University of Connecticut University of UC Title Fallback Connecticut

CGI Policies

CGI_ISG
Center for Genome Innovation Policies and Procedures

Effective 01 December 2014

The following policies apply to all CGI equipment and space located at both CGI locations unless otherwise noted:

Main Location: 354 Mansfield Road (Beach Hall), UCONN Storrs Campus
Satellite Location: 400 Farmington Avenue, Farmington, UCONN Health

Main Contents:
A. CENTER FOR GENOME INNOVATION (CGI) STAFF
B. LABORATORY ACCESS TO THE CGI – STORRS LOCATION
C. INSTRUMENT ACCESS
D. TRAINING
E. INSTRUMENT RESERVATION
F. CGI ROOM RESERVATIONS – STORRS LOCATIONS ONLY
G. FEE-FOR-SERVICE
H. INSTRUMENT ACCESS FEES – STORRS AND UCONN HEALTH LOCATIONS
I. DATA RETURN/DATA STORAGE
J. COLLABORATION/LETTERS OF SUPPORT
K. CITATION OF THE CGI IN GRANT PROPOSALS AND RESULTING PUBLICATIONS

A. Center for Genome Innovation (CGI) Staff

Dr. Rachel O’Neill, Director
Rachel.Oneill@uconn.edu

Dr. Bo Reese, Senior Facility Scientist
Bo.Reese@uconn.edu

Lu Li, Research Associate III
Lu.Li@uconn.edu

B. Laboratory access to the CGI – Storrs location

The CGI will be accessible to users during normal working hours (9:30am – 5:00pm daily). CGI staff (Bo Reese and Lu Li) have offices in the main laboratory. The Center will be locked for security purposes when CGI staff is not present.

CGI users can reserve time and bench space to work in the laboratory. These reservations must be made at least 24 hours in advance with either Bo Reese or Lu Li.

C. Instrument Access

With the appropriate training, anyone can use the 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.

D. Training

The CGI will hold hands-on, laboratory training for many applications supported by the Center equipment and staff, including but not limited to NextGen sequencing and Affymetrix genotyping. Individuals (students, faculty and staff) across all UCONN campuses are eligible to participate in CGI sponsored training. All training fees go directly toward instrument maintenance, service contracts and reagents/consumables for training. Participants can bring a sample of their own for training if desired, allowing for participant data collection that can be used as proof of principle or preliminary data for grant submissions, etc. Trainings are offered throughout the year based on demand for specific instrumentation and will be advertised via email announcement and on the CGI website.

E. Instrument Reservation

All major equipment in the CGI is accompanied by a Google Calendar for reservations. You can check the reservation schedule online by contacting either Bo Reese or Lu Li for read-only access to the Google Calendars. NOTE: UConn Health Center users are asked to contact Isolde Bates (bates@uchc.edu) 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)

F. CGI Room Reservations – Storrs locations only

The conference room (room 205) and main ballroom (room 209) can be reserved for laboratory meetings, journal clubs, seminars and other university-related events. These reservations must be made in advance of the event through either Bo Reese or Lu Li. Priority for booking will be given to CGI sponsored events. There is no charge to book either of these rooms.

G. Sample Preparation Services

In addition to instrument and laboratory space access, the CGI will offer many NextGen sequencing, microarray and single cell genomics services. Additional services may be available upon request:

• Cytoscan HD Array kit for the Affymetrix GeneChip
• WT Expression Array kit for the Affymetrix GeneAtlas
• GS FLX+ General Rapid Library
• GS FLX+ cDNA Rapid Library
• GS FLX+ Paired End Rapid Library (3Kb)
• GS FLX Amplicon Library
• Illumina TruSeq Stranded Total RNA Library Prep
• Illumina TruSeq Stranded mRNA Library Prep
• TruSeq DNA Nano Library Prep (low input)
• EpiGnome Methyl-Seq Library Prep
• TruSeq Small RNA Library Prep
• Fluidigm Single Cell RNA-Seq on the NextSeq 500 (*)

(*) = NOTE: The Fluidigm fee-for-service workflow for Single Cell RNA-Seq on the NextSeq 500 is currently undergoing cost analysis. As such, this particular service is not yet available through the CGI fee-for-service program. As soon as fees are established, they will be posted to this site; anticipated start date Spring 2015.

Fee-for-Service Rates:

A full list of services and associated costs can be found by visiting the CGI Service Rates – FY 2014 – 2015 page. Services to non-UCONN scientists are provided, subject to availability, and offered in accordance with service center charges under UCONN Financial Management Policy (**).

(**) = External Rates: If a service center provides services to individuals or organizations outside of the University, the billing rates must include institutional indirect costs even though these costs are not included in the rates for internal University users. The FY14-15 rate adds an additional 58% to billable services.

Budgets/Quote Requests:

Formal quotes or detailed budgets (i.e. for internal or external proposals/grants, developing project design within budget limits, etc) for all experiment types can be requested by contacting Bo Reese. PI’s/students/staff can also request quotes for projects that go beyond the number of samples listed in the posted list of standard services (i.e. more than 10-12 samples depending on the workflow). The CGI staff can work with you to develop your budget as well as discuss your experimental design prior to initiating work on CGI equipment.

H. Instrument Access – Storrs and UCONN Health locations

As part of the fee-for-service program, the CGI will charge users a nominal access fee for some of the instruments located in the Center. Usage fees are one-time fees that fall under two categories: “Assisted” or “Unassisted” rates. “Assisted” instrument access fees are incurred when users are not able, or are not cleared by CGI staff, to operate the equipment without the direct supervision of the CGI staff. “Unassisted” instrument access fees are incurred when users have been given clearance by CGI staff to operate the equipment without CGI supervision. The instruments included in this access program are:

• Illumina MiSeq (Storrs and UCONN Health 400 Farmington Ave. locations) (^)
• Illumina NextSeq 500 (Storrs and UCONN Health 400 Farmington Ave. locations) (^)
• ABI 3130 Capillary Sequencer
• BioRad CFX 96 Real-Time System
• Roche 454 GS FLX+
• ABI SOLiD 5500xl
• Affymetrix Gene Chip
• Affymetrix Gene Atlas
• Fluidigm C1 Single-Cell Auto Prep (^^)
• Fluidigm BioMark HD 3 (^^)
• Fluidigm Access Array systems 3 (^^)

(^) = Users can make reservations for both Illumina sequencers located at the UConn Health Center, 400 Farmington Avenue by contacting Isolde Bates (bates@uchc.edu).

(^^) = NOTE: The Fluidigm instrumentation and associated protocols are currently being evaluated for cost analysis by CGI staff. As such, an approved fee structure for access or fee-for-service has not been established. As soon as fees have been approved, they will be posted to the website; anticipated start date of Spring 2015.

Instruments that do not require usage fees for access include:

• Agilent Bioanalyzer
• Agilent Tapestation
• BioRad Experion
• NanoDrop
• Hydroshear

Instrument access fees are assessed on a per-use basis and internal billing will be compiled into one invoice (per KFS number) at the end of each month.

User-prepared samples/Modified protocols:

Users may prepare their own samples and bring user-supplied reagents/consumables to the CGI. NOTE: Users are responsible for proper quality assessment of their own samples. The CGI is not responsible for poor data quality if experimental failures can be directly attributed to sample-related issues.

Users can perform experiments where self-modified protocols are implemented (i.e. library preparation, sample denaturation and/or sample pooling protocols not supported by the manufacturer). NOTE: If the data generated from these “non-traditional” methods does not meet desired expectations, additional runs and/or troubleshooting may be required by the user.

Instrument Failures:

In case of an instrument failure/malfunction where data is compromised, instrument access fees will not be charged to the user. Troubleshooting the instrument failure will be the sole responsibility of the CGI staff. CGI staff will work with the appropriate vendor to determine root cause of the failure. When applicable, replacement kits/reagents will be requested from the vendor and the sequencing run/genotyping experiment/real-time experiment will be repeated.

I. Data Return/Data Storage

Upon completion of any experiment where data is generated, users must return to the CGI with an external hard drive (or comparable) to retrieve data. If preferred, user data will be made available to them through a secure FTP site. Data will be uploaded to the FTP site by CGI staff and users will be notified when their files are available for download. Files will be kept on the FTP site for 2 weeks, after which the data will be deleted. Prior to deletion, the user will be contacted by CGI staff to ensure that they have downloaded their data and checked to make sure the files are not corrupt, etc.

Data generated by the Affymetrix GeneAtlas or the GeneChip will not be backed up by the CGI. NextGen Sequencing data (raw data files) will be backed up by the CGI for a period of 1 year (or until the allocated backup storage space is full). After 1 year, the user will be notified that data will be removed from the CGI server. Data will not be deleted until the user has been notified and agrees to permanent deletion.

In the case of data generated by the NextSeq 500, all user runs will be created and managed through BaseSpace (Illumina cloud storage). Runs will be initiated through CGI accounts belonging to either Lu Li or Bo Reese. Upon completion of the sequencing run, the ownership (which includes access to run performance metrics reports as well as sequencing data) will be transferred over to the user. Transferring ownership is only possible if the user has an active BaseSpace account. Therefore, prior to beginning a project that will require multiple sequencing runs, the user should create a BaseSpace account. Note that it is not a requirement that users create a BaseSpace account to use the NextSeq 500. If users do not have a BaseSpace account, they must return to the CGI with an external hard drive to collect their data.

J. Collaboration/Letters of Support

CGI staff can serve as collaborators on proposals and grants if desired. Similarly, CGI staff is available for consultation on project design, sample requirements, timeline and feasibility, and can draft budgets at no charge. The CGI staff can work with you to develop detailed budgets and experimental design outlines prior to initiating work on CGI equipment (i.e. for internal or external proposals/grants, developing project design within budget limits, etc.) for small as well as large-scale projects.

The CGI can provide letters of support for proposals and grants that require CGI access or services. The CGI can also be included as a supporting facility. Please contact Rachel O’Neill or Bo Reese for letters of support requests and/or text that can be used in proposals and grants describing the facility. Please allow for 3-5 days for letter requests to be processed if possible.

K. Citation of the CGI in grant proposals and resulting publications

Researchers are required to acknowledge the CGI as follows: Center for Genome Innovation, Institute for Systems Genomics, University of Connecticut. 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.