Clinical Trials Services
We will work closely with investigators and their clinical trials office to ensure patient-facing support for your study. The Microbiome Core does not reproduce clinically oriented services offered by other ISOs, but we can facilitate connecting investigators to services. Services performed by the CTO, UMGC, CISS, or other ISOs will be billed separately by them.
Courier Services [$106.11/trip]
Staley lab students/staff will pick-up samples from UMMC/CSC and transport to the lab for storage or deliver supplies for sample collection.
Fecal sample collection kits [$133.63/12 kits]
We will provide kits for bulk stool collection in 30mL collection tubes. Kits will be provided in increments of 12.
Swab collection kits [$125.61/12 kits]
We will provide kits for surface (e.g. skin) swabs or fecal samples. Surface swabs will be provided with a sampling buffer (0.15M NaCl, 0.1% Tween 20) and a storage buffer (0.15M NaCl, 0.1% Tween 20, 10% glycerol). Swabs for fecal samples will be provided in 95% ethanol.
Same-day sample processing [$106.46/sample]
The lab will receive samples and aliquot them to cryovials for freezer storage within 4 h of receipt (if received before 3pm). We will maintain an internal database of samples on Box. Any additional administrative reporting/oversight is the responsibility of the contact PI.
Microbiome Analytics Services
We work closely with UMGC and MSI to facilitate quality sequencing and bioinformatics analyses. Services provided by UMGC will be billed separately, but we can handle submission and paperwork if provided a chartstring.
DNA extraction [$344.03/12 samples]
We will extract DNA from samples using QIAGEN's DNeasy PowerSoil Pro kit on the QIAcube platform. DNA will be quantified using the Qubit double-stranded DNA high sensitivity kit. For studies needing high-throughput (>100 samples at one time) DNA extraction services, please contact UMGC.
Sequencing submission [$311.48/plate]
We will complete submission paperwork, aliquot DNA to sequencing plates, and deliver plates to UMGC for sequencing.
Amplicon sequence processing and analysis [$4,244.22/dataset]
We will process amplicon sequence data (16S rRNA/ITS) for prokaryotes or fungi using mothur. We will provide standard outputs that include a table of taxa abundances with a genus-level summary, alpha diversity measures, an ordination plot, and SourceTracker source similarity calculations, if applicable. Data will be provided as Excel workbooks. Additional statistical analyses are offered as a separate service.
Expedited service [$6,116.40/dataset]
Amplicon sequencing processing and analysis will be performed by Dr. Staley with a TAT <2 weeks for standard workflows.
Shotgun sequence processing and analysis [$8,182.62/up to 100 samples]
We will process shotgun data using tools from the Biobakery to perform taxonomic and functional annotation. We will provide stratified taxonomic, gene family, and gene pathway tables as well as clean species table. Data will be screened to remove host contamination prior to annotation, and gene families can be annotated to as Enzyme Commission (EC) or KEGG pathways. Note: this workflow is in the process of being updated to use Kraken2 for taxonomy annotation. Additional statistical analyses are offered as a separate service.
Expedited service [$12,232.80/up to 100 samples]
Shotgun sequence process and analysis will be performed by Dr. Staley with a TAT of ~1 month.
Statistical analysis [$2,122.11/dataset]
We will perform statistical analyses integrating the microbiome data with (clinical) metadata and do specialized statistical analysis based on study goals. Service will include up to two meetings with collaborators to understand study goals and explain the data interpretation. Additional requests for statistical analysis after the first consultation will be billed as a separate analysis.
Custom bioinformatics [$4,244.22/analysis]
We will work with investigators who wish to use new or emerging tools for microbiome analysis. Currently available custom services include co-occurrence network analysis; however, we are open to trying new tools and will add to these services as our skills expand.
Training by student [$98.46/meeting (up to 1 h)]
One of our PhD students in the BICB program will work with you or your student/staff to train them in microbiome analytics methods. PIs should have established accounts with the Minnesota Supercomputing Institute (MSI). Investigators needing to set up MSI accounts (free of charge) can find instructions here.
Training by Dr. Staley [$152.91/meeting (up to 1 h)]
Dr. Staley will work with you or your student/staff to train them in microbiome analytics methods. PIs should have established accounts with the Minnesota Supercomputing Institute (MSI). Investigators needing to set up MSI accounts (free of charge) can find instructions here.
Investigators requiring additional or specialized analyses should email Chris [cmstaley@umn.edu] to discuss his availabilty to collaborate.