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 [$63.24/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 [$88.12/12 kits]
We will provide kits for bulk stool collection in 30mL collection tubes. Kits will be provided in increments of 12.
Swab collection kits [$80.79/12 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 [$63.67/sample]
The lab will receive samples and aliquot them to cryovials for freezer storage within 1 h of receipt (if received between 10am - 3pm)
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 [$235.82/12 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) DNA extraction services, please contact UMGC.
Sequencing submission [$185.60/plate]
We will complete submission paperwork, aliquot DNA to sequencing plates, and deliver plates to UMGC for sequencing.
Amplicon sequence processing and analysis [$2,529.42/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 basic statistical analyses (one pass only). Data will be provided as Excel workbooks. We will work with the investigator to understand the main study questions to guide analysis, but we will only perform one round of analyses under this service.
Shotgun sequence processing and analysis [$4,797.42/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. We will perform basic analysis for differential abundances in categorical variables using MaAsLin3.
Investigators requiring additional or specialized analyses should email Chris [cmstaley@umn.edu] to discuss his availabilty to collaborate.