CORE Director: Richard Cripps, PhD
Manager: George Rosenberg, MS
Bioinformatics Specialist: Lijing Bu, PhD
Phone: (505) 277-4278
The Molecular Biology Core located within the Department of Biology at the University of New Mexico, provides genetic sequencing services to University investigators and maintains a repository of equipment for use by faculty, staff and students to carry out molecular biology experiments. A Bioinformatics Specialist is also on staff to assist with data analysis.
Illumina NextSeq 500 sequencing
Sanger Sequencing and DNA Fragment Analysis
Services Offered by CETI’s Bioinformatics Support Group
- RNASeq: Differential gene expression analysis, de novo transcriptome assembly and annotation.
- Genome/DNA Sequencing: De novo genome assembly, annotation, genome variation analysis.
- High-Throughput Data Analysis: Improved efficiency using CETI high-performance computer servers (24 cores/48 threads CPUs + 128 GB RAM; 20 cores/40 threads CPUs + 1 TB RAM), and parallel computing on computer clusters (120 nodes/960 cores with 32 GB RAM/core) at the UNM Center for Advanced Research Computing (CARC).
- Maintain the local Bioinformatics cloud based on the Galaxy platform (developed by Galaxy team of the Penn State University) - a web server containing over 700 different Bioinformatics tools. As a collaboration project with UNM CARC, the server named Pluto (http://pluto.alliance.unm.edu) is open to UNM researchers and collaborators for free. We offer hands on workshops at CARC regularly for new users as well as online workshop materials.
- Data processing, statistics and visualization using Unix/Linux shell, R, Perl, HTML and Python.
In addition, we are happy to discuss with potential users any special bioinformatics needs they may have with respect to next-gen sequencing, metagenomics analyses, environmental DNA surveys or molecular phylogenetic reconstruction.
General Use EquipmentIllumina NextSeq 500
ABI 3130-XL Sanger Sequencer (2)
Roche 454 GS-FLX+
Bio-Rad CFX96 RT-PCR (2)
ABI 7000 RT-PCR
MJ Research Tetrad Thermocycler
Eppendorf EP Gradient Thermocyler (6)
BioRad ChemiDoc Touch
BioRad GelDoc XR+
Kodak Image Station 440
Kodak Gel Logic 200 Digital Imaging System
Kodak Gel Logic 2200 Digital Imaging System
Packard Cyclone phosphoimager
Beckman J2-HS Preparative Centrifuge
Beckman L-70 Ultra-Centrifuge
Eppendorf 5810 Refrigerated Tabletop Centrifuge (2)
Jouan CR412 Swinging Bucket Centrifuge
Labconco Centrivap Concentrator (2)
Agilent 2100 Bioanalyzer
Qubit 3.0 Fluorometer
Quantifluor ST Fluorometer
Nanodrop 1000 Spectrophotometer
Nanodrop 2000c Spectrophotometer (2)
Beckman 640B Spectrophotometer
Qiagen TissueLyser II
Covaris M220 Focused-ultrasonicator
Blue Pippin Fragment Collector
Digilab DNA Shearer
Airclean PCR Workstations (2)
Milli-Q Plus Water System (2)
Casy DT Cell Counter
Robbins Scientific Hydra96 Multichannel Dispenser
Bio-Rad CHEF Gel System
Orbital shakers and Incubators
Dell workstations (5) for DNA analysis