‘Omics

Revolutionary approaches to DNA sequencing have significantly impacted our ability to query large amounts of nucleic acid sequence, leading to a scientific revolution in Biology and Medicine. These platforms collectively known as massive parallel DNA sequencing encompass a combination of sophisticated enzymology, chemistry, high-resolution optics, nanotechnology, hardware, and software engineering. Flexible and scalable performance levels allow a wide range of applications.

Here we summarize our capabilities in several areas, with emphasis on NGS applications.

Available Next Generation Sequencing Platforms:

• Life Technologies Ion Proton
• Illumina HiSeq2500
• Illumina MiSeq
• PacBio RS SMRT

• De novo Genome Scaffold Construction
• mRNA sequencing
• miRNA sequencing
• Sequencing of other non-coding RNA species
• Genome assemblies
• Whole or partial exome re-sequencing
• Targeted genome and transcriptome (re-)sequencing using both amplification- and capture-based methods
• Biomarkers: Variant Discovery and Calling (SNP’s, Insertions, Deletions, Gene Duplications, etc)
• Metagenomic Sequencing
• CHiP-Seq – Identifying and characterizing Protein-DNA interactions
• Methylation Sequencing
• DNase-Seq – Sequencing of DNase I hypersensitive sites
• FAIRE-Seq (Formaldehyde-Assisted Isolation of Regulatory Elements)
• CLIP-Seq (Cross-Linking Immunoprecipitation, for Genome-wide RNA binding sites)

• Experimental Design and Consultation
• Read Quality Control
• Biomarker and Variant Discovery and Genotyping (Variant Calling)
• RNA-seq Analysis
• Differential Gene Expression
• eQTL Analysis
• Genome Annotation
• Coding sequences
• Non-coding RNA
• Gene Ontology
• Pathway Analysis
• Visualization tools for results display and graphic summarization (Heatmaps, GO Graphs)
• Cross-platform gene expression integration
• Development of customized bioinformatics pipelines
• iCOPâ„¢: ArrayXpress’ proprietary integrated Systems Biology platform (integration and co-analyses of genetic, transcriptomic, epigenetic, proteomic and metabolomic data sets)

• DNA and RNA Extraction
  • Genomic DNA/RNA purification from plant tissues, bacteria and other microorganisms
  • Plasmid DNA Purification
  • In vitro transcription
• Quality Control
  • Agarose and Polyacrylamide Gel Electrophoresis (PAGE)
  • Nanodrop ND-1000 - Spectrophotometer
  • Agilent 2100 Bioanalyzer Lab-on-a-Chip Quality Control Analysis: Integrity, Sizing, Quantification from DNA to protein
  • Kappa qPCR Sequencing Library Quantification
• Nucleic Acid Analysis
  • Sanger sequencing
  • Northern blot
  • Southern blot
  • Electrophoretic mobility shift assays
  • DNase I footprint assays
• Molecular Cloning
  • Restriction enzyme digestion and ligation
  • TA cloning
  • PCR cloning
  • TOPO and Gateway cloning
  • Blunt end cloning
  • Long fragment cloning
• Real-Time PCR
  • Absolute quantification
  • Relative quantification
  • Allelic discrimination
  • Presence/Absence for detection of specific targets
• Protein Services
  • Heterologous Protein Expression
    • Bacterial systems
    • Eukaryotic
      • Fungal
      • Mammalian
      • Plant
    • Heterologous Protein Purification
      • Poly-Histidine tagged
      • Glutathione S-transferase tagged
      • Affinity Separation
      • High Performance Liquid Chromatography (HPLC)
    • Protein Analysis
      • Native and denaturing (SDS) PAGE
      • Western blotting
        • Chemiluminescent detection
        • Fluorescent detection
      • ELISA
    • Enzymatic Assays (solution and in-gel native PAGE assays)

• Plant Genetic Engineering
  • Plant transformation
    • Agrobacterium-mediated transformation
    • Microparticle bombardment
  • Gene expression
    • Synthetic promoter design
    • Engineering of transcriptional trans-modulators
  • Multigene transfer and large constructs assembly for gene stacking
  • Site-specific transgene integration: see Emerging technologies
  • Transient gene expression assays
• Metabolomics
  • Biochemical identification
  • Quantification through statistical analysis
  • Data interpretation
• Emerging Technologies – evolving tools for Genome Engineering and Targeted Gene Manipulation
  • TALEs: TAL Effectors-based Nucleases and Transcription Factors
    • Modulation of gene expression
    • Site specific, directed homologous recombination for targeted insertions or deletions
  • CRISPR/Cas9: Site specific, directed gene mutagenesis, knock-outs and deletions; targeted insertions or gene replacements
• Functional Genetics
  • Protein-Protein interaction
    • Yeast two-hybrid screening
    • Split-ubiquitin yeast two-hybrid
    • In planta Förster resonance energy transfer (FRET) and Bimolecular fluorescence complementation (BiFC)
  • RNAi and other non-coding RNA – siRNA, shRNA, miRNA, lncRNA analyses
  • Co-suppression
  • Promoter screening: Quantitatively test and compare promoter constructs over-time in a plant-tissue based system using a fluorescent reporter gene. This semi high-throughput method allows for promoter constructs containing various control elements to be tested in the host tissue before the timely process of stable transformation.
  • VIGS (Virus-Induced Gene Silencing): Uses the plant’s natural homology-based defense mechanisms triggered by viral infections as a reverse genetics tool for studying gene function through gene silencing.