Getting Started with CHOP Microbiome Center



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Working with us is easy. Here are the steps to get started:

Project Consultation
Step 01

Project Request and Consultation: Fill out our project request form. After reviewing your project, we will schedule a 30-minute consultation to discuss the project scope. In this meeting, we will go over potential pitfalls and special considerations for microbiome research.

Estimate and Billing
Step 02

Estimate and Billing: We will send you an estimate for our services. (If you are outside of CHOP and Penn, a representative from our legal team will contact you to initiate the contracting process.) You will then submit your billing information using iLab.

Step 03

Scheduling: Email Lisa Mattei to schedule your project. Please contact us early — our queue is typically two months. Rush projects can be scheduled for an additional charge.

Step 04

Sample Metadata and Sending Samples: A sample metadata sheet is required to begin work on your project. Please use this template and instructions. The form can be complicated and revisions should be expected. Please send samples to the sequencing lab overnight on dry ice for receipt Monday through Friday, excluding holidays


Frequently Asked Questions

Yes. Please fill out our project request form, and we will be in touch to schedule a meeting.

Our consultation meetings are designed to advise people on this question. Please fill out our project request form. Our 2017 review article, “Optimizing methods and dodging pitfalls in microbiome research” gives a run-down of common mistakes and things to watch out for.

Our queue is typically two months long. If your project comprises less than one instrument run, there may be a wait while we prepare other projects to fill out the run. Rush projects can be scheduled for an additional charge.

We are unable to pre-bill for services. 

Sequencing turnaround time is queue- and project-dependent. Once we initiate your project, it is generally two to three weeks for 16S projects, four to six weeks for shotgun metagenomics projects, and six to eight weeks for whole genome sequencing projects. Please let us know in advance if you require a faster turnaround time (special pricing may apply). 

Analytical turnaround time is dependent on how well we can collaboratively develop a detailed analysis plan. We will send you a basic bioinformatics report within one to two weeks of sequencing data transfer. Following this first report, we will meet with you to review the sequencing data and set goals for the first round of follow-up analysis. Our policy is to check in and realign with our collaborators, either in person or by email, at least once for every eight to 10 hours of analysis work on a project. We take a strategic approach to prioritizing parts of the analysis to meet deadlines or to inform time-sensitive decisions.

Yes. Our goal is to work collaboratively to generate a manuscript or presentation that is as accurate and impactful as possible. We allocate time in our analysis plans for manuscript writing and figure preparation.

Our goal is to have each run collect the highest quality and quantity of data possible. Each Illumina NGS platform delivers a maximum output dependent upon the type of flow cell and reagents used. In practice, this output can also be affected by the DNA source and the type and diversity of the library. 

We guarantee a minimum of 70 percent of the maximum number of possible reads if we complete all quality control (QC) on submitted DNA and perform the library prep, pooling, and final library QC. All libraries used must pass QC in order for the run to be guaranteed.

We guarantee a minimum of 60 percent of the maximum number of possible reads if the user submits final library preps generated using the CHOP Microbiome Center or standard Illumina protocols and we complete the final library QC. All libraries must pass QC for the run to be guaranteed.

We cannot guarantee a minimum data output if custom sequencing/indexing primers are used in replacement of Illumina-provided reagents, or if a run includes experimental libraries that have not been previously tested at our Center or by Illumina.

Here are the specifications for the MiSeq and HiSeq 2500 instruments. 

The CHOP Microbiome Center should be acknowledged in publications or presentations. The nature of our collaboration warrants authorship if personnel at the CHOP Microbiome Center make an intellectual contribution that meets the authorship guidelines of the journal to which the work is submitted and will be part of any contractual arrangements.