Facilities & Resources
UR Genomics Research Center
The UR Genomics Research Center (URGRC) is located in the Cardiovascular Research Institute (CVRI) on the Bailey Road campus and provides core laboratory support, technical advice, assistance with experimental design and data analysis for investigators using high-throughput genomic sequencing, genotyping and gene expression in their research programs. The URGRC currently provides support for RNA-Seq, CHiP-Seq, Exome/Genome sequencing, Sanger sequencing, qRT-PCR, Affymetrix microarrays, processing of RNA/DNA, as well as custom applications and approaches. In addition, URGRC staff lead collaborative projects with URMC investigators to develop new methodologies and incorporate emerging genomic technologies into the URGRC workflow. The URGRC has a faculty-level director, a faculty-level Associate Director, a Lab Manager, three technicians and a Bioinformaticist/data analyst. Dedicated computational support for hardware, data analysis and storage of high-throughput sequence data is provided by the Center for Integrated Research Computing (CIRC).
The following major equipment is located in the URGRC: one Illumina HiSeq2500 high-throughput DNA sequencer, one ABI 7900HT real-time PCR instrument with autoloader and microfluidic card module, one ABI 3730 Capillary Electrophoresis DNA sequencer, two ABI 9700 PCR machines, two BioRad DNA Engine PCR machines, two Thermo Hybaid MBS PCR machines, CAS 1200 liquid handling robot, two Agilent 2100 Bioanalyzers, one BioRad gel documentation system, one Qubit, and multiple NanoDrop ND-1000 spectrophotometers.
NGS Data Processing and Alignment
Raw reads generated from the Illumina HiSeq2500 sequencer are demultiplexed using configurebcl2fastq.pl version 1.8.3. Low complexity reads and vector contamination are removed using sequence cleaner (“seqclean”) and the NCBI univec database, respectively. The FASTX toolkit (fastq_quality_trimmer) is applied to remove bases with quality scores below Q=13 from the end of each read. Processed reads are then mapped to the NCBI XXX genome build XXX with SHRiMP version 2.2.3 and differential expression analysis is performed using Cufflinks version 2.0.2; specifically, cuffdiff2 and usage of the general transfer format (GTF) annotation file for the given reference genome.
Please contact the URGRC with any questions you have have.