCF section headings, including solicitation/contract subject matter where feasible.)

The purpose of this amendment is to post questions and answers, and extend the response date to April 21st, 2023 at 5:00 PM EST. There are no other changes to this solicitation.

Q. What are the data output requirements for both platforms?

A. Looking at the NovaSeq S4 flowcell 2x150bp with estimated output of 2,250M reads/675Gbp for the shotgun Illumina sequencing and standard V3 Miseq 2x300 with 13-15M reads.

Q. Are there estimated batch or volume sizes per submission?

Batch sizes will likely vary, but would be enough samples for a multiplexed runs, e.g., 12 metaG samples

Continued ...

16A. NAME AND TITLE OF CONTRACTING OFFICER (Type or print)15A. NAME AND TITLE OF SIGNER (Type or print)

15C. DATE SIGNED 16B. UNITED STATES OF AMERICA 15B. CONTRACTOR/OFFEROR 16C. DATE SIGNED

(Signature of person authorized to sign) (Signature of Contracting Officer)

KENDA C. TUCKER

STANDARD FORM 30 (REV. 11/2016)

Prescribed by GSA FAR (48 CFR) 53.243

Previous edition unusable

Except as provided herein, all terms and conditions of the document referenced in Item 9 A or 10A, as heretofore changed, remains unchanged and in full force and effect .

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12905B23Q0036/0001

A. What type of sample will be submitted to us (gDNA? cells? environmental samples?)

Samples for NovaSeq will be submitted at gDNA or

DNA-depleted RNA, Nextera barcoded multiplexed libraries for MiSeq, HMW DNA for Nanopore

Q. How many estimated samples?

A. Estimated 36 metaG, 24 metaT, 6 multiplexed metabarcoding libraries

1. What are the data requirement?

Q. Metabarcoding is typically 16S sequencing.

Please confirm if this is correct.

A. Both 16S and LSU sequencing for fungi, using Nextera barcoding preps from Illumina, would be sent multiplexed separately for sequencing, and the sequences generated are different lengths.

Q. Metabarcoding typically generates about 100K reads per sample, please confirm if this is sufficient.

A. For these samples, this coverage is more than sufficient, and we would likely aim for >96 samples per run, with the understanding that depth per sample would be lower.

Q. Please specify how much data is required for metagenome using Illumina platform.

A. Aiming for ~50Gbp per sample for metaG, 25Gbp per sample for metaT.

Q. Please specify how much data is required for metagenome using Nanopore platform. Coverage for medium bacterial genomes (~6Mb) plus potential fungal isolates.

A. We estimate that a single PromethION run will be more than sufficient for the seven bacterial isolates with the remaining runs for fungi of unknown size.

Q. Please specify how much data is required for metatranscriptome using Illumina platform.

A. See above.

Q. Please specify how much data is required for metatranscriptome using Nanopore platform.

A. We are not planning for metaT for Nanopore.

Q. Is data analysis required? If not, only the sequencing data in the form of FastQ format will be provided as the deliverable.

A. FASTQ files processed via the Illumina software will be sufficient for analysis.

Q. What starting material you would like to Continued ...

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12905B23Q0036/0001 provide for the Sanger sequencing work?

A. The starting material would be either cleaned or raw PCR products depending on services available.

Q. Would you like our team to design primers for the target regions? Alternatively, will you provide the primer design or primer aliquots?

A. Primers used are standard for 16S and the fungal LSU, and sequences/aliquots could be provided if needed.

Q. Is subcontracting allowed?

A. There is not a general restriction on subcontracting, but any subcontracting must be in accordance with the laws and regulations such as the Federal Acquisition Regulation (FAR).

Q. If all but one services can be performed, can a quote be submitted or is this an ¿all or none¿ endeavor?

A. Evaluation will be based on the requirement being completely satisfied.

NSN 7540-01-152-8067 OPTIONAL FORM 336 (4-86)

Sponsored by GSA

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