I.            Sequencing Process

Initial Consultation

1. The Genomics Core (GC) will schedule an initial consultation to discuss your research goals and project expectations with core personnel and faculty researchers.
2. If needed, the GC will provide assistance and guidance with project design, however, final decisions regarding experimental design will be the customer’s responsibility.

Pre-processing

1. The project will be placed into the GC sequencing queue and processed by core personnel once all required forms have been completed and submitted.
2. All samples will be quality control checked prior to preparing sequencing libraries to determine suitability. Please note that we cannot guarantee that your sample will perform well in downstream procedures even if it passes all quality control checks. If your sample passes our quality control tests, but fails to provide satisfactory sequencing data, we will request a replacement sample and repeat sequencing at no cost to you.

Sample Preparation

1. Prepared libraries will be run on the Agilent 2100 Bioanalyzer and qPCR-verified prior to sequencing. 
2. If at any point during the library preparation, the GC staff finds that the sample is insufficient quality or quantity for downstream sequencing, the customer will be notified and a replacement sample will be requested. If additional sample is not available or cannot be provided, the customer will have the option to proceed with the current sample or forego sequencing; if the customer decides to proceed with sequencing against the advice of the GC, the customer must agree that the data obtained will be "as-is".

Sequencing Run

1. Depending on the type of sample submitted and sequencing requested, the GC will either prepare libraries for sequencing on the MiSeq in-house or submit prepared libraries to the outsourcing facility for sequencing on the HiSeq. If samples are run in-house on the MiSeq, the GC will ensure that the instrument is running optimally. We will re-run any samples if there is an instrument malfunction or error determined to be the fault of the GC. 
2. If samples are outsourced to be run on the HiSeq, the EBC will be the liaison between the customer and the outsourcing facility if there are any questions for the project. Likewise, the GC cannot guarantee satisfactory results received from the outsourced facility. The GC will work with the outsourcing facility to obtain the best possible sequencing results and provide a reasonable response to under performing runs.   

II.            Post Run

1. Raw sequencing data from MiSeq experiments will be retrieved from Illumina’s BaseSpace. The GC will obtain HiSeq sequencing data from the outsourcing facility.
2. The GC will provide FASTQ files for all sequencing runs. If samples were pooled using Illumina adapter indexes, then the samples will be demultiplexed into separate files. 
3. Sequencing data will be made available to the customer over a secure server and stored both locally and backed-up on our server.

III.            Expectations

1. The customer will provide an adequate amount of sample necessary to proceed with the requested experiment. Guidelines for sample submission and input requirements can be found on the GC website. Additionally, Illumina’s website provides sample preparation guides and protocols for all Illumina library preparation kits. 
2. All samples will be quality control checked prior to preparing sequencing libraries to determine suitability.We cannot guarantee that your sample will perform well in downstream procedures even if it passes all quality control checks. If your sample passes our quality control tests, but fails to provide satisfactory sequencing data, we will request a replacement sample and repeat sequencing at no cost to you.
3. If at any point during the library preparation, the GC staff finds that the sample is insufficient quality or quantity for downstream sequencing, the customer will be notified and a replacement sample will be requested. If additional sample is not available or cannot be provided, the customer will have the option to proceed with the current sample or forego sequencing; if the customer decides to proceed with sequencing against the advice of the GC, the customer must agree that the data obtained will be "as-is".   

I hereby acknowledge receipt of the Epigenetics Bioinformatics Core Sequencing Policy. I have read the policy and acknowledge that work for my project will begin after an initial consultation has taken place and the Sample Submission form has been completed and submitted to the core. I acknowledge that adequate sample concentrations and volumes are required for library preparation methods and that samples must be of sufficient quality to provide satisfactory sequencing results. I acknowledge that the core cannot guarantee that my samples will perform well in downstream sequencing even if the sample passes all quality control checks. If my samples are deemed of insufficient quality/quantity, and I decide to proceed with sequencing against the advice of the core, I agree that the data obtained will be "as-is".