Attachment 2 - Statement of Work (SOW).pdf

Statement Of Work RNA-Seq of 140 Samples from the Pig Intestine

Scope:

USDA, Agricultural Research Service (ARS), Animal Biosciences and Biotechnology Laboratory (ABBL) requires a service which will produce a set of RNA-Seq sequencing reads for 140 samples from the pig intestinal tissue.

Background:

RNA-Seq is the sequencing of all RNA present in a sample. We will examine all RNA in samples from the pig intestinal epithelium 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.

Technical Requirements/Tasks:

140 RNA samples will be provided by ARS-ABBL scientists to the Contractor, who will in turn perform RNA quality assessment, poly-A tail enrichment library construction, library QC, pooling, and normalization, and DNA sequencing.

Tasks:

1. Assess RNA quality – RNA quality will be assessed using a method which determines both the quality and quantity of RNA, including the differentiation of genomic DNA and RNA using electrophoresis. Results of the RNA quality testing will be compiled in a document for delivery to researchers.

2. Prepare sequencing libraries - High quality RNA will be used to prepare sequencing libraries. Libraries will be constructed via enrichment of poly-A tails, and the construction will be performed such that the directionality of the RNA molecules is accounted for. QC of libraries will be performed.

3. Pool and normalize libraries - High quality libraries will be pooled in equal volumes and normalized.

4. Sequence libraries – Normalized libraries will be sequenced on a next-generation platform to produce high quality DNA reads (~30 million read pairs per sample, paired-end reads 2 x 150bp, at least 80% of reads have a base call error probability of less than 1 in 1000). Metrics assessing DNA read quality will be generated by software associated with the sequencing platform and provided to researchers as a final DNA sequencing QC report. Raw sequence data for each sample will be delivered to researchers within ARS- ABBL, along with sequencing QC report.

Deliverables:

• RNA QC report - generated from results of RNA quality testing (task 1)

• FASTQ files for each of 140 samples (~30 million reads per sample) – generated after library preparation and QC, library pooling and normalization, and sequencing of libraries on a next-generation platform (tasks 2,3,4)

• DNA sequencing data QC report – generated via the next-generation sequencing platform (task 4)

Delivery:

Raw sequence data for each sample will be delivered to researchers within ARS-ABBL, along with RNA and final sequencing QC reports within 270 days of award. All data files will be transferred digitally using a secure method or mailed to ARS via a hard drive.