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BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center

Directors: Bhasin, Manoj, Ph.D.; Libermann, Towia, Ph.D.

Location: 1st Floor, Room 107, 3rd floor, Room 380E, Simon C. Fireman Research North Building, 99 Brookline Ave, Boston, MA 02115

Summary:

The BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center provides all of the tools of modern functional genomics and proteomics combined with in depth bioinformatics and systems biology analysis, for academic and corporate clients alike. Equipped with State-of-the-Art technologies for high throughput transcriptional profiling, genotyping, protein quantitation, protein profiling and identification, real-time PCR and robotics and various systems biology tools. The BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology center is a core proteomics facility for the Dana-Farber/Harvard Cancer Center.

New Services:

• In-house developed workflows and algorithms for analysis of next-generation sequencing data including RNA-Seq, ChIP-Seq, Epigenetics-Seq and DNA seq
• Comprehensive workflow for analysis of Microbiome sequencing data
• Integrated systems biology analysis of transcriptome, miRNA, epigenome, metabolomics and proteomics data
• Coming soon on in-house development pipelines: MALDI Tissue imaging and targeted quantitative proteomics.

Affiliations:

People:

Resources:

Instruments

  • ABI 4800 Plus MALDI-TOF/TOF analyzer ( Mass spectrometer )

    Identifies and quantitates low-abundance proteins in complex biological samples, using iTRAQ Reagents. Handles up to 8 samples at a time (8-plex workflow).

  • Affymetrix GeneChip High Throughput Array Station ( Microarray platform )

    Used for labeling, hybridization, washing and staining.

  • Affymetrix GeneTitan High Throughput Array Plate Scanner ( Genotype analysis platform )

    "Affymetrix GeneTitan Instrument for fully automated 16, 24 and 96 well Affymetrix ArrayPlate whole genome expression arrays The BIDMC Genomics and Proteomics Center has upgraded the Affymetrix capabilities further by acquiring the fully automated GeneTitan instrument that enables hybridization of 16, 24 or 96 samples per run in a 96 well plate format. Various expression arrays for human, mouse and rat are available for the GeneTitan. We offer all 16, 24 and 96 well Affymetrix ArrayPlate whole genome expression arrays at highly competitive prices (significantly lower price per sample than any regular Affymetrix cartridge array) and expand the line of arrays to gene 1.1 ST and U219 ArrayPlates."

  • Agilent 1100/1200 HPLC ( High performance liquid chromatography instrument )

  • Agilent 2000 autosampler ( Autosampler )

  • Agilent fraction collector ( Fraction collector )

  • Amersham Lucidea arrayer ( Arrayer )

    Allows printing of custom slide arrays for both RNA and protein.

  • Beckman Coulter Biomek FX laboratory automation workstation ( Liquid handler )

    Handles both 8- and 96-well formats.

  • BioMicro Systems MAUI automatic hybridization station ( Hybridization station )

  • GeneChip Fluidics Station 450 ( Microarray wash station )

    Lab contains two copies of this instrument.

    "The GeneChip® Fluidics Station 450 is used for the wash and stain operation of Affymetrix GeneChip® arrays. The instrument includes design advancements to provide improved ease of use and true walk-away freedom dramatically improving efficiency in your genetic analysis.

    The GeneChip Fluidics Station 450 is 110V- and 220V- compatible."

  • GeneChip Hybridization Oven 640 ( Hybridization oven )

    Lab contains two copies of this instrument. To be used for hybridization after the plate comes out of the array station. Supports 96-well plate.

  • GeneChip Scanner 3000 7G ( Array scanner )

    "The GeneChip® Scanner 3000 7G is an extension of the GeneChip® Scanner 3000 (GCS 3000) series that allows you to scan next-generation higher-density arrays, including SNP arrays with up to 900,000 SNPs, tiling arrays for transcription and all-exon arrays for whole-genome analysis.

    The GCS 3000 7G combines space-saving and other design improvements with speed, superior performance and lower scanner-to-scanner variation to dramatically improve throughput and efficiency in your genetic analysis. The GCS 3000 7G also provides enhanced auto-focus and more consistent scanner-to-scanner biological performance to improve data integrity and data sharing between researchers."

  • Perkin Elmer ScanArray Express HT Laser Scanner ( Array scanner )

  • ScanArray Express HT ( Microarray platform )

  • SpectraMax 190 microplate reader ( Microplate reader )

    For nucleic acids and proteins.

  • StepOnePlus Real-Time PCR ( Real-time PCR machine )

    96-well format with capability for 384-well format.

  • Synergy Mx Monochromator-Based Multi-Mode Microplate Reader ( Microplate reader )

    Reads from 200 to 900 nm (wavelength) without filters/.

  • UltiMate Plus nanoLC ( Liquid chromatography instrument )

Protocols

Reagents

  • CytoScan® HD Cytogenetics Solution ( Microarray )

    "The CytoScan HD Solution provides the broadest coverage, highest performance, and most genotype–able single nucleotide polymorphisms (SNPs) for detecting human chromosomal aberrations with high-density coverage of all OMIM and RefSeq genes. This single array includes more than 2.6 million copy number markers of which 750,000 are genotype–able SNPs and 1.9 million are non–polymorphic probes."

Services

  • Affymetrix Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates ( Material analysis service )

    We are now introducing the Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates for comprehensive whole-transcript expression analysis. These arrays measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA). These whole-transcript array designs provide a complete expression profile of mRNA as well as the intermediary lincRNA transcripts that impact the mRNA expression profile. There is ample evidence that differential expression of lincRNAs plays an important role in the genesis and progression of disease and that aberrant expression of these molecules have also been linked to cancer. Recent advancements in transcriptome profiling provided evidence of the association of lincRNAs in a diverse range of cellular functions:

    1. Regulation of mRNA transcription
    2. Regulation of mRNA post-transcriptional modifications
    3. Occlusion/recruitment of transcription factor binding
    4. Activation and transportation of transcription factors
    5. Interaction with accessory proteins
    6. Guide protein complexes to locations in the genome

  • Bioinformatics and Systems Biology analyses offered ( Data analysis service )

    • Experimental design assistance for OMICS studies
    • Analysis of high throughput sequencing, microarray, proteomic and metabolomics data.
    • RNA-Seq analysis (mRNA expression/alternate splicing/isoforms/novel transcripts or gene/ Gene fusion/ detection of RNA editing)
    • Variation discovery/allele analysis (CNV/SNP) from Exome or DNA-Seq data
    • Analysis of epigenomics, ChIP-Seq and DNA Methylation data
    • Comprehensive workflow for analysis of Microbiome sequencing data
    • Integrated analysis of transcriptome, miRNA, epigenome and proteomics data
    • Functional Genomics analysis of data including pathway and functional enrichment analysis
    • Systems biology analysis of data to identify potential therapeutic targets or biomarkers.
    • Development of predictors using Bayesian, SVM, ANN, and KNN Algorithms for diagnosis and prognosis of disease.
    • Target design for enrichment and deep sequencing
    • Antigenicity and subcellular localization prediction
    • Data and text mining from Public databases and literature
    • Personalized consulting
    • Customized data analysis and interpretation

  • Gene expression profiling service ( Material analysis service )

  • Next Generation Sequencing Service ( Material analysis service )

    We are now offering full service for your next generation sequencing needs including in depth bioinformatics and systems biology analysis.

  • Proteomics analysis service ( Material analysis service )

    The Proteomics Core will provide a comprehensive array of services pertaining to the design, performance and analysis of proteomic studies. The core not only offers the ability to implement and validate previously developed proteomic methods to profile proteins in biological fluids and tissues, to quantitate proteins, to identify proteins and posttranslational modifications, and to study protein-protein interactions, but also the capability to modify or develop entirely new assays when warranted.

    A consultative service provided by key members of the core will be available to investigators to assess the rationale and feasibility for undertaking specific projects, designing proteomic studies, process and protocol development, proteomic data analysis, and the interpretation of results.

  • Real-time PCR service ( Material analysis service )

    Real-time PCR provides a highly accurate means of quantitating RNA or DNA in solution. It is often used as a validation technique for microarray data. The Genomics Center provides RTPCR services, including primer design and assay optimization if necessary. Online ordering is not available at this time. To order a real-time PCR experiment, please download the order form and fax it to us.

Software

  • Affymetrix Expression Console ( Software )

    Genomics Software. "Affymetrix® Expression Console software supports Probe Set summarization and CHP file generation for both 3' Expression (GeneChip® Human Genome U133 Plus 2.0 Array) and Exon Arrays (GeneChip Human Exon 1.0 ST Array)."

  • Affymetrix GeneChip Operating Software SDK ( Software )

    "The Affymetrix® GCOS SDK is a set of application programming interfaces (API) used to access the Affymetrix GCOS system. The GCOS SDK is a very thoroughly documented collection of software libraries, application programming interfaces, and sample code that illustrate and enable the use of and integration with the Affymetrix GCOS by external programs."

  • Bioconductor ( Software )

    "Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, more than 460 packages, and an active user community."

  • CLC Bio Software ( Software )

  • Cytoscape ( Software )

    "Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data." Systems biology analysis software. Uses Java.

  • Gene Set Enrichment Analysis ( Software )

    "Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states." Systems biology analysis software.

  • GeneGo ( Software )

    Web-based systems biology analysis software.

  • GEXPAS ( Software )

    Web-based genomics software. It also works with the following types of files: cel, dat, text, CSV, Excel.

  • GEXPAS ( Software )

    Web-based genomics software. It also works with the following types of files: cel, dat, text, CSV, Excel.

  • Ingenuity IPA ( Software )

    "IPA is software that helps researchers model, analyze, and understand the complex biological and chemical systems at the core of life science research.

    IPA helps you understand biology at multiple levels by integrating data from a variety of experimental platforms and providing insight into the molecular and chemical interactions, cellular phenotypes, and disease processes of your system. Even if you don’t have experimental data, you can use IPA to intelligently search the Ingenuity®Knowledge Base for information on genes, proteins, chemicals, drugs, and molecular relationships to build biological models or get up to speed in a relevant area of research. IPA provides the right biological context to facilitate informed decision-making, advance research project design, and generate new testable hypotheses."

  • JMP Genomics ( Software )

    "Whether you’re working with large data sets from next-gen sequencing studies or microarrays, JMP Genomics provides the tools you need to analyze rare and common variants, detect differential expression patterns, discover reliable biomarker profiles, and incorporate pathway information into your analysis workflows. In addition, our latest release extends the software’s capabilities for creating and manipulating genetic linkage maps, and then utilizing these maps in downstream QTL mapping for important agronomic crops.

    The unique pedigree of JMP Genomics combines dynamically interactive JMP graphics and robust SAS® Analytics, so you can see and explore your data from every angle, understand it and share analysis results with colleagues.

    JMP Genomics automatically organizes results into tabbed reports and lets you customize your view of analysis options. With capabilities for integration with R, Excel and other tools, JMP Genomics becomes your analytic hub."

  • m2iRNA ( Software )

    Custom software that will analyze correlations between mRNA and microRNA species.

  • m2iRNA ( Software )

    Custom software that will analyze correlations between mRNA and microRNA species.

  • Mascot ( Software )

    "Mascot is a powerful search engine which uses mass spectrometry data to identify proteins from primary sequence databases. While a number of similar programs available, Mascot is unique in that it integrates all of the proven methods of searching. These different search methods can be categorised as follows:

    * Peptide Mass Fingerprint in which the only experimental data are peptide mass values.

    * Sequence Query in which peptide mass data are combined with amino acid sequence and composition information. A super-set of a sequence tag query.

    * MS/MS Ion Search using uninterpreted MS/MS data from one or more peptides."

  • MATLAB ( Software )

    "MATLAB® is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran."

  • MATLAB ( Software )

    "MATLAB® is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran."

  • Partek Genomics Suite ( Software )

    "Partek® Genomics Suite™ is a comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noisy data. The software is unique in supporting all microarray and next generation sequencing technologies including gene expression and digital gene expression (DGE), exon/alternative splicing and RNA-Seq, copy number and association, ChIP-chip, ChIP-seq, and microRNA in a single software package allowing for analysis of multiple applications in one complete solution."

  • ProteinPilot ( Software )

    Proteomics software that analyzes protein expression data.

  • R ( Software )

    "R is a free software environment for statistical computing and graphics."

  • SAS ( Software )

    Statistical package.

  • SEQUEST ( Software )

    SEQUEST is a tandem mass spectrometry data analysis program used for protein identification. Sequest identifies collections of tandem mass spectra to peptide sequences that have been generated from databases of protein sequences.

  • SPSS ( Software )

    "IBM SPSS Statistics is a comprehensive, easy-to-use set of data and predictive analytics tools for business users, analysts and statistical programmers."

  • SYBYL 8.0 ( Software )


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Last updated: 2015-11-19T14:32:12.296-06:00

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The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016