127EAU26Q0078 Statement of Work.pdf

Statement of Work (SOW)

RNA-Seq Library Preparation and Sequencing Services

1.0 Scope of Work:

The USDA Agricultural Research Service (ARS) requires RNA-Seq library preparation and sequencing services for up to 176 poultry RNA samples.

The Contractor shall provide all labor, reagents, consumables, equipment, sequencing, quality control, and data delivery necessary to perform stranded mRNA sequencing.

2.0 Background:

The USDA Agricultural Research Service (ARS) requires RNA-Seq library preparation and sequencing services for up to 176 poultry RNA samples in support of ongoing research.

3.0 Technical Requirements/Tasks:

The Contractor shall perform the following:

Sample Submission

• Provide preferences for RNA sample volume and concentration so that

USDA can prepare the samples to be submitted.

• Provide any templates or instructions needed for USDA to share sample/library naming and experimental group assignments.

Library Construction

• Prepare stranded mRNA-Seq libraries from up to 176 RNA samples.

• Utilize library construction method that incorporates strand specificity and poly(A) enrichment (stranded mRNA-seq). If rRNA depletion, or another suitable method is proposed instead of mRNA-seq, it must have been validated to be effective for poultry transcriptome analysis, as identified in the proposal.

• Incorporate unique dual indexes or equivalent sample indexing to minimize sample misassignment and index hopping.

• Perform necessary quality control to assess and confirm library quality prior to sequencing.

• Share with USDA the product info (kit name and vendor) used for library construction for bioinformatics and recordkeeping purposes.

Sequencing Requirements

• The Contractor shall perform sequencing using Illumina technology meeting the following minimum specifications:

• Platform: Illumina NovaSeq X, or equivalent Illumina instrument

• Read configuration: Paired-end reads with 2 × 100 bp or 2 x 150 bp.

• Library type: Stranded mRNA-Seq.

• Minimum sequencing depth: 50 million paired-end reads per sample.

• Minimum quality threshold: ≥80% of bases at Q30 or higher.

• To minimize lane, flow cell, and batch effects, libraries shall be randomized across sequencing lanes and/or pooled such that either all individual samples are run in technical replications across all needed lanes or flow cell partitions to achieve sufficient read depth or individual samples from each experimental group are distributed balanced (or as close as possible) across each lane or flow cell partition. Samples shall not be sequenced in a manner that confounds experimental groups with lane, flow cell, or sequencing run assignment. If multiple sequencing runs are required, samples shall be balanced across runs such that experimental treatment groups are not confounded with sequencing batch. The Contractor shall describe the strategy used to minimize technical variation attributable to sequencing lane, flow cell, and batch effects.

• Provide route via which USDA can access and download the resulting data.

• Share with USDA the sequencing run information (instrument, flow cell type, lane usage) for bioinformatics and recordkeeping purposes.

4.0 Government Furnished:

The USDA will provide extracted RNA and will perform all pre-submission RNA quality control and quantification. The USDA will provide sample names and group metadata.

5.0 Deliverables / Schedule:

Item No.

Deliverable

Objective

Due

1 Data Demultiplexed compressed FASTQ files (*.fastq.gz) for each sample. Each sample must have at least one forward and one reverse file;

additional file pairs may be provided if samples are run in multiple lanes.

90 Days after date of award

6.0 Data Rights:

USDA shall retain unlimited rights in the data produced and delivered under this contract, including the RNA sequencing data, sample identification information, and quality control (QC) data generated in the performance of the requirement.

For purposes of this requirement, the data includes, as applicable, raw and processed RNA sequencing files, sequencing run information, sample/library identifiers and associated metadata, library construction and QC results, and other sequencing-related data required to be delivered under this SOW.

USDA shall have the right to retain, use, reproduce, disclose, distribute, and provide such data to other USDA personnel, laboratories, researchers, or contractors for Government purposes, including future research and analysis.

7.0 Inspection and Acceptance:

The Government will review the sequencing data and quality control documentation to ensure the requirements of this SOW are met.

Acceptance will be based on the following:

• FASTQ files are provided for each sample.

• Each sample meets the minimum sequencing depth of 50 million paired-end reads.

• At least 80% of bases are Q30 or higher.

• Sample information matches the USDA-provided sample information.

• Required sequencing and quality control information is provided.

If the sequencing results do not meet the requirements due to Contractor performance, the Contractor shall correct or repeat the affected work at no additional cost to the Government.

Payment will not be approved until the Government has reviewed and accepted the sequencing data and required quality control documentation.

8.0. Period of Performance:

90 Days from Date of Award

3.0 Technical Requirements/Tasks: