GRC Descriptions for Grant Proposals and Data Management

Facilities & Resources

UR Genomics Research Center
The UR Genomics Research Center (GRC), located at the James P. Wilmot Cancer Institute, provides core laboratory support, technical consultation, assistance with experimental design and data analysis for investigators using high-throughput genomic sequencing, genotyping and gene expression in their research programs. The GRC currently provides support for RNA-Seq, CHiP-Seq, Exome/Genome sequencing, Single-cell genomics applications, spatial profiling and transcriptomics, ATAC-Seq, whole genome and reduced representation bisulfite sequencing (WGBS, RRBS), 16S rRNA sequencing, qRT-PCR, processing of RNA/DNA, as well as custom applications and approaches. In addition, GRC staff lead collaborative projects with URMC investigators to develop new methodologies and incorporate emerging genomic technologies into the GRC workflow. The GRC has a faculty-level Director, a technical director, an operations director, one Staff Scientist, two Lead Research Specialists, two Research Specialists and seven Bioinformaticians/data analysts. Dedicated computational support for hardware, data analysis and storage of high-throughput sequence data is provided by the Center for Integrated Research Computing (CIRC) with 37 24-core compute nodes and 300TB of space dedicated solely for GRC analyses.

The following major equipment is located in the GRC: one Illumina NovaSeq X PLUS high-throughput DNA sequencer, one Illumina NovaSeq6000 high-throughput DNA sequencer, one Illumina NextSeq 2000 high-throughput DNA sequencer, one Illumina MiSeq DNA sequencer, one Fluidigm C1 Single-Cell AutoPrep System, one 10X Genomics Chormium iX Controller, one 10X Genomics Chromium Controller, one Xenium in situ Analyzer, one Visium CytAssist Instrument, one Illumina iScan array scanner, one QuantStudio 12K FLEX real-time PCR instrument with autoloader, microfluidic card module, and open array module for digital PCR, one BioRad QX100 digital droplet PCR system, one Sage Science PippinPrepHT size fractionation system, one Sage Science PippinPrep size fractionation system, one Covaris E220 Focused-ultrasonicator, two ABI 9700 PCR machines, six BioRad DNA Engine PCR machines, one Perkin Elmer Sciclone G3 liquid handler, one Eppendorf EpMotion 5075 liquid handler, three Opentrons OT-2 liquid handlers, two Agilent 2100 Bioanalyzers, one Agilent TapeStation 4200, one Agilent Fragment Analyzer, one BioRad gel documentation system, one Qubit Flourometer, one Qubit Flex, one NanoDrop One spectrophotometer, and one NanoDrop Eight spectrophotometer.

Data Management

NIH has issued the Data Management and Sharing (DMS) policy (effective January 25, 2023) to promote the sharing of scientific data. Sharing scientific data accelerates biomedical research discovery, in part, by enabling validation of research results, providing accessibility to high-value datasets, and promoting data reuse for future research studies.

In partnership with Miner Library, the GRC has developed template Data Management Plans and a Data Size Estimator to help support researchers with their grant submissions. 

Data Size Estimation Tool*

 DMPStorageEstimationTool_1

*This estimation tool is meant as a guide and is based on the project deliverables provided by the GRC. While we attempted to slightly overestimate the storage need for each project types and consider as many scenarios as possible, there may be situations or circumstances (e.g., custom library type or sequencing) where this estimator provides an underestimate. We strongly encourage consulting the GRC is any questions arise or to help with finalizing any information pertaining to your project.

Template DMPs for common GRC services:

10X scRNA Sequencing: GRC_DMP_10XscRNAseq_012023

Bulk RNA Sequencing: GRC_DMP_Bulk_RNAseq_012023

Whole Genome Sequencing: GRC_DMP_WGS_WES_012023

ChIPseq/ATAC Sequencing: GRC_DMP_ChIPseq_ATACseq_012023

CUTandRUN/CUTandTAG Sequencing: GRC_DMP_CUTandRUN_CUTandTAG_012023

Metagenome and Metatranscriptome Sequencing: GRC_DMP_MGX_MTX_DMP_112823

Need help with High-throughput sequencing Data Storage and deposition to NIH public repositories? 

We can help, contact us with questions on how and cost. GRC policy is to archive all data we generate for a period of 5-year, longer in many cases. We have access to local and cloud-based storage solutions approved for use by University IT that includes high risk/legally restricted data. If you would like us to help with data deposition, it is much easier for us to to also store these data on our secure systems. 

Please contact theGRC with any questions or to receive specific methods or estimated storage sizes for your project.

Additional University of Rochester Data Management Resources

Click here for access to a guide to storage solutions that are available to researchers. 

Please note: we are not able to transfer sequencing data to external storage devices (with the exception of Apricorn Drives). Please contact us if you are interested in alternative storage strategies. 

Data Security Classification Policy

For more information about the types of data that are considered high, medium, and low risk, please visit the UR IT website. 

User’s Guide to Data Security Classifications

For more information about the minimum requirements for the different types of data, please visit the UR IT website. 

Data Delivery

**Effective July 1, 2024**

On July 1st 2024, URMC Genomics Research Center will begin delivering sequence data via direct delivery using SMDNAS (specifically SMDNAS02) for internal university users. This change in delivery method is being introduced to streamline delivery of data away from links that expire, links that are otherwise accessible by anyone (unsecured), to ensure long term data storage, and to ensure data storage within a legally-restricted and more secure data transfer system. It is UR security and management policy to not use hard drives for data longevity and security for any UR research generated data. This new process is a partnership between the GRC and Research IT to better align with University and NIH data security/management policies as well as reduce the financial and technical burden on UR investigators. Our collective goal is that investigators will find this storage solution useful and continue to use it for their data storage needs related to large omic datasets.

What you need to know:

• Every PI will have a dedicated share on SMDNAS02 for GRC to transfer all data and results files directly. 
• GRC will send a notification email when project deliverables are transferred and ready to access.
• Access to the SMDNAS02 data storage shared will require active directory (AD) credentials (login for email). More information on how to access can be found here: https://www.protocols.io/view/delivery-via-smdnas02-261ge5d97g47/v2?step=1 .
• Initial access will be given to PI only and it will be the responsibility of the PI to request access permissions for other lab members or internal collaborators using this form: https://is.gd/SMDNASRequest .
• These data storage shares are meant for GRC delivery and storage of genomics data/results generated by the GRC. *Note: data generated by the GRC prior to July 1, 2024 can be transferred to this data storage platform upon request of the PI. If you wish to use these data storage shares for storing other data (non-genomics data), please contact Research IT (SMDIThelp@urmc.rochester.edu) to discuss.
• The SMDNAS02 server share is approved for storage of legally restricted data such as human sequence data.
• Any questions can be directed to URgenomics@urmc.rochester.edu or John_ashton@urmc.rochester.edu.