FAQ | Microbiome Core

Yes, we happily take external clients from domestic and international institutions. There is a surcharge for all external clients. 

If you are outside of the United States, please contact us for additional shipping info.

Troubleshooting of 9 samples per plate is included. Clients will be contacted if more than 9 samples per plate fail to amplify. Before moving forward to normalization we will do one round of troubleshooting. 

For projects using standard PCR conditions, we will test two input conditions (a 4-fold increase and decrease of template concentration). 

Touchdown PCR projects will have the DNA template volume increased to 5 ul from 3 ul. 

Internal clients can login to your MiCores account and fill out a service request. External clients are asked to use our Qualtrics survey.

Yes, please submit at least 15 ul of volume per sample. Our shipping guide has more information on preparing plates for shipping. 

We will keep DNA for 60 days after submission; samples will be disposed after this period.  If you are an external client and have sent in samples for DNA extraction, we will ship your DNA back at cost to you.  We are not responsible for DNA that was not claimed and disposed after the grace period.

It is best practice to submit an aliquot of your DNA for submission and keep the remaining volume for other applications.

Yes, you can download a copy here.

We do not add samples to the Bead Plate.  We feel it is best that the client adds the samples as this reduces the risk of error.

Instructions can be found in our MiCores service request forms (specifically in ‘Community Analysis Submission’ or ‘Stand-alone DNA Isolation Service’).

250 uL or 0.25 g can be added to each well.  Please seal well with the provided silicone mat provided before returning to the Core.

A biohazard hood using appropriate personal protective equipment.

For samples that have amplified well, the average is 20K reads per sample on the Nano 500v2 flowcell and 15-20K per sample on the standard 500v2 flowcell.  However, this cannot be guaranteed as many factors can influence average reads/sample.

Yes, if you do not have an entire plate you are still responsible for the cost of the entire plate. On the plus side, you will receive more coverage of those samples than if you submitted a full plate.

It is not necessary, but recommended.  If quantifying the sample, please use a fluorescence-based assay such as Picogreen and not the Nanodrop.

The touchdown program is modified from the standard program as the initial annealing temperature is higher than the optimal Tm of the primers and is gradually reduced over subsequent cycles until the Tm temperature or “touchdown temperature” is reached.  This increases specificity and sensitivity in PCR amplification as described here. Additionally, after 20 rounds of touchdown PCR, another 20 rounds of standard PCR are performed.

Touchdown is a great tool for low biomass samples, but should  used with caution as any trace amounts of 16S will amplify including that in the negative controls.

The mock community used is commercially produced ZymoBIOMICS Microbial Community DNA Standard (cat# D6306), which is a mixture of genomic DNA extracted from pure cultures of eight bacterial and two fungal strains.  This mock community can be used for error analysis (see: Mothur Wiki).  The FASTA file for this mock can be found in a downloadable file below. 

FASTQ files

Yes.

All sequencing project data will be transferred on Illumina’s BaseSpace website. For an additional cost, you may request the data also be transferred to a USB.

You need to open an account using your email and include the email address in your service request form.

We keep backups of data for six months so if you lose your USB or delete your BaseSpace run within this time frame, we will likely have a backup copy. A fee of $75 will be charged to retrieve your data.

The standard workbook contains a methods sheet, your plate map, the PCR conditions for each of your samples, any troubleshooting conditions, post-PCR QC results, a summary of run metrics, and how well your samples indexed.

Most of our clients use Mothur to analyze their data.  The MiSeq SOP on the Mothur wiki page is an excellent resource.  Additionally, Pat Schloss offers numerous workshops throughout the year.

We do not currently provide analytical support for external clients at this time. For clients within the University of Michigan Medical School, we can provide a list of resource for analytical support.

We ask that all publications and presentations of research results supported by the Microbiome Core contain the following (or equivalent) acknowledgement:  "This research was supported by work performed by The University of Michigan Microbiome Core"

Please let us know as soon as you have an article accepted for publication, poster, or meeting presentation which has received Microbiome Core support. Early notification helps us to track the activities being supported by the Microbiome Core.  Submit your notifications by email to [email protected]. Be sure to include a copy of the presentation abstract or complete accepted article.