Proposal Resources

The Bioinformatics Consulting Group at The University of Texas at Austin provides access to computational approaches for advancing biological knowledge to researchers at the university and beyond. The group strives to provide analysis support for researchers using high throughput biological data, to train and educate on computational approaches to empower researchers to conduct high quality biomedical research and to serve as a centralized knowledge base of tools and best practices in computational biology.

The group is comprised of four bioinformaticians with over 15 years of experience in providing analysis support, with a demonstrated publication record in high impact journals such as Science, PNAS, PLOS One and Nature. The group brings expertise in a variety of areas including whole transcriptome profiling (bulk, single cell and spatial), variant calling, transcriptome and genome assembly, algorithm development, motif discovery, machine learning and biostatistics. The group’s offerings span walk-in consultations, full-service bioinformatics pipelines for common analyses, hourly projects for well-defined problems or long-term consulting for more involved, collaborative projects.

The group supports training in computational biology and bioinformatics through a mix of short 3-hour courses and an annual Big Data in Biology Summer School. The short courses typically run for a few hours to a half-day (2–4 h) and cover essential skills such as programming in Python or R, using UNIX/Linux, data visualization, next-generation sequencing (NGS) fundamentals, and other bioinformatics techniques. The summer school is a more intensive option: over several consecutive days, participants can take multi-day workshops ranging from introduction to computing and NGS tools to RNA-Seq analysis, machine learning for bioinformatics, and data visualization in R.

The group works closely with several other CBRS cores, including the Genome Sequencing and Analysis Facility (GSAF) and Biomedical Research Computing Facility (BRCF) and helps researchers with strong biological expertise but limited computational background to conduct complex data-driven biology research.

The Center for Biomedical Research Support (CBRS) Biological Mass Spectrometry Facility is housed in dedicated instrumentation laboratories located in the Institute for Cellular and Molecular Biology. We provide proteomics and metabolomics services and collaborate on research projects.

Researchers are supported by three full-time, PhD staff scientists who provide consultations on experimental design, conduct data acquisition and processing and training on the self-service instrumentation.

Proteomics instruments and software:

• Thermo Orbitrap Tribrid Ascend mass spectrometer with Vanquish Neo ultra high pressure liquid chromatography systems (UHPLC) with CID, HCD, and ETD MSn analysis for fragmentation options and extended mass range
• Thermo Orbitrap Tribrid Fusion mass spectrometer with Ultimate 3000 RSLCnano UPLC and high flow Ultimate 3000 HPLC
• Intavis DigestPro MSi robot is used for automated digest and desalting for low level samples in a 96 well format
• Evosep One chromatography system for reproducible, high throuphput quantitative proteomics with in-line desalting
• Proteome Discoverer for protein identification and quantitation using SequestHT for database search, with XlinkX crosslinking analysis node
• Scaffold for data visualization and validation
• Spectronaut for DIA quantitation
• PEAKS for de novo sequencing
• Byonic for specialized searches

Metabolomics instruments and software:

• Thermo Orbitrap Tribrid IQ-X mass spectrometer with Vanquish Flex Duo UPLC with Dual column compartments and split sampler
• Thermo Orbitrap QExactive mass spectrometer with Vanquish Flex Duo UPLC for column switching
• Compound Discoverer for metabolite feature detection, assignment, and quantitation
• TraceFinder for detection and targeted quantitation
• LipidSearch for characterization of lipids
• Mass Frontier for structural characterization

MALDI instrument:

• Bruker Autoflex maX MALDI-TOF/TOF mass spectrometer for self-service usage

Overview

The University of Texas at Austin (UT Austin) is the flagship school of the University of Texas System, which includes nine academic universities and six health institutions statewide. UT Austin was established in 1883 with one building, eight professors, and 221 students; now UT Austin has 18 colleges and schools, more than 51,000 students and over 3,000 tenure/tenure track faculty. UT Austin now ranks as one of the top 10 public universities, according to U.S. News & World Report. Over the last 2 years, the Genomic Sequencing and Analysis Facility has supported 92 independent principal investigators, 15% of which are NSF-funded.

Campus and Infrastructure

The grounds of UT Austin consist of the original forty-acre campus north of the Texas state capital which has expanded and now covers more than 350 acres. Also, part of the UT Austin campus is the J. J. Pickle Research Campus, a 476-acre tract that houses research organizations in engineering and science and is the home of the Texas Advanced Computing Center (TACC); the Marine Science Institute at Port Aransas; and the Dell Medical Center which is co-located on the main UT Austin campus.

Colleges and Schools within UT Austin Utilizing GSAF

Within the College of Natural Science (CNS) there are 13 Departments, five of which have faculty users of GSAF. Usage by CNS members accounts for ~40% of the total usage of the GSAF in fiscal year 2024, which is why five out of the eight GSAF Advisory Board members are from CNS. CNS has 390 faculty and over 900,000 sq ft of assignable space across 11 buildings, most within walking distance of the GSAF. The Marine Science Institute at Port Aransas, Texas, is administratively housed in CNS and is regular user of GSAF.

The Cockrell School of Engineering (CSE) has 7 Departments, three of which have faculty who have utilized the GSAF, and CSE accounts for ~20% of the total usage of the facility. CSE has 280 faculty members and over 600,000 sq ft of assignable space in buildings adjacent to the GSAF. In addition to the Colleges and Schools listed above, GSAF has supported research in the College of Liberal Arts, College of Pharmacy and the Dell Medical School.

Institutional Core Facility Relevant to Instrument Acquisition

Genomic Sequencing and Analysis Facility (GSAF) is a full-service genomics core offering next-generation library prep services on samples ranging from formaldehyde-fixed paraffin embedded (FFPE) tissues to single cells. Services include short read sequencing, in-situ spatial transcriptomics, and DNA methylation array services. The facility provides the community with technical expertise and experience to support ongoing research projects.

Organizational Structure: GSAF falls under the umbrella for the Center for Biomedical Support, a center that oversees 10 university core facilities providing expert research support. The GSAF director and Co-PI Jessica Podnar reports to the CBRS Deputy Executive Director Katherine Hale and Executive Director of the CBRS Dr. Hal Alper, who report to the Assistant Vice President of Core Facilities, Julie Hayes, who in turn reports of Dr. Daniel Jaffe, Vice President for Vice President for Research, Scholarship and Creative Endeavors at UT Austin.

Laboratory: The Genomic Sequencing and Analysis Facility is housed in the Neural and Molecular Science (NMS) and Moffett Molecular Biology Building (MBB) space overseen by the College of Natural Sciences. GSAF has approximately 2000 square feet. NovaSeq X will be housed in the GSAF on the main campus of UT Austin, in the Neural and Molecular Science Building room 1.208. The building is within walking distance of the main lab spaces of all major users, allowing for transport of samples to the instrument. The 1.208 lab currently houses a NovaSeq 6000, which will be retired and removed from the room before the installation of the NovaSeq X. Because this lab is already equipped with NGS sequencing instruments, no renovation is needed. The port the instrument will connect to is currently a CAT6 but will require an upgrade to support 10Gig, this upgrade is supported and approved by the College of Natural Sciences IT department. As a dedicated instrument room, the required socket NEMA L6-20R is already in place and the instrument will come with a dedicated UPS for backup. The room is 271 square feet in area and has sufficient electrical and HVAC for the instrument.

Funding: GSAF is funded through recovering fees. All costs, including personnel, supplies, software licenses, and maintenance, are recalculated regularly. If user fees are insufficient to cover facility costs, CBRS is willing to undertake the responsibility of maintaining and operating the instrument for the benefit of a community of users engaged in research and research training.

Personnel: GSAF has seven full-time staff at the facility. GSAF director Jessica Podnar, oversees all operations at the facility. GSAF Program Manager, Gabriella Huerta, oversees daily lab operations for the NGS platforms. Two Research Engineering/Scientist Associate III, Aditi Karmakar and Maria Jose Gomez, and a Research Engineering/Scientist Associate II, Coral Lookerman, report to Ms. Huerta. Together they execute simple and complex protocols related to next generation sequencing (NGS) and operate and maintain a wide range of equipment used for preparing sequencing libraries, sequencing run management and set up. Drs. Holly Stevenson and Sylvie Beaudenon-Huibregtse are Research Engineering/Scientist Associate IV’s in GSAF and report directly to the GSAF director. They assist researchers with the execution of specialized experiments using published methods also independently operate and maintain a wide range of equipment including those used for NGS, single cell library production, and microarray equipment. The salary and fringe costs for these personnel are recovered through usage fees with partial support from CBRS. GSAF is also supported by an administrative assistant responsible for billing and ordering and a Systems Administrator to help with data storage and IT support.

Data Management: GSAF holds a BaseSapce Sequence Hub Professional Subscription, a secure cloud-based system used for sequencing run setup, monitoring and data transfers. Working closely with the Biomedical Research Computing Facility (BRCF) and its Director Anna Battenhouse, once sequencing runs complete, the data and selected meta data is downloaded to local servers and then archived for a minimum of 7 years at the Texas Advanced Computing Center (TACC) on their Ranch magnetic tape storage system.

Support services: GSAF has a custom-built LIMS through Salesforce to track project submissions and samples, create reports regarding facility usage, store account information, and track project submitted and completion dates. The system is secure requiring dual authentication.

The Center for Biomedical Research Support (CBRS) Microscopy and Flow Cytometry Facility (MFC) has several high-end light microscopes, flow cytometers, and cell sorters that are available for use by UT Austin and external researchers.

The MFC is housed in three locations: the main UT Austin campus, the Dell Medical School, and the Dell Pediatric Research Institute, with over 5,500 sq ft of space.

Users of the facility are supported by full-time, expert staff specialists, who offer one-on-one training sessions on equipment, as well as consultations on experimental design and post-acquisition image analysis. The facility offers licenses and support for analysis software packages, including Imaris, NIS-Elements, ZEN, FlowJo, and FCS Express.

The MFC is a designated Nikon Center of Excellence. This partnership includes a suite of light microscopes, as well as the ability to test novel technologies, thereby supporting cutting-edge research efforts.

The MFC’s instruments include:

• Nikon AXR upright and inverted confocal microscopes
• Nikon NSPARC super-resolution
• Zeiss LSM 980 confocal microscope with Airyscan super-resolution
• Leica Stellaris cryo-confocal microscope
• Nikon W1 spinning disk confocal microscope
• Nikon large format multiphoton microscope
• Multiple epifluorescence compound microscopes
• Nikon TIRF microscope
• Nikon N-STORM super resolution localization microscope
• Cytek Aurora and Northern Lights spectral flow cytometers
• BD LSRFortessa SORP and Accuri C6 Plus conventional flow cytometers
• BD FACSAria Fusion SORP cell sorter
• Sony MA900 and SH800 automated cell sorters

The Mouse Genetic Engineering Facility (MGEF) at The University of Texas at Austin, located in the Animal Resource Center, serves as the university’s central resource for developing transgenic mouse models. Its mission is to provide expert consultation and to generate, archive, and rederive mouse models for biomedical research.

The facility occupies approximately 600 sq. ft. in the ARC Annex, with dedicated areas for molecular biology, microinjection, and embryonic stem (ES) cell culture. Two barrier rooms support animal housing for production and breeding.

The MGEF is fully equipped to generate transgenic mice. Dedicated equipment used by the core includes: 

• Olympus IX70 microscope fitted with Eppendorf micromanipulators for injecting embryos with DNA, CRISPR reagents, and ES cells.
• Sutter Instrument P-1000 micropipette puller for making microinjection needles.
• Narshige MF-900 microforge for polishing and bending microinjection needles.
• BIO-RAD Gene Pulser XCell electroporation apparatus for electroporating CRISPR reagents into mouse embryos.
• BioCool controlled-rate programmable freezer for cryopreserving mouse embryos.
• Forma 1300 Series Tissue Culture hood for handling mouse ES cells.
• Forma 3110 water-jacketed incubator for culturing embryos and mouse ES cells.
• Nikon TS100 tissue culture microscope for use in mouse embryonic stem cell culture.
• Multiple Thermo Forma Cryo storage dewars for cryostorage of mouse embryos, sperm, and ES cell lines in duplicate. The core also stores a percentage of its cryopreserved mouse lines at an off-site location, Cryogene, for additional security.
• Stereomicroscopes for the isolation and transfer of mouse embryos.

In addition to the microinjection and ES cell culture equipment, the core is equipped for wet lab work, including:

• Eppendorf Mastercycler PCR machine for genotyping transgenic mice.
• Nandrop 2000 spectrophotometer for quantifying DNA/RNA for embryo microinjection.
• Fotodyne UV transilluminator and Canon digital camera for visualizing and documenting DNA gels.
• Eppendorf 5415C microcentrifuge for isolating DNA/RNA.
• Jouan CR312 bench centrifuge for concentrating mouse ES cells.

Core personnel stay up to date on the latest technological advances by participating in the International Society for Transgenic Technology and the Society for Developmental Biology, serving on the External Advisory Committee for the NIH’s Mutant Mouse Resource and Research Centers, and conducting independent research.