Service Description
Our CRISPR-Cas9 Editing Analysis service is an extension of our existing amplicon sequencing service. Using the same rapid, cost-effective approach, coupled with a refined analysis, we are able to provide a comprehensive report of the editing outcomes from your CRISPR-cas9 experiment. This service is capable of analyzing outcomes from non-homologous end joining (NHEJ) and homology-directed repair (HDR).
Runs are twice a week – Monday and Thursday!
Access our Interactive Submission Guidelines and get the exact guidance you need to prepare, label, and deliver your samples.
Drop-off at Biotech Center outside room 1360 or WIMR outside room 7162. Shipping, pick up times, and more can be found in the Interactive Submission Guidelines.
If you can’t find the information you’re looking for, please contact us at nextgen-seq@biotech.wisc.edu
CRISPR-Cas9 Editing Analysis Pricing
Effective 4/1/25
| Flat rate is charged for any submission in a 96-well plate, even if <96 samples. |
| Prices are subject to change without notice. Please email nextgen-seq@biotech.wisc.edu to request a quote. In the absence of a valid quote, prices from our current price books will be applied at the time of the service request. Prices may differ from those listed on this page. |
Important Notes and FAQs
What do I get back from UWBC? We will provide a CRISPResso2 report and FASTQ files of passed reads.
What size do my amplicons need to be? For greatest success, your amplicon should be >500bp and your primers should be designed at least 200bp away from your edit. The reference sequence you provide should begin with your forward primer and end with your reverse primer. Your reference sequence should be the WT sequence to which your expected edits will be compared.
Does UWBC perform QC of my amplified DNA? No upfront QC of the input DNA or QC of the final library is performed. Ensure the following before you submit.
- Optimize your reaction to avoid primer dimer, spurious products, over-amplification/heteroduplex formation, or weak enrichment.
- Check for effective target amplification. Verify the presence of the intended product and absence of primer dimers or spurious products by visualization on an agarose gel. Any and all dsDNA products submitted to us have the potential of being sequenced.
- If you are having trouble with your initial amplification, contact the DNA Sequencing facility before you submit.
Do you hold onto my amplicon and can I get it back? Once the data is delivered, we dispose of the amplicon. We suggest you retain sufficient product for your needs as we will not send it back to you.
When can I expect results? Runs are scheduled every Monday and Thursday. Provide samples at least a day before a run and you can expect data the following day after that run. The exception may be weeks with intervening holidays where the facility is closed. If the sample is received later than 8am on Monday or Thursday, it will be processed the following run cycle. Please note that shipments received the day of a run will not reach us in time – please plan shipments accordingly.
How do I access my data? Our preferred method to distribute data is through Globus (external clients) and ResearchDrive (internal clients). More information can be found here. You will receive an email when your data is available and it will contain instructions on how to access it.
How long do you store my data? We store your data for 60 days. After 60 days, it is deleted from our servers. Please download your data as soon as you receive the data delivery notification!
Do you guarantee success or read counts? Following our guidelines gives the highest chance of successful amplicon sequencing. High quality inputs that meet specifications are very likely to get more than sufficient coverage. We don’t guarantee variant detection, phasing of variants, minimum read count, or minimum/even amplicon coverage. If you aren’t seeing what you expect in your data, there may be issues other than quality and quantity to consider such as complexity of the amplicon (specifically, but not limited to, homopolymeric regions). This may be addressed with other methods – we’re here to help!
Do you still charge if no data is generated? Each amplicon will be charged, even if no data is generated. Refer to our guidelines for the best chance of a successfully analyzed amplicon.
What type of basecaller is used? Guppy basecaller with the Super accurate (SUP) model is used, which is the most accurate model available for Oxford Nanopore data.
Why do I not see what I expected in the report I received? Reasons you may not see expected results vary but are likely due to the provided product not being what you intended to amplify (spurious amplification or pseudogene), insufficient product provided, or incorrectly provided/oriented sequences.
Unless otherwise specified, all data and reagents distributed by the University of Wisconsin Biotechnology Center DNA Sequencing Facility are intended for research purposes only. They are not intended nor certified for diagnostic or clinical use. Clinical services are provided through our collaboration with the UW Collaborative Genomics Core.