Scope

Bioinformatics analysis – we provide timely and accurate analysis of high-throughput sequencing, gene expression, proteomics, metabolomics, and other biological data.

DNA sequencing – we offer a variety of DNA sequencing methods such as:

• • • • Complete genome re-sequencing – may be used to determine the sequence of individual genes, larger genetic regions (i.e. clusters of genes or operons), full chromosomes or entire genomes, of any organism.
      • ChIP-seq – is a method used to analyze protein interactions with DNA combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest.
      • DNase-seq – identifies the location of regulatory regions based on sequencing of regions sensitive to cleavage by DNase I.
      • FAIRE-seq  – determines the sequence of DNA regions associated with regulation. FAIRE-seq can analyze any cell type and doesn’t require the permeabilization of cells or isolation of nuclei.
      • ATAC-seq – is a method used to determine the accessibility of chromatin across the genome.
      • Metagenomics Sequencing – is used to study the genetic material from an environmental sample. By using PCR directed sequencing or “shotgun”, we are able to get widespread coverage of all genes within the sampled communities thus learning more about microbial diversity.

RNA sequencing – we offer a variety of RNA sequencing methods such as:

• • • • RNA-seq (RNA sequencing) – also called whole transcriptome shotgun sequencing (WTSS), uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment in time. RNA-Seq facilitates the ability to look at alternative gene spliced transcripts, post-transcriptional modifications, gene fusion, mutations/SNPs and changes in gene expression over time, or differences in gene expression in different groups or treatments. There are a variety of approaches to transcriptome sequencing, the best approach will depend on your needs.
      • MicroRNA sequencing (miRNA-seq) – a type of RNA-Seq, is the use of next-generation sequencing to sequence miRNAs. miRNA-seq differs from other forms of RNA-seq in that input material is typically enriched for small RNAs. miRNA-seq allows researchers to examine tissue-specific expression patterns, disease associations, and isoforms of miRNAs.
      • Single-Cell RNA-seq(scRNA-seq) – measures the gene expression level in each individual cell. scRNA-seq can reveal complex and rare cell populations, uncover regulatory relationships between genes, and track the trajectories of distinct cell lineages in development.¹

Microscopy Imaging Analysis – we provide expertise in processing, analysis, interpretation and final presentation of imaging data with a strong emphasis on quantitative image analysis. Our experience includes but is not limited to:

• • • • Analysis of 2D and 3D images based on segmentation (for example cell counts, area and volume measurements, foci detection or translocation analysis).
      • Particle and cell tracking in time-lapse series.
      • Co-localization analysis.
      • Dimensionality reduction analysis for multiplex single cell imaging.
      • FRET (Forster Resonance Energy Transfer) analysis.
      • FRAP (Fluorescence Recovery After Photobleaching) analysis.
      • Super-resolution image analysis.
      • Image data annotations.
      • Image registration and alignment.
      • Noise and background correction.
      • Experimental design to validate new fluorescence biosensors.
      • Script-writing to automate the analysis procedure and create analysis pipelines.
      • Development of automated and semiautomated tools for custom analysis performed directly by investigators.
      • Microscopy data visualization and presentation.
    • We also provide expert training in use of free, open-source image analysis software Fiji (ImageJ) and CellProfiler, as well as support in image analysis script development in Matlab and Python.

Application development – our team of experts will assist you with development of custom applications, including custom pipelines, databases and/or visualization.

Referrals—for projects beyond the expertise of our team, we will assist in the definition of the need and assist in locating relevant expertise on and off campus.