The CHOP Microbiome Center (Sequencing and Analytical Resource)

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

High throughput sequencing.  Infrastructure for deep sequencing includes two Illumina HiSeq instruments, a MiSeq instrument, and a Pacific Biosciences long read single molecule sequencing instrument.  The facility is housed in specially-built space in the Colket Building at CHOP.  Wet lab space (three modules) is in the adjoining Abramson building.  The wet lab is staffed by a lab director, co-director, and two research assistants. 

Analytical center. The analytical center is staffed by three full time programmer/analysts and supported by a network of consulting statisticians.  The center is located in prime office space at the Roberts Center for Pediatric Research., a few blocks from the wet lab facilities.  High capacity network lines connect the analytical center to the sequencing center, and to the CHOP supercomputing facility in Allentown PA.

Interacting with the Microbiome Center can take two forms. 

1)  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.

2)  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.

For more information about the CHOP Microbiome Center please visit the website








Contact/Project Information

Please fill out this form and send to:

Lisa Mattei ( and Cathy Engelman (

Pricing: Under development



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