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CHOP Microbiome Center (Sequencing and Analytical Resource) (CHOP)

eagle-i ID


Resource Type

  1. Core Laboratory


  1. Resource Description
    The CHOP Microbiome Center is the sequencing resource of the PennCHOP Microbiome Program. The Center is comprised of a Sequencing Core and an Analytical Core. Together we provide end-to-end solutions for microbiome research. The Sequencing Core provides expertise in next-generation sequencing of microbiome samples. Services include sample aliquoting, DNA extraction, quantitative PCR, library preparation, and sequencing. All protocols and workflows are optimized for individual sample types. Infrastructure for deep sequencing includes an Illumina HiSeq 2500 instrument, MiSeq instruments, and Oxford Nanopore technology. The sequencing facility is housed in the Colket Translational Research Building at CHOP. The wet lab is located in the adjoining Abramson Research Center and it includes dedicated pre- and post-PCR spaces. The labs are well equipped with the latest instruments including two automated liquid handling robots for high-throughput processing. The Sequencing Core is staffed by a laboratory manager and three research technicians. The Analytical Core provides expertise in large-scale bioinformatics analysis of microbiome datasets. Core services start with a thorough quality check and review of sequencing results. This includes removal of host genomic sequences and other DNA added during the sequencing protocol. Automated pipelines assess the bacterial, fungal, and viral taxa found in each sample. Alignments to genes of known function are summarized, and the data are queried against a curated collection of full genomes for microbes of interest. The primary mission of the Analytical Core is to follow up basic bioinformatics analysis with targeted bioinformatics and statistical approaches that are unique to each study. Rather than applying a one-size-fits-all approach, our goal is to collaborate with other researchers and draw conclusions from the sequence data about which we have high confidence and which reflect the original goals of the experiment. The Analytical Core is located at the CHOP Roberts Center for Pediatric Research. High capacity network lines connect the Analytical Core to the Sequencing Core, and to the CHOP supercomputing facility in Allentown, PA. The Core is staffed by three full time programmer/analysts and is supported by a network of consulting statisticians.
  2. Contact
    Bittinger, Kyle., PhD
  3. Contact
    Mattei, Lisa., PhD
  4. Affiliation
    PennCHOP Microbiome Program
  5. Performs Technique
    Metagenomics analysis
  6. Performs Technique
    Next generation DNA sequencing
  7. Performs Technique
    Data analysis
  8. Website(s)
Provenance Metadata About This Resource Record
  1. workflow state
  2. contributor
    ggrant (Gregory Grant)
  3. created
  4. creator
  5. modified
Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016