This is home to all the standard protocols, procedures and services of the PennVet Center for Host-Microbial Interactions (CHMI).
Edit me

Site overview

This website provides convenient access to all the standard protocols and procedures the PennVet Center for Host-Microbial Interactions (CHMI). If you’re a member of my lab, then clicking on the “Edit me” button above (and on each page) will take you to GitHub where you can collaboratively edit any protocol page. This wiki-style approach gives us a central place to develop our lab protocols, while always keeping the most up-to-date protocol in one convenient and publicly accessible place. If you’re not part of CHMI, no worries, you can still peruse the site to see our protocols. Comments and feedback are welcome!

Printing protocols

We made the site as visually clean as possible, so that your laptop or iPad could be used for following protocols at the bench. However, each page is also formated for printing or saving as a PDF. Simply hide the navigation sidebar by clicking ‘Nav’ button at the top of the page and print.

Protocol tags

Notice that each protocol is tagged at the bottom of the page. Clicking on a tag allows you to easily find all protocols related to a certain topic (e.g. library prep, transcriptomics, single cell genomics, and much more!).

Technology available at CHMI


CHMI does not charge for labor (I know, I know, we’re awesome). We do, however, charge for consumables and apply a run fee to each use of our sequencer, which helps offset the cost of our annual service contract on the machine. To avoid unnecessary administrative overhead, we ask that you purchase your own consumables for any work done with CHMI. Of course, we can guide you on what exactly to purchase. See our CHMI invoice template for a detailed list of charges.