Sequencing and Genomic Technologies

Program Leadership

Holly Dressman, PhD
Director

Overview

The Sequencing and Genomic Technologies Shared Resource brings all of the robust genomic technologies on campus under a single organization and enables comprehensive consultation, seamless management of complex projects that span multiple services, enhanced operational flexibility, and economies of scale for support services. Assistance is also provided to investigators with regard to data quality control, versioning, statistical analysis, and dissemination for all of these services. A major goal of many cancer genome projects is to characterize key genetic alterations in cancer and discover therapeutic targets through comprehensive genomic profiling of the cancer genome. The Sequencing and Genomic Technologies Shared Resource provides researchers with comprehensive genomic solutions with the latest and most complementary technologies readily available.

Services

  • Sample processing  (RNA/DNA extraction, QC,  Covaris Shearing)
  • Gene Expression Analysis  (RNAseq, Targeted RNAseq, microarrays, qRTPCR, ddPCR) 
  • Sequence Analysis (Functional, Variant Detection, De Novo, Chomatin IP, DNA modification)
  • Single cell isolation and gene expression profiling
  • Microbiome profiling

Accessibility and Scheduling

The majority of services provide sample processing and data analysis. The workflow for these services begins with an initial consultation with Dr. Dressman that covers the most appropriate genomic technology for the project, experimental design, sample preparation requirements, data analysis, and data storage. When samples are ready for processing, investigators fill out an on-line submission form and drop off their samples. Samples are processed in order of receipt, with DCI investigators given priority over other users. Samples are tracked throughout processing by Shared Resource staff using the LIM systems. Investigators can log in at any time through a web portal to follow their samples throughout the steps of processing. Once the data have been generated, they are checked against quality control benchmarks and some preprocessing may be done with the data (depending on the particular service and specifications from the investigator), the LIM systems send an email to the investigator informing them that their data set is ready to be downloaded from the secure server. Once the data have been retrieved, Dr. Dressman follows up with the investigator to ensure that they are satisfied with the service and to provide any needed assistance with data analysis and storage. After sufficient time has elapsed for the investigator to analyze the data, Dr. Dressman follows up again to offer any needed assistance with submitting data to public repositories such as GEO and Dryad.

Fees

Initial consultation, routine discussions, and assistance with manuscript and grant proposal preparations are free to DCI members. Fee for services is discussed during initial consultation and sequencing rates/quotes are provided through the web portal. 

Location and Contact for Services

Service Location Contact
DNA sequencing 119 BioSci sequencing@duke.edu
RNA sequencing 119 BioSci sequencing@duke.edu
Chromatin Immunoprecipitation Sequencing 119 BioSci  sequencing@duke.edu
DNA Modification Sequencing 119 BioSci sequencing@duke.edu
Microarray - Agilent and Affymetrix 2208B CIEMAS microarraylab@duke.edu
Single cell isolation and profiling  2208B CIEMAS microarraylab@duke.edu
Microbiome profiling 2208B CIEMAS microarraylab@duke.edu
Sample Processing & QC - Covaris Shearing 2208B CIEMAS microarraylab@duke.edu
Sample Processing & QC - DNA/RNA extraction 2208B CIEMAS microarraylab@duke.edu
Sample Processing & QC - DNA/ RNA QC 2208B CIEMAS microarraylab@duke.edu
Sample Processing & QC - Beta Globin Reduction 2208B CIEMAS microarraylab@duke.edu
RT-PCR – ABI 7900 HT and Fluidigm RT-PCR 2208B CIEMAS microarraylab@duke.edu
droplet digital PCR-Biorad QX200 2208B CIEMAS microarraylab@duke.edu
Instrument & Software Usage 2208B CIEMAS microarraylab@duke.edu

EQUIPMENT & TECHNOLOGY 

  • Three Illumina high-throughput DNA sequencers (HiSeq4000, HiSeq2500, HiSeq 2000, and MiSeq)
  • Pacific Biosciences RSII third-generation DNA sequencer with SMRT technology
  • Two LifeTechnologies IonTorrent high-throughput DNA sequencers (PGM and Proton)
  • Fluidigm C1 Single-Cell Auto-prep and IFC HX and MX controller system
  • Affymetrix GeneChip workstation with four GeneChip Fluidic 450 stations, two Affymetrix hybridization systems, and one Affymetrix GeneChip 7G scanner
  • One Agilent C and two Axon GenePix 4000B scanners
  • Life Technologies ABI 7900HT RT-PCR machine with autoloader, one Applied Bio RT-PCR Machine (steponeplus), Fluidigm BioMark HD RT-PCR 
  • Bio-Rad QX200 Droplet Digital PCR System