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

Directors: Bittinger, Kyle, PhD; Ravi, Kandasamy, PhD

Summary:

The CHOP Microbiome Center supports planning microbiome projects, DNA purification, library preparation, high throughput sequence analysis, and bioinformatic analysis of the output."

"To request pricing or core services, please complete this form and send to:

Jessi Erlichman erlichman@email.chop.edu

Requests for pricing must be submitted at least 4 weeks prior to grant deadline.

Affiliations:

People:

    Member: Erlichman, Jessi, MPH
    Role: Administrative Director, PennCHOP Microbiome Program, Manager, GI Center and Research Development, CHOP

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: 2016-02-01T15:05:53.028-05:00

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