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 (or equivalent; email to Hilary)
Keck personnel are not responsible for size-selecting or pooling samples

For shotgun projects, please email a spreadsheet (or tab-delimited text file) with your sample ids and indexes used to Hilary (hmorrison1981@gmail.com). Also provide a valid cost center number or AR account number, and type of run requested (PE, HT, etc.)

VAMPS project submission is required for all projects, both amplicon and shotgun genomic/metagenomic

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 (currently Bailey Fallon; 2022)
PI must provide all reagents OTHER than the Miseq kit itself
Run must be preceded by email or discussion with Hilary
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 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)

NextSeq Operation

Samples must be provided as above
Small sample ‘spike in’ will be done at our discretion
Distribution of samples across lanes will be done at our discretion in order to optimize data recovery from both amplicon and shotgun libraries
Keck personnel are responsible for data transfer and amplicon processing