Microbiome Research
Sequencing Facilities
Core: JHMI Deep Sequencing and Microarray Core
Director: Haiping Hao, Ph.D.
This core offers Illumina HiSeq and MiSeq Next Generation Sequencing (NGS) and Third Generation Sequencing (PacBio Single Molecule Real-Time (SMRT)) sequencing platforms. Other available techniques include DNA and RNA extraction from tissue samples, library preparation. Fecal DNA or RNA preparation is not done. These approaches are useful for microbiome 16S rRNA sequencing and metagenomics sequencing as well as whole genome sequencing of bacterial strains. RNA preparation for RNA-seq is done in this Core (samples are subsequently sequenced in the Scott/Mohr GRCF core below). Please see link below for a complete description of this core’s service portfolio.
Core: Genetic Resources Core Facility (GRCF)
Directors: Alan F. Scott, Ph.D. and David Mohr, Ph.D.
This core offers Illumina HiSeq and MiSeq Next Generation Sequencing (NGS) and ‘traditional’ Sanger or pyrosequencing (Qiagen) sequencing platforms. Other available techniques include DNA and RNA extraction from biologic and FFPE samples. DNA library preparation, Exome, and custom capture sequencing are offered. RNA library preparation and non-standard library preparation can be coordinated with the JHMI Deep Sequencing and Microarray Core above. Fecal DNA and RNA preparation is offered. These approaches are useful for microbiome 16S rRNA, metagenomics and transcriptomic (RNASeq) sequencing. Please see link below for a complete description of this core’s service portfolio.
Core: Next Generation Sequencing Center
Director: Vasan Yegnasubramanian, Ph.D.
This newly formed core integrates the Next Generation Sequencing, Microarray, Bioinformatics, and Genomics Educational activities and services in the Cancer Center, and provides these services across all of JHU. The Next Generation Sequencing lab in the core houses Illumina HiSeq and MiSeq, SOLiD 5500 and Wilfire instruments and integrates computational analytical services. This Core provides microbial whole genome sequencing and RNASeq as available applications, among a number of custom and flexible microbiome and metagenomics applications. DNA and RNA extraction is not done currently, but will be supported in the future. DNA and RNA library preparation is available for multiple standard and custom applications. Until the newly created Experimental and Computational Genomics Center website is officially launched in the coming weeks, please see the link below for more complete information.
Metabolomics Facilities
Core: Johns Hopkins Institute for Clinical & Translational
Research: Metabolomics Program
Director: Namandje Bumpus, Ph.D.
This core offers targeted metabolomics analysis of endogenous small molecules and development of custom targeted mass spectrometry-based metabolomics assays as well as identification of drug metabolites. Please see link below for a complete description of this core’s service portfolio.
Core: Center for Resources in Integrative Biology (CRIB) & Molecular Determinants Core (MDC)
Director: David Graham, Ph.D.
This core focuses on metabolomics analyses. Discovery metabolomics (METLIN workflow, best for non-polar metabolites)) is offered as well as a pipeline better suited for profiling of polar metabolites. Semiquantitative targeted metabolomics assays are available as well as absolute quantitation of free amino acids. A lipidomics pipeline is available originally developed in the Agilent Center of Excellence in Delaware by Sumit Shaw. Please see link below for a complete description of this core’s service portfolio.
Proteomics Facilities
Core: Mass Spectrometry and Proteomics Facility
Director: Robert Cole, Ph.D.
This core focuses on mass spectrometry-based proteomics to identify, quantify or characterize proteins and their post-translational modifications in gel bands or spots, or in complex protein extracts from cells, tissues or body fluids. Please see link below for a complete description of this core’s service portfolio.
Computational Core
Core: Computational Biology Consulting Core
Directors: Liliana Floria, Ph.D.
Steven Salzberg, Ph.D.
This core offers state of the art computational biology services. The core offers comprehensive analysis of sequencing data for a variety of genomics and other sequencing based experiments. This includes 16S rRNA, RNA-seq and metagenomic sequence analysis among others. Please see link below for a complete descriptions of this core's service portfolio.
Dejea et al. PNAS 111:18321, 2014.
False colorized scanning electron micrograph of the surface of a biofilm-covered colorectal cancer.