Attachment 2 - Statement of Work (SOW).pdf

Statement of Work

Project: Next-generation sequencing of nucleic-acid libraries

GENERAL INFORMATION

1.0 Scope of Work: A contractor must be able to provide next-generation sequencing of nucleic acid libraries using stated cycling and sequencing arrangement.

2.0 Background: In order to understand the immune status of cells with and without treatment, interrogation of both gene expression and DNA epigenetic status is important.

To perform such an analysis requires a large amount of nucleic acid sequencing on prepared libraries in a manner that minimizes batching of samples. Only certain Illumina sequencers and flow cells are amenable to the sequencing required.

CONTRACTOR REQUIREMENTS

3.0 Technical Requirements/Tasks:

• Contractor utilizes Illumina Novaseq X Plus to perform next generation sequencing of already prepared illumina libraries.

• Must be able to perform the following sequencing runs:

o Run 1 - acquire approximately 1.5B read pairs total with a single library pool with the following cycling required for whole-transcriptome assay - Read 1: 51 cycles, Read 2: 71 cycles, Index 1: 8 cycles; PhiX spike-in at 1%. Run would typically be performed as 1.5B flow cell (both lanes) or two lanes in a 10B flow cell at 2x150 or 300 cycles.

o Run 2 – acquire approximately 3.25B read pairs total with a single library pool with the following cycling required for whole-transcriptome assay - Read 1: 51 cycles, Read 2: 71 cycles, Index 1: 8 cycles; PhiX spike-in at 1%. Run would typically be performed using a single lane on a 25B flow cell or two lanes in a 10B flow cell at 2x150 or 300 cycles.

o Run 3 – aquire approximately 25B read pairs total using entire flow cell (8 lanes) on a NovaSeq X/X Plus 25B using specific cycling parameters for 4 lanes (Read 1: 50 cycles, Read 2: 50 cycles, Index 1:

8 cycles, Index 2: 60 cycles, PhiX spike in at 1%) with one pool for whole transcriptome and another set of cycling parameters for the other 4 lanes (Read 1: 51 cycles, Read 2: 71 cycles, Index 1: 8 cycles; PhiX spike-in at 1%) on a second pool for ATACseq. Run would require entire 25B flow cell comprised of 8 lanes.

• Each sequencing Run must be performed sequentially, with data provided from each run prior to samples being submitted for next sequential sequencing run. A quality report for the sequencing run and FASTQ files are deliverable for each Run.

• Library quantitation may be performed by sequencing facility.

4.0 Government Furnished: N/A

5.0 Deliverables/Schedule:

• Each sequencing run must be completed and data provided within 14 days of contractors receipt of samples.

• A quality report for the sequencing run and FASTQ files are deliverable for each

Run.

6.0 Evaluation Factors: Both price and ability to deliver in timely manner will be factors used for evaluation.

7.0 Technical Point of Contact: Should there be technical questions, please contact Dr.

Crystal Loving, at 515-337-7364 or via email at crystal.loving@usda.gov.

8.0 Place of Delivery: Data made available for download via cloud or harddrive.