Illumina Sequencing Requirements

This document specifies requirements for the submission and sequencings of Illumina libraries through the Keck Facility.  Because we are not a core facility, we have been open to users wishing to sequence less than a full lane, but this level of accommodation requires cooperation by all.

 

Sample Requirements

Samples must be ready for Kapa qPCR quantitation and clustering
Samples must be accompanied by a Bioanalyzer trace (email to Joe)
Keck personnel are not responsible for size-selecting or pooling samples
Exceptions must be requested via the Illumina sequencing request

Illumina Sequencing Request Form

This form is required for all types of Illumina sequencing; complete it well in advance of the run
This form is required for all users, including Keck personnel
All samples should be delivered to Joe by the date specified in the sequencing request to hold your space reservation
Any materials provided by Sogin lab or Keck facility, e.g. Qiagen clean up plates, must be identified in the sequencing request for charge back
Information on average insert size and indices used for shotgun libraries is requested and required on the sequencing request
Lane fractions allowed are 0.25, 0.5, 0.75 only

VAMPS project submission is required for amplicon projects

Provide a valid cost center number
Be certain the project description and dataset names are as you wish to see them in VAMPS (renaming requires a VAMPS reload).
Failure to submit required forms in a timely way may result in the exclusion of your samples from the expected run

 

Miseq Operation

End-user operation

PI may elect to have an RA trained in the operation of the Miseq and perform their runs
RA must be trained either directly by Illumina personnel or by one of the Keck facility RAs (Bette, Sharon, Joe)
PI must provide all reagents OTHER than the Miseq kit itself
Run must be preceded by Illumina sequencing request
Run information must be entered into the log on the Miseq desktop on the day of the run
PI’s lab personnel are responsible for data transfer and backup and for amplicon processing

Keck personnel operation

Run will be performed by one of the Keck facility RAs with time charged to end user’s cost center OR at monthly billing
Any additional reagents used, i.e. Kapa qPCR, will be charged at monthly billing along with usual run charge
Run must be preceded by Illumina sequencing request
Run information must be entered into the log on the Miseq desktop on the day of the run
Keck personnel are responsible for data transfer and amplicon processing
Keck facility will retain a copy of the unprocessed data (/sequencing)

Hiseq Operation

Joe is the only person who will operate the cBot and Hiseq
Samples must be provided as described in I
Small sample ‘spike in’ will be done at Joe’s discretion
Distribution of samples across lanes will be done at Joe’s discretion in order to optimize data recovery from both amplicon and shotgun libraries
Keck personnel are responsible for data transfer and amplicon processing

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