SPECIFICATIONS_FOR_SEQUENCING.docx

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Attached to
RNA Sequencing Federal contract opportunity
Solicitation number
1232SC18-927459
Issued by
Department of Agriculture Agricultural Research Service Central Program Planning Coordination and Support

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SPECIFICATIONS FOR LIBRARY PREP AND CONSTRUCTION AND SEQUENCING

USDA, ARS shall provide the following:

1)ARS provide 172 RNA samples (sets of 20-24 samples per Illumina cartridge per submission).
2) Samples will be packed on dry ice in a cooler and pay for the overnight shipping
3)The USDA, ARS shall provide an email to the Contractor with the shipping tracking number on the date the samples are shipped.
4)Replacement samples will be provided upon request. (is there a time limit from when samples are originally received – there should be no time limit?
5)The USDA, ARS shall collect the results as raw sequencing data provided by the FTP or other means of transferring large data sets. The provider will deliver data within two weeks from sample submission.

The Contractor shall provide the following:

1. cDNA library preparation:

1. DNase treatment on total RNA samples.

1. rRNA Depletion using ribo-zero kits.

1. Perform QC to assure RNA quality is suitable for cDNA library construction.

1. RNA library construction (Produce cDNA libraries for HTS).

1. High throughput sequencing:

a.Ability to Multiplex samples for sequencing with unique barcodes
b.Perform sequencing using Illumina NextSeq, HiSeq2500 or HiSeq4000 system.
c.Produce raw data reads (75 bp single-end reads). Expected number of raw data reads per sample are 25, 000, 000 to 50, 000, 000
d.Electronic access to a LIMS (Laboratory Information Management System) based system for access to sequencing data once sequencing is completed.
3.Provide an email notice for: 1) Access to LIMS; and 2) When the work has been completed.
4.Submit the (consolidated) monthly Invoice, in arrears after the services have been completed through the Invoice Processing Platform (IPP) System.
5.Provide a final release of claims with the final invoice.

Delivery of Services:

The Contractor will notify Dr. Dimitre Mollov by email at dimitre.mollov@ars.usda.gov and Lynn Hults, the Contracting Officer, at lynn.hults@ars.usda.gov when the results are completed and available for access through LIMS.

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