The Core focuses on the acquisition and development of new technologies and applications to advance the analysis of the impact of the environment on the “Cell Landscape”, from genotype to phenotype. Members of the QBC have many years of experience with a full range of Genomics, Bioinformatics, Biostatistics and Computational Biology applications and are engaged at multiple levels in the training activities, applications development and research activities. The central goal of the QBC is to offer CTEHR investigators with prioritized access to Genomics, Bioinformatics, Biostatistics and Computational Biology resources and personnel.

QBC Core Flyer 2

Director

Ivan I. Ivanov, Ph.D.
Ivan I. Ivanov, Ph.D.Clinical Associate Professor
VTPP, Texas A&M University

979-739-4328

Webpage

Co-Director

Robert S. Chapkin, Ph.D.
Robert S. Chapkin, Ph.D.Distinguished Professor, Regents Professor and University Faculty Fellow
Texas A&M University

979-845-4426

Webpage

Lab Members

The Quantitative Biology Facility Core provides the following services to Center Members:

RNA/DNA QualityMicroRNA DetectionReal Time PCRSequencing Library PrepCellular BioenergeticsStatistical Analyses

RNA quality can be accurately assessed on an Agilent 2100 Bioanalyzer. The Agilent 2100 Bioanalyzer is the method of choice for determining nucleic acid quality. The instrument uses microfluidics technology to separate charged molecules by size. Total RNA, polyA RNA, microRNA and DNA can be analyzed on the Bioanalyzer, 10-12 samples per chip.

RNA/DNA Quality Submission Requirements

  • Samples should be in water or dilute buffer (i.e. 10 mM Tris, 0.1 mM EDTA)
  • RNA should be 25-500 ng/µl for a Nano chip or 0.2-10 ng/µl for a Pico chip
  • Genomic DNA and sequencing libraries at 0.1-50 ng/µl can be run on a DNA chip
  • 3 µl of each sample is requested
  • Results should be available within two days

Detection and quantification of small RNA species (microRNA, siRNA, tRNA, snRNA) can be performed using the Agilent 2100 Bioanalyzer.

microRNA Submission Requirements

  • RNA should be in water or dilute buffer (ie 10 mM Tris, 0.1 mM EDTA)
  • 3 µl of each sample is requested
  • Results should be available within one day

An ABI 7900HT Real Time PCR machine is available for use. Consultation for training in experimental design, primer design, optimization and troubleshooting available. Traditional 96-well format is available as well as a 384-well low density array format. Supplies needed for use with the ABI 7900HT can be ordered through Applied Biosystems or from the Biochemistry Stockroom. Assays are available for all human, mouse or rat genes.

Illumina library preparation services are available for RNA, DNA, and ChIP.

The Seahorse XF Analyzer measures fatty acid oxidation and metabolism of glucose and amino acids for kinetic metabolic information. Adherent cells, primary cells, suspension cells and isolated mitochondria can be analyzed

These activities fall under the core initiative in Systems Biology to model, understand, and ultimately engineer at the molecular level the dynamic relationships among biological molecules that define living organisms. This takes advantage of our cross-disciplinary activities in Genomics, Biostatistics, Bioinformatics and Engineering.

We also provide a central facility for the evaluation, acquisition of and training in specialized bioinformatics software for analysis of expression data.

SERVICES PROVIDED

AGILENT BIOANALYZER

Chip Type                          Cost per chip              Number of samples/chip
RNA Nanochip                        $60                                            11
RNA Pocochip                         $65                                            10
DNA High Sensitivity             $95                                             11
DNA 1000                                $65                                             12

REAL TIME PCR (includes training and troubleshooting)

Cost per plate

96-well PCR Plate                   $45
384-well LDA Plate                $60

PIPPEN PREP

No Dye
3% Gel $100/cassette
2% Gel $100/cassette

Each cassette holds 5 samples

Please contact for availability of other gel percentages

LIBRARY PREP

for a set of 1-24 samples
Illumina TruSeq RNA $265/set + $130/sample
Illumina TruSeq DNA $180/set + $130/sample
Illumina TruSeq ChIP $265/set + $125/sample
Bioo Scientific ChIPSeq $265/set + $100/sample

OTHER EQUIPMENT AVAILABLE

Axon Scanner Use $10/slide
Nanodrop Use $10/set (1-20 samples/set)
BioRad Imager $10/use (1-2 gels/use)
Seahorse XF Analyzer $150 per run plus $60 consumables
Accuri C6 Flow Cytometry $75/hour of instrument use
BioPlex Immunoassays $500/plate for labor and instrument charges
Bioruptor Sonicator $40/use (12-0.6 mL tubes, 6-1.5 mL tubes)

Wet lab training – consultation fee $75/hour
Data Analysis/Bioinformatics Requires a consultation to determine scope of the request and create a quote

Assistant professors can request consideration for a 1:1 match from the center ( i.e for each $100 spent, $50 would come from the PI and $50 from the center).

Associate and Full professors can request consideration for a 1:4 match from the center (i.e. for each $100 spent, $75 comes from the PI and $25 from the center)

Name of the person submitting this form:
Contact Phone Number
Contact Email
Name of PI
Title of PI (Full professor, associate professor, assistant professor)
Investigator Level
SeniorJunior
Institution
Department
Mailing Address

MEMBERSHIP DETAILS

Membership Status
Full MemberAssociate MemberAffiliate MemberNon-Member
Are you a CTEHR pilot project program award recipient?
YesNo
Do you anticipate requesting matching funds for services?
YesNo
Research Project Title
Brief Description of the Research Project
CTEHR Core this service request is directed to
Quantitative BiologyAdvanced ImagingIntegrative Health SciencesTargeted Genomics
Does your project include human subject research?
YesNo
Is there an animal use protocol associated with your project?
YesNo
Additional Information/Comments:

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