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 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 HiSeq2000 platforms (only before 2015), please acknowledge us as follows:
“This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 Instrumentation Grants S10RR029668 and S10RR027303.”
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 or HiSeq2500 Rapid 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 email@example.com, 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, either by email (send PMCID) or by using this form.
Please also link your papers to our NIH grants in eRA commons, RePORTER, etc., through myNCBI. Instructions on how to do so can be found here.
Illumina-Compatible Library Preparation
1. How much starting material do you need?
Please see our Submissions page with more information regarding our starting material requirements. 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 to finish?
The general turnaround time for library prep sample is 2-3 weeks. This can be shorter or longer depending on our current queue.
1. What concentration do you need samples to be for submission?
Please provide us with at least 10uL of minimum 10nM sample. For the HiSeq4000, we will need 5ul at 3nM per sample as measured by qPCR, so provide >10nM as measured by Qubit to account for ligation inefficiencies. For the HiSeq2500/MiSeq, samples that measure lower than 0.5nM post qPCR must be resubmitted. If you have a low concentration sample please submit more than the requested 10ul. Please also submit samples in water when possible, this will help if we need to concentrate your samples.
2. Can I use custom sequencing primers?
Custom sequencing primers are accepted for all reads on the MiSeq and the 2500. Custom R1 primers are also accepted for the HiSeq4000, index and R2 primers can be accepted but we must review the sequences first. Please contact us prior to submission; additional charges may apply for single lane only custom primer use on the 2500.
3. What’s the turnaround time for sequencing projects?
Generally, turnaround time for HiSeq2500 lanes is 3-4 weeks depending upon the run type. Users that can fill an entire flow cell (2 lanes same run type) generally see data within 1-2 weeks. 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 or 3-5 100SR and 150PE run types. Submitting 8 lanes for the same run type can result in data the same week. MiSeq data is generally returned within 1-3 weeks. Please contact us if you have time-sensitive samples to discuss your options.
4. What are the benefits of the HiSeq2500 rapid vs HiSeq4000?
The HiSeq2500 can perform a 250PE run while the HiSeq4000 maxes out at 150PE, there is also a 150SR lane type on the 2500 but wait-times can be long. The HiSeq4000 is cheaper per base and results in more than double the throughput per lane but per lane the 2500 is cheaper if you do not need the high depth of the 4000. The 2500 also requires far less DNA than the 4000.
5. How do you provide your sequencing data?
We provide users with access to our FTP server, which will have your data 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.
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.
7. Do you archive submitted samples?
Samples will be stored at -20 degrees C for no more than 1 year past the data of submission. The GSL facilities will not under any circumstances store user’s samples beyond this point. Please arrange pick-up of your samples within ONE month of data return if you require them or provide a FedEx account number if you require samples to be returned. It is not a good idea to provide the GSL with your entire sample volume unless specifically required to meet minimum submission requirements.