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

Summary:

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.

Affiliations:

People:

      Member: Bittinger, Kyle., PhD
      Role: Assistant Professor of Pediatrics at the Children's Hospital of Philadelphia, Lab Core Director, Analytics Core, CHOP Microbiome Center (Sequencing and Analytical Resource)

      Member: Mattei, Lisa., PhD
      Role: Laboratory Manager, Sequencing Core

    Resources:

    Instruments

    Services

    • High throughput sequencing service (Collaboration) ( Material analysis service )

      "Customers can collaborate with Microbiome Center staff for help with designing and analyzing microbiome-related projects. In the second format, customers will collaborate with the center to design and carry out complete projects. In this work flow, customers will begin by meeting with Center staff. Initial consultation on experimental design will be free of charge, subsequent use of Center Resources will be charged according to our cost schedule. The analysis will be fully planned, including sample size assessment and construction of the statistical framework for analysis. Customers will be provided with a cost estimate. Customers will then prepare complete metadata tables for the analysis, and present written documentation of IRB approval. Samples are then sent to the Center, DNA is purified, sequencing libraries are prepared, and sequence is determined. The pre-specified analysis is then carried out, and reported to customers. Any unused sample is also returned to customers. Additional analysis is available on a fee for service basis."

      "The core has three work-flows for sequence acquisition:

      1. High throughput shotgun metagenomic analysis of large microbiome sample sets. Sequencing will take place on the two HiSeq 2500 instruments.

      2. High throughput analysis of amplicons, such as 16S rRNA gene tags to characterize bacterial community membership. Sequencing will take place on the MiSeq instrument.

      3. Complete characterization of bacterial genomes. Sequencing will take place on the PacBio RS II instrument.

      Click here to get general sample submission guidelines and specific PacBio instructions."

    • High throughput sequencing service (Fee-for-service) ( Material analysis service )

      "Customers can send samples for fee-for-service sequencing and take delivery of output sequences. In this setting, customers will analyze the data independently of the Center."

      "The core has three work-flows for sequence acquisition:

      1. High throughput shotgun metagenomic analysis of large microbiome sample sets. Sequencing will take place on the two HiSeq 2500 instruments.

      2. High throughput analysis of amplicons, such as 16S rRNA gene tags to characterize bacterial community membership. Sequencing will take place on the MiSeq instrument.

      3. Complete characterization of bacterial genomes. Sequencing will take place on the PacBio RS II instrument.

      Click here to get general sample submission guidelines and specific PacBio instructions."

    • Nucleic acid sample quality assay service ( Material analysis service )

      • quality assay by gel electrophoresis
      • quality assay by Bioanalyzer/Fragment analyzer
      • nucleic acid purity measurements by UV spectrophotometry


    Web Links:

    Last updated: 2019-10-09T13:50:13.883-04:00

    Copyright © 2016 by the President and Fellows of Harvard College
    The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016