The CGI will be accessible to users during normal working hours (9:30am – 5:00pm daily). The Center will be locked for security purposes when CGI staff are not present.

With the appropriate training, anyone can use the non-sequencing instrumentation in the CGI. Depending on the instrumentation, the extent of training can range from a brief, one-on-one informal session to a multi-day workshop. For example, training on the Agilent Bioanalyzer can be done in a one-on-one informal session, while usage of all NextGen sequencing instrumentation requires participation in either a multi-day workshop or one-on-one training. Even after training, users can request supervision if they are not comfortable working independently with the equipment or protocols. Granting unsupervised access to users is at the discretion of CGI staff.

Users will not be allowed to use equipment in the CGI after-hours. Special requests for after-hours access can be made by contacting Bo Reese. However, granting after-hours access is made on a case-by-case basis and permission is granted at the discretion of CGI staff.

After completing the training required for facility access, users may reserve instruments for use. 

Storrs users: All major equipment in the CGI is accompanied by a Google Calendar for reservations. You can check the reservation schedule online by contacting Bo Reese for read-only access to the Google Calendars.

UConn Health Center users are asked to contact Isolde Bates to make reservations for equipment located on the UCONN Health campus.

Due to high usage volume of most of the equipment, we ask that individuals adhere to the schedules and cancel any reservations if they are no longer needed at least 24 hours in advance. Only CGI staff will be able to make and cancel reservations. Users who routinely make reservations without using the instrumentation will be penalized after 5 occurrences by being charged the instrument’s assisted instrument access fee.

All reservations are made on a first-come first-served basis. There are no restrictions on how far in advance reservations can be made. When reservations are made, the following information must be provided:

• Name of user

• Name of PI

• Department

• Contact information (email or phone number)

• KFS number for instrument access fee billing (if applicable)

• Type of experiment/sequencing run (so that the appropriate number of days can be reserved)

Researchers are required to acknowledge the CGI. 

At a minimum, manuscripts should include the following statement in the Acknowledgements section: Work [you can be specific or general here: “sequencing and data delivery”; “genomics activities”] was performed in the Center for Genome Innovation and Computational Biology Core in the Institute for Systems Genomics at the University of Connecticut, Storrs, USA. 

Citation should be given in grant applications and publications where findings were enabled by the Center’s resources, staff and/or services. Inclusion of the Director and/or specific facility members as co-authors on manuscripts may also be warranted if significant intellectual contributions are made to the resulting work; such collaborations are available through discussion with the CGI Director and staff as needed.

Guidelines and Requirements for Acknowledging Contributions from the CGI in publications and grants

All publications and grants that include work performed in the CGI or by CGI staff must include an acknowledgement of the core’s contribution. 

The existence of core facilities at UConn depends in part on proper acknowledgment in publications. This is an important metric of the value of our core facility to the University; proper acknowledgment is a way to track our contributions to the research at UConn, other non-profit universities and agencies, and for-profit entities.

Such acknowledgements are necessary to obtain financial and other support so that the CGI may continue to provide essential services and keep pace with technological advances in genomics. Moreover, acknowledgement of the CGI helps our personnel advance in their careers, adding to the overall health of the core facility.

Acknowledgement or Co-Authorship??

The Association for Biomolecular Resource Facilities (ABRF) recommendation was previously published in Angeletti et al. in 1999 (FASEB Journal, 13:595), stating:

“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.”

The CGI must charge for services rendered according to cost accounting practices established at the University of Connecticut. However, charging for services does not preclude authorship on manuscripts provided the CGI 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 CGI researcher are cognizant of each other’s criteria.

CGI 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.

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

RAW DATA STORAGE/BACKUP FOR IN-HOUSE SEQUENCING: Fastq files from sequencing platforms will be delivered to the customer via (1) the Illumina Basespace cloud storage server (if possible), (2) symlink from the CAM/Xanadu HPC, (3) secure file sharing software like Globus (for users not able to create CAM/Xanadu accounts), or (4) data may also be collected from the instrument using a customer supplied hard drive disk (select instruments only).  Please note that Basespace run folders will contain all raw data images needed for fastq file regeneration, different from project folders that contain raw fastq files.  The CGI is not able to retain copies of runs and/or projects in Basespace due to the storage limitations of Basespace accounts.  After 2 months, Basespace runs and associated projects will be deleted from the CGI basespace account or as soon as sequencing run information is moved to the CAM/Xanadu server.  

Raw sequencing data is backed up to the CAM/Xanadu server and stored for 1 year.  After 1 year, all raw data images (run folders) and all raw fastq files will be deleted from the server.  The CGI is not responsible for re-sequencing customer samples or providing data for customer samples as a results of the customer’s failure to properly back-up or archive their own data.

SAMPLE STORAGE: DNA and RNA samples will be properly stored in the CGI for up to (1) month after libraries are made unless it is specified by the customer on the Sample Submission form that DNA/RNA samples are to be Destroyed.  NGS stock libraries, library dilutions and sample pool dilutions will be stored by the CGI for up to (6) months after sequencing is complete unless it is specified by the customer on the Sample Submission form that libraries are to be Destroyed.  Customers can request to have their samples returned to them at any time.  The CGI is not responsible for sample loss due to power failures.  All samples will be destroyed by the CGI after (6) months of project completion.

COST ESTIMATES: Fee-for-service cost estimates prepared by the CGI are based on current vendor pricing for the reagents and consumables needed to complete the services requested for the indicated number of samples being submitted. The costs reflected in this document may not be identical to the final billed amount as samples may be added/removed from project and/or if other services are added/removed from the project. If any changes are needed to the project cost estimate, the original document will be edited and sent to the PI for approval before proceeding .

FINAL INVOICING: Upon completion of the project, final invoice totals may need to be adjusted to reflect additional discounts and/or pricing increases for reagents and consumables used as well as shipping and handling charges incurred if items were special ordered. A final invoice will be sent to the customer upon completion of the project (i.e data delivery).

SAMPLE QUALITY: The quality of DNA and RNA samples should be checked (if possible) by the customer prior to delivery to the CGI for sample processing. However, the CGI will QC all customer samples regardless of previous QC results prior to starting library preparation (included in the cost for library preparation unless otherwise noted). The CGI will alert the PI to any sample quality issues and potential impact on data quality before proceeding with library preparation. The CGI is not responsible for library preparation failures and/or data quality issues that can be traced back to poor input sample quality.  If the CGI is instructed to proceed with library preparation using poor quality samples by the PI, the PI will be financially responsible for re-preparation and/or re-sequencing of these samples regardless of the data quality of the samples. 

PROJECT DELIVERABLES: Data delivery estimates will be communicated to the customer prior to the start of a project and staff will work to adhere to the delivery estimation given.  The CGI is not responsible for any delays in data delivery due to backorder or shipping delays for reagents/consumables from outside vendors, or for equipment malfunctions during the lirbrary preparation or sequencing process. 

CONTRACT LABOR WORK: Contract Work Hours and Safety Standard Act (40 U.S.C. 327-333) – Where applicable, if order involves the employment of mechanics or laborers, the contractor shall comply with Sections 102 and 107 of the Contract Work Hours and Safety Standards Act (40 U.S.C. 327-333), as supplemented by Department of Labor regulations (29 CFR part 5).