Services Offered


Nucleic Acid Purification

Qiagen Qiacube (Contact: Felicia Waller)

Application Capabilities Advantages Disadvantages Recommendations
Nucleic acid isolation and purification Total RNA; miRNA; DNA; All prep (all nucleic acid) 2-12 samples per run Fully automated; DNase over column; Flexible to handle cells and tissues Efficiency of columns limited Specialized methods needed for miRNA. Appointment and training required

Nucleic Acid Quantification and Quality Control

Agilent Bioanalyzer (Contact: Felicia Waller)

Application Capabilities Advantages Disadvantages Recommendations
Quality Control Profiles for total RNA; enriched mRNA; enriched small RNA; DNA fragment up to ~10kb; Measure integrity and quantity of DNA and RNA; samples sizes down to ~100pg Quantification not as accurate as other methods; salt skews results Samples must be in nuclease free water.

Nanodrop Spectrophotometer (Contact: MRC @ 901-448-6191)

Application Capabilities Advantages Disadvantages Recommendations
Nucleic acids quantification and quality control Absorbance for nucleic acids; calculating concentrations and purity; A260/A280 ratios; and A260/A230 ratios Able to see contamination of organics and proteins; requires only 1µl of sample Loses accuracy at concentrations below 20ng/µl and above 1500ng/µl. Concentrations affected by purity. Nucleic acids only

Qubit (Contact: Lorne Rose)

Application Capabilities Advantages Disadvantages Recommendations
Quantification of nucleic acids Florescence detection for concentration of nucleic acids Organic contamination not usually a problem; high sensitivity Does not allow determination of sample purity. Needs 1µl of sample

Spectra Max M2e Plate Reader (Contact: Felicia Waller)

Application Capabilities Advantages Disadvantages Recommendations
Quantification of nucleic acids and proteins Absorbance; fluorescence; luminescence for DNA; RNA; and protein assays Reads plates or cuvette with a wide range of wave lengths User must provide plates or cuvette Works with any flat bottom 96 well plate. Prior training necessary.

Gene Expression and Genetic Variation (High Throughput)

Life Technologies Ion Torrent PGM (Contact: Bill Taylor or Caitlin Costelle)

Application Capabilities Advantages Disadvantages Recommendations
Next generation sequencing; genetic variation and discovery ChIP seq; miRNA seq; targeted seq; genome seq 1-96 samples; scalable coverage Good for discovery experiments; lower cost with high throughput; very flexible Restricted amount of coverage; data analysis is challenging Arrange for bioinformatics analysis before run. Prior consultation with MRC required.

Life Technologies Proton (Contact: Bill Taylor or Caitlin Costelle)

Application Capabilities Advantages Disadvantages Recommendations
Next generation sequencing; genetic variation and discovery ChIP seq; miRNA seq; targeted seq; genome seq
1-96 samples; scalable coverage
Good for discovery experiments; lower cost for higher throughput; very flexible Data analysis is challenging Arrange for bioinformatics analysis before run. Prior consultation with MRC required.

Affymetrix Microarray (Contact: Lorne Rose)

Application Capabilities Advantages Disadvantages Recommendations
Gene expression and genetic variation Differential gene expression; alternative splicing; genotyping; cytogenetics; miRNA; 1 sample/ array Whole transcript (no 3’ bias); high correlation values; gene level and exon level data; excellent for iRNA detection; data easy to analyze Restricted to probes tiled on the array; hybridization based application; less reliable for low expression Requires validation. Prior consultation with MRC required.

ABI 3130XL Sequencing (Contact: Tom Cunningham)

Application Capabilities Advantages Disadvantages Recommendations
DNA sequencing Sequencing of plasmids; PCR product; genomic DNA; fragment analysis Sensitive; over 700bp’s can be sequenced per run Sample quality affects sequencing data; proper primer concentrations are necessary for optimal results Check with MRC for available standard primers.

Real Time PCR and Genetic Variation

Roche LC480 (Contact: Felicia Waller)

Application Capabilities Advantages Disadvantages Recommendations
Real-time PCR Gene expression; genotyping; HRM; Taqman UPL library®;
Sybr Green 96- and 384-well formats
Highly sensitive; reproducible and flexible UPL Library available for human; mouse and rat Sybr green assays prone to errors from primer dimers and nonspecific amplification Reference gene assays available. UPL probes and controls need to be tested. Samples should be run in triplicate

Fluidigm Biomark (Contact: Jian Yan)

Application Capabilities Advantages Disadvantages Recommendations
Real-time PCR qRT-PCR; digital PCR; genotyping Taqman UPL library®; Sybr green Various high throughput formats Cost effective for high throughput; low sample input requirements; highly sensitive Defined formats determine number of samples and genes Samples must be pre-amplified

Affymetrix Quantigene 2.0 Mµltiplex Assay (Contact: Jian Yan)

Application Capabilities Advantages Disadvantages Recommendations
Multiplexed gene expression assays; CNV Gene expression; DNA copy number;
multiplex 3-50 targets;
1-96 samples
Flexible multiplexing assays; measure directly from cell homogenates without RNA isolation Best for large sample sizes ~3000 cells required per sample; or ~100ng total RNA

Other Services

Eppendorf epMotion 5075 (Contact: Lorne Rose)

Application Capabilities Advantages Disadvantages Recommendations
Liquid handling robot Liquid transfer to 384 well plates Able to quickly set up 384 well plates for Roche LC480 Must dispense either single or 8 channels Prior appointment necessary

Transnetyx Genotyping (Contact: Felicia Waller)

Application Capabilities Advantages Disadvantages Recommendations
Genotyping Knockouts; transgenic mutations; SNP detection using real-time PCR Fully automated process; mail in mouse tail or ear NA Check with company for acceptable tissues to send; drop off kiosk located at MRC

Zeiss Axiophot Photomicroscope (Contact: Felicia Waller)

Application Capabilities Advantages Disadvantages Recommendations
Fluorescence microscopy Fluorescence detection assays; photo documentation available Progres® software able to take color pictures of fluorescence detection assays Limited resolution. Dyes limited to Red (PE’s); Green (Fitc); DAPI or dyes with similar spectra Prior appointment and training necessary

MRC Services Offered Comparison Chart and Quick Reference Guide

Genetic Variation and Discovery Workflow Suggestions