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Illumina 1G High Throughput Sequencing Run Policy

CGRB Illumina 1G Service Description

The Center for Genome Research and Biocomputing (CGRB) offers a service to sequence DNA samples on the Illumina 1G platform. Due to the nature of the technology, the CGRB 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. As detailed below, several things must be in place at least 2 days prior to this date or your spot in the CGRB Illumina job queue will be forfeited.
  1. Payment terms must be established prior to submitting biological samples to the CGRB. Contact Rosa Hill () for details. Payment terms must be in place at least 2 working days prior to the scheduled Illumina run.
  1. Although the overall design of the project using data from the 1G is the responsibility of the submitting parties, CGRB staff can provide specific details related to sample submission and data acquisition. For questions related to biological samples, contact Mark Dasenko. For questions about data acquisition, contact Steve Drake ().
  1. At least 2 days prior to the scheduled Illumina run, an order should be placed using the CGRB online ordering system (http://www.cgrb.oregonstate.edu/weborder). As part of this process, the submitting parties need to provide a reference genome file in FASTA format (if available) to be used by the Solexa data analysis pipeline (see 10). Contact Steve Drake for details of submitting the file. The reference genome file must be received at least 2 working days prior to the scheduled Illumina run.
  1. Biological samples should be submitted to Mark Dasenko at the CGRB at least 2 days prior to scheduled Illumina run:

    Mark Dasenko
    Center for Genome Research and Biocomputing
    Oregon State University
    Corvallis, OR 97331-7303

  1. Parties from outside Oregon University System (OUS) must purchase reagent kits from Illumina and send them to Mark Dasenko at least 2 days prior to scheduled Illumina run. For a normal Illumina sequencing run, the kits required are the cluster station kit and the SBS kit. For Illumina expression profiling, different kits may be necessary; please discuss your specific run details with Mark Dasenko.
  1. Mark Dasenko will prepare the samples and run them on the Illumina 1G sequencer.
  1. Primary data from the 1G will be transferred to a central repository within the CGRB computational infrastructure. All primary data and data generated by the Solexa data analysis pipeline (see 10) will reside in the central repository for a maximum of 2 weeks from the time of transfer.
  1. Primary data will be archived to digital tape.
  1. Primary data will be run through the Solexa data analysis pipeline.
Analysis of the 1G data is a major consideration. The CGRB does not maintain adequate staff to do any analysis of 1G data other than what is generated by the Solexa data analysis pipeline. The Solexa data analysis pipeline extracts DNA sequence data from the image files generated by the 1G as it cycles through the samples. Therefore, the CGRB will deliver all the primary data generated by the 1G and the DNA sequence data generated by the Solexa 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 CGRB does not currently provide these steps as a service.
  1. Graphical and Tabular summaries of the data will be available on a website maintained by the CGRB. The URL for the data will be emailed to the submitting parties. These data will be available for as long as the data reside on the central repository file system (roughly 2 weeks). Summary data will remain on the CGRB online ordering system indefinitely (under the “View Data” link). Please please see additional comments about data analysis, above (see 10). Mapping and run quality data from the current Illumina pipeline will be inaccurate if adaptor or non-reference sequences are included in reads.
  1. All primary data and the data generated by the Solexa data analysis pipeline will be delivered on a portable USB hard drive supplied by the submitting parties. This hard drive must be supplied at least 2 days prior to the scheduled Illumina run. The hard drive should have enough storage capacity to contain all the data, which is roughly 1TB per flowcell. Data will not be available for direct download due to network limitations. Send hard drives to:

    Mark Dasenko
    Center for Genome Research and Biocomputing
    Oregon State University
    Corvallis, OR 97331-7303

     

Checklist for CGRB 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 CGRB Illumina queue.

Contact Mark Dasenko () to schedule Illumina run
Establish payment terms with Rosa Hill ()
Place order using CGRB online ordering system (http://www.cgrb.oregonstate.edu/weborder)
Submit fasta file of reference sequence to Steve Drake ()
Submit biological samples to Mark Dasenko
Send Mark Dasenko the necessary Illumina reagent kits
Send USB hard drive to Mark Dasenko