Loren Data's SAM Daily™

SAMDAILY.US - ISSUE OF JULY 23, 2023 SAM #7908
SOURCES SOUGHT

99 -- Metagenomic Sequencing of Pig Fecal Samples and RNA Sequencing of Pig Intestine Samples

Notice Date

7/21/2023 10:35:08 AM
 

Notice Type

Sources Sought
 

NAICS

541380 — Testing Laboratories
 

Contracting Office

USDA ARS NEA AAO ACQ/PER PROP BELTSVILLE MD 20705 USA
 

ZIP Code

20705
 

Solicitation Number

1105622-SS
 

Response Due

8/1/2023 6:00:00 AM
 

Archive Date

08/16/2023
 

Point of Contact

Elizabeth Wilson
 

E-Mail Address

elizabeth.wilson2@usda.gov
(elizabeth.wilson2@usda.gov)
 

Description

Sources Sought Notice Metagenomic Sequencing of Pig Fecal Samples and RNA Sequencing of Pig Intestine Samples Sources Sought #1105622-SS This is a Sources Sought notice Only.� This is NOT a solicitation for proposals, proposal abstracts, or quotations. �This Sources Sought is issued for information and planning purposes only as part of USDA ARS market research and does not itself constitute an RFQ. Metagenomic Sequencing of 672 Pig Fecal Samples Background USDA, Agricultural Research Service (ARS), Animal Biosciences and Biotechnology Laboratory (ABBL) requests a Contractor from which to purchase a service which will produce a set of shotgun sequencing reads for 672 pig fecal samples.� Shotgun sequencing is the sequencing of all DNA present in a sample.� In this case, it is the sequencing of all microbial DNA present in piglet fecal samples.� ARS scientists will use these data in various downstream bioinformatics analyses including the assignment of sequences to species to determine the taxonomic composition of the samples, and the identification of genes and pathways each species contains.� Furthermore, this large scale sequencing project will provide the data required to develop novel machine learning algorithms which elucidate the complex associations between the microbiome members and the piglet host.� Thus, production of this highly dimensional dataset will result in multiple final outcomes which will contribute to the meeting of multiple National Program objectives. Requirements 672 DNA samples will be provided by ARS-ABBL scientists to the Contractor, who will in turn provide shotgun metagenomic library preparation and sequencing on these samples (~20 million read pairs per sample).� DNA should be quantified using the Qubit system, normalized, and then processed into sequencing libraries using SeqWell kits and sequenced on the recently released Illumina Nova X sequencer.� The reliability and accuracy of each of these methods is supported in the scientific literature.� Raw sequence data for each sample will be delivered to researchers within ARS-ABBL. Schedule of Line Items Line Item 0001 �library preparation and sequencing of 672 piglet fecal samples Deliverable will include raw sequence reads for each of 672 piglet fecal samples RNA Sequencing of 60 Samples from the Pig Intestine Background USDA, Agricultural Research Service (ARS), Animal Biosciences and Biotechnology Laboratory (ABBL) requests a Contractor from which to purchase a service which will produce a set of RNA-Seq sequencing reads for 60 samples from the pig intestinal tissue.� RNA-Seq is the sequencing of all RNA present in a sample.� We will examine all RNA in samples from the pig intestine to better understand gene expression as it relates to both intestinal functions such as digestion as well as how the gut microbiome interacts with pig intestinal tissues to promote pig health and growth.� This information will contribute to the meeting of multiple National Program objectives. Statement of Work 60 RNA samples will be provided by ARS-ABBL scientists to the Contractor, who will in turn provide poly-A tail enrichment library construction and sequencing on these samples (~50 million read pairs per sample).� RNA should be quantified via Qubit fluorescence-based assays and visualized using Agilent TapeStation.� Samples should then undergo poly-A tail enrichment, using the New England Biolabs Poly(A) kit, which reduces the amount of uninformative ribosomal RNAs in the sample.� This tailored sample then undergoes library construction and sequencing on the Illumina Nova X sequencer using the 10B flowcell.� Raw sequence data for each sample will be delivered to researchers within ARS-ABBL. Schedule of Line Items Line Item 0002 �library preparation and sequencing of RNA from 60 piglet intestinal samples Deliverable will include raw sequence reads for RNA from 60 piglet intestinal samples Delivery Address: Attn: Cary Davies USDA ARS ABBL BARC-East; B307 10300 Baltimore Ave. Beltsville MD 20705 The Contractor Shall: This Sources Sought is only for the purpose of identifying potential sources as part of USDA ARS market research. The Government does not intend to make an award based on responses to this inquiry. This notice does not constitute a commitment by the Government. Responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible.�� The purpose of this notice is to obtain information regarding the availability and capability of qualified sources including any Small Businesses; HUBZone small business; service-disabled, veteran-owned small business; 8(a) small business; veteran-owned small business; woman-owned small business; or small disadvantaged businesses. Please state if you are a large business or a small business according to the NAICS code listed in this Sources Sought. All information submitted in response to this announcement is voluntary, and the Government will not pay for information requested nor will it compensate any respondent for any cost incurred in developing information provided to the Government. Any organization responding to this notice should ensure that its response defines how it can specifically meet the specifications for the items requested.� Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted.� After review of the responses received, a Combined Synopsis solicitation notice may be published on Sam.gov. Submit the Following: Your response should define how you can specifically meet the technical requirements in the Statement of Work. Identify if you are a large business or a small business with NACIS 541380. Original Point of Contact: All responses to this Sources Sought Notice must be received by August 1, 2023, by 9:00 AM EDT, the specified due date and time to be considered.� Email responses to Elizabeth Wilson at Elizabeth.Wilson2@usda.gov. Responses will not be returned. Responders are solely responsible for all expenses associated with responding to this Inquiry. Do not submit pricing information in response to this Request.
 

Web Link

SAM.gov Permalink
(https://sam.gov/opp/fc2e1ba3ddef4bd08a6fc50a4dc2e144/view)
 

Place of Performance

Address: Beltsville, MD 20705, USA

Zip Code: 20705

Country: USA
 

Record

SN06759585-F 20230723/230721230050 (samdaily.us)
 

Source

SAM.gov Link to This Notice
(may not be valid after Archive Date)

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