Cite the Vincent J. Coates Genomic Sequencing Facility
1. How should I acknowledge your services in my publications?
All work performed by the Vincent J. Coates Genomics Sequencing Laboratory and Functional Genomics Laboratory should be acknowledged in reports, presentations, posters, papers, and other publications. Your acknowledgment is a measure of our facility’s impact, and is essential to our funding and continued operation.
For genomic sequencing using the HiSeq4000 platforms, please acknowledge us as follows:
“This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant.”
There is no NIH grant reference required for MiSeq, NovaSeq, or PacBio sequencing ; however, we do ask that you reference the facility in your Materials and Methods sections for all services provided by the facility. For methods details please contact firstname.lastname@example.org, please provide the facility with enough time to compile the information specific to your project (a minimum of 14 days).
Please also let us know if you have a publication that cites data from our laboratory by emailing the full citation of PMCID.
1. How much starting material do you need?
Please see our Submissions pages for requirements for all prep types. If you have less than our requested amount, please contact us to discuss. We may still be able to generate libraries for you.
2. How long does it take for library preps + sequencing to finish?
The general turnaround time for library prep through sequencing is 4-6 weeks (Illumina). This can be shorter or longer depending on our current queues and your sample counts. For PacBio and iTag this is a moving target. Please inquire for your project if you need data faster than within 4 weeks.
3. What’s the turnaround time for Illumina sequencing only projects?
Generally, turnaround time for NovaSeq and HiSeq4000 lanes is 2-3 for all run types. The HiSeq4000 wait time is based on the rate to fill an 8 lane flow cell; but the wait is normally 2-3 weeks for 50SR and 100PE run types. Novaseq flowcells require 2 lanes (except S4 flowcells have 4 lanes) and tend to fill quickly. Submitting a full flowcell can result in data the same week. MiSeq data is generally returned within 1-3 weeks but can be longer if there are many 300PE samples in the queue. Please contact us if you have time-sensitive samples to discuss your options. Samples that are submitted with minimal QC requirements generally move through the queue faster. Submissions that have not passed QC (bioanalyzer, qPCR, and cleans) will be passed over in the line for later submission that have already passed. So submitting a single tube with a Bioanalyzer traces per lane will result in the fastest turnaround.
4. Can I use custom sequencing primers?
Custom sequencing primers are accepted for all reads on the MiSeq. Custom R1 primers are also accepted for R1 on the HiSeq4000. The NovaSeq can run custom primers but they must be applied to the entire flowcell not just a single lane. Please contact us prior to submission and understand that the facility is never responsible for run failures deemed due to custom primers by Illumina technical support. You must clearly indicate on your submission form that you need custom primers if that is the case. It is never assumed that they are required and we will not look if it’s not indicated on your submission form in the comments section.
5. How do you provide your sequencing data?
We provide users with access to our secure FTP server, which will have your ata files in FastQ format. These data are available on the server for one month. Reposts after the one-month download window will incur a fee. Data is not stored indefinitely and may not be available for repost. The FTP is a secure transfer point with password protected access to individual data sets per user.
6. Do you archive sequencing data files on your servers?
We guarantee that we will have sequencing data for 3 months on a backup server. In most cases, we have the capacity to hold data files for up to 6 months. It is your responsibility to backup your data and ensure that your files have not been corrupted upon download. Md5check sums are generated for your reference.
7. Do you archive submitted samples?
Samples will be stored at -20 degrees C for no more than 1 year past the date of seqeuncing. Samples that are never sequenced are not stored. If you cancel a run you must collect your samples or they will be discarded quickly. The GSL facilities will not under any circumstances store user’s sequenced samples beyond one year. Please arrange pick-up of your samples within THREE months of data return if you require them. It is not a good idea to provide the GSL with your entire sample volume unless specifically required to meet minimum submission requirements. Please join the GSL User email list to get notifications regarding annual sample purges. You can request old samples be returned at that time for a fee if you forgot to get them previously.