^{Shared Resources}

Hartwell Center
for Biotechnology

Hartwell Center for Biotechnology supports St. Jude investigators with state-of-the-art tools for biomedical discovery. The center provides highly specialized services that cannot be easily reproduced within an individual laboratory.

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OVERVIEW

The Hartwell Center for Biotechnology is a unique integration of high-throughput biotechnology resources, designed with the mission to provide St. Jude investigators state-of-the-art tools for biomedical discovery. Services include DNA Sequencing, Genome Sequencing, DNA Genotyping, Macromolecular Synthesis, and Microarray Analysis. The Hartwell Center is supported by the Cancer Center, investigator program funds, and by ALSAC. Services are highly cost-effective and chargeback fees are designed to recover only the cost of reagents.

IMPACT

The Hartwell Center provides extraordinary breadth of support across the St. Jude research community. Virtually all research laboratories utilize at least one of the services. The Hartwell Center also provides highly specialized services that cannot be reproduced readily within a research laboratory. The staff has a unique blend of skills across a diverse range of biotechnology platforms, protocol methods, instruments, and software systems. Their engagement and dedicated expertise are essential to the outstanding quality of services. The Hartwell Center provides access to biotechnologies that accelerate the pace of scientific discovery. Publications supported by this resource have a median impact factor >10, illustrating the significance of those research findings. These biotechnologies support novel discovery within the molecular processes contributing to pediatric cancers, as well as those responsible for normal development and response to infectious diseases.

One area in which St. Jude is so far ahead of everyone is the application and ease with which next- generation sequencing projects can be done, and new technologies can be adopted.

Paul Thomas, Member

Services and instrumentation

Genome Sequencing

WGS, WGBS, WES, RNA-Seq, RNA Iso-Seq, scRNA-Seq, ChIP-Seq, ATAC-Seq and custom target and amplicon sequencing
- (3) NovaSeq X Plus genome-scale production systems
- (1) NextSeq 2000 mid-range sequencer
- (5) MiSeq
iSeq 100 benchtop systems
Sequel IIe system
Pacific Biosciences Revio
- Library methods are available in automated high throughput formats running on the Hamilton STAR and PerkinElmer Sciclone NGSx liquid handling systems
- High-throughput fragment analysis systems
Agilent TapeStation 4200
- Agilent 96-capillary Fragment Analyzer
- Agilent Femto Pulse system
- Sample processing methods
  - DNA shearing (Covaris LE220, Diagenode Megaruptor 3
  - Bisulfite conversion of DNA
  - Target enrichment by hybridization, poly(A) mRNA enrichment, ribosomal RNA depletion, etc.
- Library production maintenance (automated robotic liquid handling systems)
Hamilton STAR
Hamilton Nimbus
- Perkin Elmer Sciclone NGSx
- Agilent TapeStation 4200 and a Biotek Synergy LX microplate reader
- Covaris LE220 system for sample shearing
- Agilent 5300 Fragment Analyzer

Sanger DNA Sequencing

ABI Big Dye Terminator chemistry coupled with capillary electrophoresis to sequence whole genome analyses, targeted genomic re-sequencing, SNP and mutation discovery
- (1) Perkin Elmer Janus liquid handling robotics system
- (11) Applied Biosystems Veriti thermal cyclers for sample preparation
- (2) Applied Biosystems 3730xl DNA Analyzers for separation and detection of fluorescently labeled products

Genotyping Analysis

DNA fingerprinting analysis by co-amplification and fluorescent detection of highly polymorphic short tandem repeat loci using the PowerPlex Fusion assay, SNP detection using the ABI SNaPshot method and Fragment Size Analysis of minisatellites, microsatellites, restriction fragment length polymorphisms, genomic insertions and deletions, copy number detection.
- (1) Perkin Elmer Janus liquid handling robotics system
- (11) Applied Biosystems Veriti thermal cyclers for sample preparation
- (1) Applied Biosystems 3500xl DNA Analyzer for separation and detection of fluorescently labeled products

Microarray Analysis

The Functional Genomics and Clinical Application Core Technology (CACT) laboratories offer a complete line of commercial and custom microarray analyses including SNP and copy number assessment, gene expression and CpG methylation profiling, CGH, and custom target enrichment methods for NextGen sequencing studies.
- (3) Affymetrix GeneChip cartridge analysis systems
  - (3) GeneChip 640 hybridization ovens
  - (8) automated GeneChip 450 fluidics wash stations
  - (3) high-resolution (7G) Affymetrix GeneChip 3000 scanners each with 48-place autoloaders.
- Illumina platform
  - (1) HiScan bead array scanner with autoloader
  - Tecan Evo robot for automated processing of arrays
  - (2) hybridization ovens
- Custom analysis supported by:
  - (1) Agilent High Resolution scanner
  - (3) hybridization stations
  - (2) Agilent Bioanalyzers
  - (2) Nanodrop spectrophotometers
  - (7) Bio-Rad Tetrad thermocyclers
- (1) Biotek Synergy LX microplate reader
- (2) Thermo NanoDrop 8000 spectrophotometer
- Agilent TapeStation 4200 for quality control assessment of RNA and DNA

Macromolecular Synthesis

Synthesis of custom peptide molecules, purification by preparative HPLC, and quality assessment by mass spectrometry and analytical HPLC.
- (2) Protein Technologies SymphonyX 24 column peptide synthesizers
- (1) Protein Technologies PurePrep Chorus peptide synthesizer
- (1) CEM Multipep 1 synthesizer
- (1) CEM Liberty Blue microwave peptide synthesizer
- (2) Freezemobile 25EL lyophilizers
- (2) Waters 2707 preparative HPLC systems
- (1) Waters Alliance 2695 semi-prep HPLC system
- (2) Waters Alliance 2695 analytical HPLC systems with a Waters 2487 dual wavelength absorbance detector and a Waters 2475 multi wavelength fluorescence detector
- Bruker Microflex mass spectrophotometer