RNA Sequencing, Gene Expression and structural variants

Description:
The USDA, ARS, NWISRL in Kimberly, ID has a requirement for Sequencing, Resequencing and Gene Expression analysis of Selected Sugar beet germplasm. We have 4 samples for whole genome sequencing and 24 samples for Gene Expression.

This is a Full and Open Combined Synopsis/Solicitation announcement for a commercial service prepared in accordance with the format in Subpart 12.6, as supplemented with additional information included in this notice.
This announcement constitutes the only solicitation. Solicitation number 901205405000815_IAE_FULL is issued as a request for quotes (RFQ).

The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 2019-005 corrections.
Interested offerers must submit their quote by filling out the attached Standard Form 18,Request for Quotation. Successful offerer will be evaluated by the evaluation factors that are included in the Standard Form 18.
The government intends to award a Firm Fixed Price Contract in September 2019.

We have 4 samples for whole genome sequencing and 24 samples for Gene Expression.
The genome size is 758MB. CLR library.
Latest version of software.
Our timeline to delivery is 10 weeks.

Objectives of the Sequencing Project:
1. To improve the whole genome sequence (WGS) assembly of BwSeq-1 (the first USDA-ARS genome assembly­ KDH13). This is targeting Beet curly top resistance genes

2. To establish the first whole genome assembly for KDH709-2 targeting resistance to rhizoctonia root rot disease.

3. To develop gene expression profiles for beet curly top and rhizoctonia root rot

Sequencing and resequencing KDH13,KDH709-2,KDH19-17, F1-13/19-17 are achieved through the following steps:

1. Samples and processing DNA extraction and perform quality control

2. Preparation of libraries (DNA fragments bank) for each sequencing analysis

3. Sequencing using different sequencing systems:
a. lllumina Sequencing platform: This is a sequencing system that produce millions of short (2x150 bp) DNA sequences (fragments).
b. PacBio sequencing platform: This is a sequencing system that produce long (8-15 KB) DNA sequences
4. Bioinformatics analysis:
a. Providing a FASTA formatted sequences
b. Develop a whole genome assembly
c. Submitting the assembly (BAMfiles) to the GenBank (www.ncbi.nlm.nih.gov) Gene Expression Profiling:
1. Sample preparation and RNA processing:
2. Preparation of Libraries and quality control
3. RNA - sequencing using lllumina system
4. Bioinformatics: developing gene expression profiles based on pair-wise comparisons.
5. Submit RNASeq to the GenBank (www.ncbi.nlm.nih.gov).

References :

lllumina DNA sequencing: https:/ / www.illumina.co ml systems/ se guencing-platforms.html PacBio DNA sequencing: https:/ / www.pacb.com/

PLEASE SEE THE SCOPE OF WORK ATTACHED FOR THE DETAILES OF THE FOUR SPECIFIC AND DISCRETE SERVICES TO BE PERFORMED.
1) PacBio Whole Genome Sequencing for KDH13
2) PacBio Whole Genome Sequencing for KDH709-2
3) Standard RNA sequencing with samples mapped as per special comments.
4) Whole Genome Sequencing, reference genome KDH13

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