DNA Analysis/Automated Sequencing & Phosphorimaging Shared Resource and Genome Sequencing & Analysis Core Facility

The Duke Cancer Institute’s (DCI) DNA Analysis/Automated Sequencing and Phosphorimaging Shared Resource and the Institute for Genome Sciences & Policy’s (IGSP) Sequencing Facility Core are collaborating to offer expanded sequencing services for cancer researchers.

Cancer Institute members are provided DCI Core Facility rates for services provided by the DNA Analysis/Automated Sequencing and Phosphorimaging Shared Resource but not the IGSP Genome Sequencing & Analysis Core Facility.

Duke Cancer Institute DNA Analysis/Automated Sequencing & Phosphorimaging Shared Resource

Services provided

Capillary sequencing

• Automated DNA sequencing to 900bp
• Combination PCR fragment purification and resequencing
• Combination Plasmid DNA prep and DNA sequencing

Fluorescent fragment analysis

• Genotyping -- microsatellites, STRs, RFLPs
• Gene expression profiling
• Human Kras, B-raf, and PIK3CA mutation screening

Real time-PCR

• TaqMan® SNP genotyping assays
• TaqMan® copy number variation (CNV) assays
• High resolution melting (HRM) analysis -- SNP identification and mutation discovery
• AmpFlSTR Human Cell Line Identification

Sample prep

• AMPure XL PCR fragment purification
• Automated QiaCube plasmid DNA preps
• Automated QiaCube mouse tail gDNA
• We can use almost any Qiagen sample prep kit. Ask us!

Other

• Phosphorimaging
• IDT oligonucleotide purchasing service

Contact
Michael S. Krangel, PhD
Faculty Director

Scott Langdon, PhD
Facility Director

135 Jones Building
E-mail:sequence@mc.duke.edu
919-613-7831

http://cancer.duke.edu/dna/

Duke Institute for Genome Sciences & Policy Genome Sequencing & Analysis Core Facility

Services Offered

Next-generation ultra-high throughput sequencing general services

The following are available on all four technologies listed below, including Sanger sequencing.

• Consultation & experimental design
• Bio-informatics consultation and support
• Quotes and support letters for grant proposals
• Educational tours for groups or classes, seminars, and guest lectures
• Sample pickup, data backups to hard drive, troubleshooting

Roche GS-FLX (454) ultra-high throughput sequencing

• Over one million reads at 450 bp for gDNA,cDNA, amplicons
• SNP detection, whole genome assembly, metagenomics, transcriptome reference
• 3kb, 8kb, 20kb paired-end sequencing
• Amplicon design, cleanup, and pooling
• gDNA libraries from 500 ng DNA, cDNA libraries from total RNA, mRNA enrichment, bar coding

Illumina Genome Analyzer II & IIx ultra-high throughput sequencing

• Over 200 million reads at 36 or 75 bases
• Paired-end sequencing
• smRNA, mRNA, ChIP, gDNA, paired-end libraries prepared and sequenced
• Barcoded gDNA sequencing
• RAD sequencing (restriction site associated detection), Bar-seq (deep barcode sequencing -- alternative to microarray)

AppliedBio SOLiD 4 ultra-high throughput sequencing

• Over 400 million reads at 50 bases
• Mate-pair sequencing
• Preparation of libraries (gDNA, mRNA, ChIP)
• Accurate mapping by 2-base encoding
• Directional RNA sequencing
• 96 barcodes available plus three slide gasketing options
• RNA barcodes
• BioScope user interface with GUI for secondary data analysis

Capillary sequencing and misc.

• Automated Sanger (capillary) DNA sequencing to 1000bp, sample pickup, troubleshooting
• Large-scale PCR cleanup in 96-well format
• Microsatellites, tRFLPs, and AFLPs (500 or 1,000 size standard)
• Sale and delivery of consumables at cost: BigDye, BigDye buffer, PCR plates (box of 25)
• Robotic liquid handling methods development and service (96 or 384 well)
• Molecular quantitation of nucleic acids
• Agilent BioAnalyzer for DNA/RNA quality