Overview of UConn MARS
The UConn Microbial Analysis, Resources, and Services facility offers training as well as fee-for-service equipment access and sample processing. Primarily we are a next-gen sequencing facility focused on high throughput sample processing. Our services are designed to meet the needs of the UConn research community but most are also available to non-UConn groups.
MARS Staff
Kendra Maas, Facility Scientist and Director
Kendra.Maas@uconn.edu
Lisa Nigro, Post-doctoral Facility Scientist
mars@uconn.edu
MARS Training Suspending due to SARS-CoV2
We offer training through MARS workshops and one-on-one informal training. The training required for equipment access is instrument specific. Trainings are offered throughout the year and are announced through emails and on the mars.uconn.edu website. Trained users as well as sample processing clients are encouraged to ask facility staff for assistance on any aspect of our services.
MARS Fee-for-service Sample processing
Microbiome and Amplicon Analysis
MARS offers several on-ramps for this analysis. Full service sample processing is available by combining DNA extraction (BSL1 only) with our DNA to data service which includes quantification, library prep, and sequencing at least 10,000 sequences per sample. If you are submitting DNA, we don’t have a hard cutoff for quantity or quality of DNA but be aware the very dilute or impure DNA could lead to difficulty amplifying and/or biased community recovered. If you submit DNA, we recommend at least 50ng in 20ul water/tris/TE. We can also sequence user generated libraries provided that they can use either MARS or Illumina standard sequencing primers (Client Amplicon library to data). Users who either want to control all of the library prep or who are investigating multiple targets, may want to use the 2-step Amplicon to data approach where the user does the initial PCR then we attach the indexes in a second PCR. If you are interested in either Amplicon library to data or 2-step Amplicon to data, please contact us *before* you do any library prep.
Genome Analysis
For BSL1 isolates, we can extract DNA from cell pellet for full service Isolate Sample to Data processing. We also accept DNA or user generated libraries with no BSL restriction.
Data management
Raw sequence data is shared with users through Illumina’s BaseSpace. The data project on BaseSpace will be shared with the email address you provide when submitting a project, please let us know if your BaseSpace account is linked to a different email. MARS also backs up all raw data for at least 1 year on a UConn secure server.
Data analysis
We can assist users with clustering amplicon data or draft assemblies of genomes for a flat rate. We also offer custom data analysis including multivariate statistical analyses and publication quality figures. These services are billed per hour and will be quoted in advance of any work.
Sample processing turnaround time
Turnaround time for our services is dependent on type of service and the number of samples submitted. Our prices are based on multiplexing many samples on each run, therefore fewer samples often take longer to process because we have to wait to fill a run. If you submit full runs of samples (95+ samples) for microbiome sequencing, they are usually completed in 4-8 weeks depending on our current queue. Projects that are different enough from our usual process that we deem it “protocol development”, we won’t be able to estimate turn around but will have regular conversations updating you on the progress.
Users that are more concerned with turnaround time than cost, please talk to us. It is often possible for your samples to be sequenced quickly on less than full runs, you would just need to pay the balance of the run cost.
MARS instrument access
MARS instrumentation can be accessed either unassisted by authorize users or with the assistance of MARS personnel. Assisted use should be arranged in advance through consultation with MARS staff to ensure that the instrument and technician are available at a given time. Currently we don’t have a specific lead time requirement but the further in advance a request is made, the more likely we will be able to accommodate it. Once a user has been trained on an instrument, fill out the Equipment request form to reserve time. Instrument access is billed per whole hour. Each piece of equipment that a user wants to access requires its’ own equipment request form complete with time needed.
Acknowledge MARS in grant proposals and publications
Researchers are requested to acknowledge MARS as follows: Microbial Analysis, Resources, and Services, Center for Open Research Resources and Equipment, University of Connecticut. Please acknowledge MARS in all grants and publications that utilize MARS generated data or MARS equipment.
Authorship Guidelines
As a core facility that provides both routine and fully customized microbiome focused analysis, we subscribe to ABRF’s authorship guidelines for fair representation in co-authorship when appropriate. Please review ABRF’s guidelines below and be prepared to agree to these guidelines prior to analysis in our laboratory.
From ABRF:
Core facilities must charge for services rendered according to cost accounting practices set up at each institution. Charging for services does not preclude authorship on manuscripts provided the Core laboratory individual has contributed to the research in a substantial way. If authorship is anticipated, it is preferably established at the beginning of the project so that both the customer and the Core researcher are cognizant of each other’s criteria.
Important reasons for acknowledging contributions from core facilities in publications, by co-authorship or by formal mention in the acknowledgments section, include:
1. Core facility personnel are scientists. When they make a substantial intellectual and/or experimental contribution to a publication they deserve to be acknowledged just as any other co-author.
2. The existence of core facilities depends in part on proper acknowledgment in publications. This is an important metric of the value of most core facilities. Proper acknowledgment of core facilities enables them to obtain financial and other support so that they may continue to provide their essential services in the best ways possible. It also helps core personnel to advance in their careers, adding to the overall health of the core facility.
The ABRF recommendation was previously published in Angeletti et al. in 1999 (FASEB Journal, 13:595), “Intellectual interactions between resource and research scientists are essential to the success of each project. When this success results in publication, a citation in the acknowledgments section of a manuscript may be appropriate for routine analysis. However, contributions from resource scientists that involve novel resource laboratory work and insight, experimental design, or advanced data analysis that make a publication possible or significantly enhance its value require co-authorship as the appropriate acknowledgment.”
Activities for which authorship are recommended:
1. Author should make substantive contributions to the project
– Conception, design of project, critical input, or original ideas
– Acquisition of data, analysis and interpretation, beyond routine practices
– Draft the article or revise it critically for intellectual content
– Write a portion of the paper (not just materials and methods section)
– Intellectual contribution
– Final authority for the approval of article
2. Each author should have participated enough to accept responsibility for the content of the manuscript
The following activities do not represent intellectual contributions to a project and would not constitute authorship:
– Providing funding (department chair who has no intellectual input)
– Collection of data (technical skill but not involved in interpretation of data)
– General supervision of research group, but no intellectual input into the project
All contributors that do not meet the criteria of authorship should be recognized in the acknowledgements section, for example:
– Paid technical help
– Writing assistance
– Financial and material support
– Scientific advice
***If you have questions as to whether or not our contribution to your project warrants co-authorship, contact Facility Director Jeremy Balsbaugh prior to submission of the manuscript.***
MARS Reagent/Consumables Request procedure
Requests need to be made at least one business day in advance. If you have a true emergency, come talk to us but we can’t promise to fulfill your request on the spot.
Your reagent/consumables request needs to explicitly list everything you need (other than pipet tips for the robots) including quantities. MARS’ stocks are fluid, if you request something that we don’t have we will let you know as soon as possible. You can either put the request list in your equipment request form or you can email it directly to mars@uconn.edu. Once your reagents/consumables are ready, we’ll email you and let you know where they are. List the volumes of reagents required, but be aware that our aliquots may be larger so you will have left over. (MARS cannot take back partial aliquots)