Protocols

This website provides access to all standard protocols and procedures used at the PennVet Center for Host-Microbial Interactions (CHMI). If you’re affiliated with CHMI or a member of the Beiting Lab, then you can collaboratively edit any of these protocols. 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!

Quantification and Quality Control

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Protocols for Quantification and Qualification of DNA, RNA, and NGS libraries

Tapestation Protocol

Qubit Protocol

Bulk RNA-seq and ATAC-seq

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Information and Protocols for all Bulk RNAseq and ATACseq library preparations and analysis currently used in the Beiting Lab

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RNA-seq FAQS

Illumina Stranded mRNA-seq

Illumina Stranded Total RNA-seq

Takara Low Input RNA-seq

Takara Low Input Degraded Total RNA-seq (Pico v3/FFPE-seq)

Illumina miRNA-seq

Illumina ATAC-seq Library Prep

Sorting cells for RNA-seq

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Bioinformatics for RNAseq/ATACseq

Single-Cell RNA-seq

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The Beiting Lab exclusively uses 10X Genomics kits and Chromium controllers to generate single-cell RNA-seq data. See below for more information and protocols currently used in the lab.

Chromium Next GEM Single-Cell Official Protocols (recommended):