Sanger Sequencing and Fragment Analysis
As announced in December 2019, the University of Michigan Advanced Genomics Core discontinued all Sanger sequencing services on March 13, 2020. The U of M research community will be better served by externals vendors for commodity Sanger needs, and the change will allow the AGC to focus on maximizing the added value of high throughput sequencing and related genomic techniques.
Sanger sequencing services are available to Michigan researchers through UM-wide relationships with Eurofins Genomics and GeneWiz.
Procurement Services announced that effective Monday, February 1, 2021 that Genewiz is now a contract supplier on the University’s M-marketsite ordering platform. Their punch-out catalog enables you to quickly and conveniently place your Sanger Sequencing orders via M-marketsite. Instructions detailing how to place orders can be found on the Genewiz Procurement Page.
- Genewiz Drop Box Locations (submission cut-off is 3:00 pm Monday through Friday):
- BSRB dock
- LSI dock
- MSRB II dock
- NCRC dock
- Genewiz Support:
- Genewiz Technical Support – Phone: (877) 436-3949 ext. 2, email@example.com
- Michael Bullard, Sales Executive II – Cell: (636) 466-1252, Email: Michael.Bullard@brooks.com
- Casey DeCesari, Sales Associate II – Cell: (619) 920-0528, Email: firstname.lastname@example.org
Procurement Services announced that effective Monday, June 1, 2020 that Eurofins is now a contract supplier on the University’s M-marketsite ordering platform. Their punch-out catalog enables you to quickly and conveniently place your Sanger Sequencing orders via M-marketsite. Instructions detailing how to place orders can be found on Eurofins Procurement Page.
- Eurofins Drop Box Locations (submission cut-off is 3:00 pm Monday through Friday):
- Brehm Tower Rm 5402
- BSRB outside Rm A852
- LSI 2452 (inside dock)
- MSRB II dock
- NCRC Building 14, Room 122
- NCRC dock
- Eurofins Genomics Support:
- North America (8:00 AM–7:00 PM, Monday–Friday, EST) – Phone: (800) 688-2248 FAX: (502) 371-0613; E-mail: GenomicsSupport@eurofins.com
- Dustin Perry, Head of Customer Support – Phone: (800) 688-2248 option 1; Email Dustinperry@eurofinsus.com
Access to old AGC Sanger Sequencing/Fragment Analysis data
Sanger data from the AGC will be available until December 1, 2020, at which time it will be permanently deleted from our system. How to get your old Sanger data (if you haven’t already):
- Have your PI contact the AGC using our consultation form: https://michmed.org/agc-consult. Yes, it has to be the PI.
- In the form, the PI can tell us they’d like their old Sanger data. In the reason field, please provide the “pilogin” that was used to access our old submission system.
- Someone from our data team will collect all of the data files we can find for that pilogin. We will share a zip of the files to the PI’s uniqname using U of M’s Google Drive.
- We’ll remove the share after about a week.
For security reasons, we cannot send data files to individual “users” in a lab; only the PI. If your PI no longer works for U of M, let us know and we’ll see if we can help you.
Tips for preparing samples for Sanger Sequencing
- How to prepare DNA.
- Why can’t I use a spectrophotometer to measure my mini-prep DNA?
- Can I directly sequence a PCR product?
- Can I get sequence from large-insert clones like BACs?
- Can I get sequence directly from bacterial genomic DNA?
- How do I design my own primers?
- What were the templates, volumes, and concentrations the Core used to process?
Sanger Sequencing Troubleshooting
- Interpretation of Sequencing Chromatograms
- Why is my text sequence slightly different than my chromatogram’s sequence?
- My primer works fine for PCR – why can’t you sequence with it?
- My samples produced only blank lanes. Why?
- The technicians reported ‘poor resolution’ for my samples. Why?
- Sequencing worked – sort of – the data aren’t very good. Why?
- What are the most common reasons for a sequencing reaction to fail?
The University of Michigan Advanced Genomics Core discontinued Affymetrix services July 2019. A list of certified Affymetrix service providers is available here: https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-partners-programs/affymetrix-service-providers.html.
QuantSeq provides cost-efficient, gene expression profiling data without the need for polyA-enrichment or rRNA depletion. Next-generation sequencing-based, reads are generated towards the poly(A) tail and directly correspond to the mRNA sequence simplifying the bioinformatic analysis. For gene expression studies, QuantSeq is an excellent alternative to microarrays and standard RNA-seq.
The University of Michigan Advanced Genomics Core discontinued all Sequenom genotyping services Spring 2019. Sequenom services are available from Agena Bioscience (formerly Sequenom) https://agenabio.com/services/
Design Taqman assays. You would need to set up the plates, but the core does have the QuantStudio needed so we can assist with running the PCR.
Custom NGS panel. You would work with a company to design a panel of amplicons that cover your SNPs of interest. The AGC can perform both the prep and accommodate the sequencing. Contact us for vendor recommendations
The University of Michigan Advanced Genomics Core discontinued PacBio services Summer 2018. A list of certified PacBio service providers is available here: https://www.pacb.com/products-and-services/service-providers/.
Linked-Read library prep barcodes HMW DNA prior to building an Illumina compatible DNA library. Analysis pipelines deconvolute the HMW barcodes to stitch the short reads from the sequencer together to generate synthetic long reads and enables phased and/or structural variant detection. The AGC can accommodate the entire workflow – prep, sequencing, and data processing. Contact us for more information.