CQLS Illumina HiSeq 3000 and MiSeq Service Description

The Center for Quantitative Life Sciences (CQLS) offers a service to sequence DNA samples on the Illumina HiSeq 3000 and MiSeq platforms. Due to the nature of the technology, the CQLS has established a formal description of the service to ensure the greatest utility to its users. The description below contains information about arranging payment, sample submission and subsequent data analysis.

  1. Initially, all projects should be discussed with Mark Dasenko. Mark will provide the date for your Illumina run, which can be viewed on the high throughput sequencer (HTS) calendarPlease note that the events listed on this calendar are for reference only, and are subject to change on a daily basis to reflect the status of the Illumina sequencer and completed runs.  Run dates will shift due to unexpected downtimes, repairs, unforeseen problems, and reruns.  As detailed below, several things must be in place at least 2 days prior to this date or your spot in the CQLS Illumina job queue will be forfeited. If you have questions about the computational requirements for downstream analysis of your data, please contact Chris Sullivan.
  2. Parties from outside Oregon University System (OUS) must establish payment terms prior to submitting biological samples to the CQLS. Contact Bo Price for details. Payment terms must be in place at least 2 working days prior to the scheduled Illumina run.
  3. Although the overall design of the project using data from the Illumina sequencers is the responsibility of the submitting parties, CQLS staff can provide specific details related to sample submission and data acquisition. For questions related to biological sample and PhiX Spike-In, contact Mark Dasenko. For questions about data acquisition or the Barcode policy, contact Matthew Peterson
  4. At least 2 days prior to the scheduled Illumina run, an order should be placed using the CQLS online ordering system.
  5. When you log in to the ordering system you will be able to see which kinds of samples are already in the queue to be run, and how many samples of each kind are needed to complete a set of 8 that is required to fill and run a flow cell. This information is also viewable on a display in ALS3012.
  6. Biological samples should be submitted to Mark Dasenko at the CQLS at least 2 days prior to scheduled Illumina run (see address in item number 12).
  7. Mark Dasenko will prepare the samples and run them on the Illumina HiSeq 3000 or MiSeq sequencer.
  8. Primary data from the Illumina sequencers will be transferred to a central repository within the CQLS computational infrastructure. All primary data and data generated by the Illumina data analysis pipeline (see 10) will reside in the central repository for a maximum of 2 weeks from the time of transfer.
  9. Primary data will be archived to digital tape.
  10. Primary data will be run through the Illumina data analysis pipeline.  Analysis of HTS data is a major consideration. The CQLS does not maintain adequate staff to do any analysis of Illumina data other than what is generated by the Illumina data analysis pipeline. The Illumina data analysis pipeline extracts DNA sequence data from the image files generated by the sequencers as it cycles through the samples. Therefore, the CQLS will deliver all the primary data generated by the HiSeq 3000 or MiSeq and the DNA sequence data generated by the Illumina data analysis pipeline. Please note that sequence reads containing adaptor or non-reference sequences will not currently run through the basic mapping feature of the Illumina pipeline. Mapping will require parsing of reads from adaptor sequence, then mapping of the parsed reads. The CQLS does not currently provide these steps as a service.
  11. Graphical and Tabular summaries of the data will be available on a website maintained by the CQLS. The URL for the data will be emailed to the submitting parties.
  12. All primary data and the data generated by the Illumina data analysis pipeline will be available for only 2 weeks on the CQLS file servers. Therefore, researchers will need to copy their data onto a file server they own or a collaborator's file server. External customers have the option of downloading their data via the web or providing an external USB hard drive. This USB hard drive must be supplied by the external customer to the CQLS (see below) at least 2 days before the scheduled Illumina run.  Please contact Matthew Peterson to determine the size of hard drive that is needed to store the flow cell data. The CQLS is not responsible for the hard drive, any data on the hard drive, or shipping costs. Send hard drives to:
          Mark Dasenko
          Center for Quantitative Life Sciences
          Oregon State University
          ALS 3012
          Corvallis, OR 97331-7303

Checklist for CQLS Illumina service:

All of the items on this checklist must occur at least 2 days prior to the scheduled Illumina run. Failure to do so will result in losing your place in the CQLS Illumina queue.

Contact Mark Dasenko to schedule Illumina run
Establish payment terms with Bo Price (non-OSU users only)
Place order using CQLS online ordering system
Submit biological samples to Mark Dasenko
Send USB hard drive to Mark Dasenko (if necessary)