FAQ

Frequently Asked Questions

Locations

Computational Biology Core
Main Location:
Torrey Life Sciences Building, Rm. 375
75 North Eagleview Road, Unit 3043
Storrs, CT 06269
Satellite Location:
400 Farmington Avenue
Farmington, CT 06030


Center for Genome Innovation
Main Location:
Beach Hall, Rm. 201
354 Mansfield Road Unit 1131
Storrs, CT 06269
Satellite Location:
400 Farmington Avenue
Farmington, CT 06030-6403


General Questions

1. What are the costs associated with the use of the facilities?

Computational Biology Core:
Use of the facility and its resources are available free of charge to affiliates of the University of Connecticut.  Users external to the University may contract services at a pre-defined hourly rate.

If you are preparing a project that will require significant computational power or storage, we ask that you discuss this with us and include the cost of this equipment in your proposal.  The hardware purchased will be available for your data and your computation, and maintained by the facility.

Center for Genome Innovation:

Yes, for some instruments.  The CGI requires usage access fees for some of the instruments located in the Center. The instruments included are:

  • ABI 3130 Capillary Sequencer
  • BioRad CFX 96 Real-Time System
  • Roche 454 GS FLX+
  • Illumina MiSeq
  • Illumina NextSeq 500
  • ABI SOLiD 5500xl
  • Affymetrix Gene Chip
  • Affymetrix Gene Atlas
  • Fluidigm C1 Single-Cell Auto Prep, BioMark HD and Access Array systems

Instruments that do not require usage fees for access include:

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

In addition to instrument access fees, the CGI also offers fee-for-service for NextGen sequencing and genotyping services.  A full list of services will be posted to the Fee-for-Services page can be found here. If you have questions or would like more information about any of the services provided by the CGI, contact Bo Reese.

2. How should the facilities be acknowledged in resulting manuscripts and grant applications?

Computational Biology Core:

The following text describing the Computational Biology Core facility is available for inclusion in proposals. Researchers should acknowledge the Computational Biology Core Facility of the University of Connecticut in all publications and grant applications that are enabled by the facilities' resources and services, or include contributions by the facility members. Include the facility heads and/or staff as co-authors when they provide a significant intellectual contribution to the published research. Include BBC facility heads and/or staff as co-PI or co-investigators in grant applications when they provide a significant contribution to the grant proposal.  

Please follow these guidelines:

phd031305s

Center for Genome Innovation:

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.

3. How is data storage handled on the facility's cluster?

Computational Biology Core: 

Except as noted for specific services, storage and backup of the users' data is the users' responsibility.  Read about long-term data storage options here.

Center for Genome Innovation:

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.

 


Center for Genome Innovation-Specific

1. When is the Center for Genome Innovation open?

Bo Reese and Lu Li have offices in the main laboratory (room 201) of the CGI, with either one or both of them present in the Center between 9:30am and 5:00pm. The Center is locked for security reasons during the times they are not there.

2. Can anyone use the instrumentation in the CGI?

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 three day workshop with other individuals. 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 a three day workshop or a one-on-one individual training.  Even after training, users can request supervision if they are not comfortable working independently.

3. How do I reserve time to use the instruments in the CGI?

All equipment in the CGI is accompanied by a Google Calendar sign-up sheet. You can check the reservation schedule online by contacting either Bo Reese or Lu Li for access to the Google Calendars. 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.

4. How do I determine which Next Generation Sequencing platform is best for my experimental needs?

Most applications are supported by all NextGen sequencing platforms, like whole transcriptome RNA-Seq for example. Having your choice of which platform to use is great because each of the NextGen platforms has a unique way of presenting the data. Although there are certain experimental questions that heavily favor using one platform over another, there are others where the choice is not as clear. For many researchers, the choice in platform comes down to three main factors: genome target, desired genome coverage and cost. The information provided in the table below compares the most frequently used NextGen platforms based on these three (and other) factors.

NGS_May2014

Because the details of each experiment are very different, we encourage you to reach out to us so that we can prepare a budget and sequencing coverage analysis for your experiment. Please contact Bo Reese with your questions.