Protocols
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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
Tapestation Protocol
Qubit Protocol
Qubit Protocol
PicoGreen Protocol
PicoGreen Protocol

Bulk RNA-seq and ATAC-seq

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.
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scRNA-seq FAQs
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10X Genomics FAQs
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Sign Up: 10X Chromium Controller and Deep Well Thermocycler

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

3’ Kit v3.1 Kit
3’ Kit v3.1 Kit
3’ Kit v3.1 Feature Barcoding Kit
3’ Kit v3.1 Feature Barcoding Kit
FLEX Kit
FLEX Kit
ATAC Kit
ATAC Kit
Multiome Kit
Multiome Kit

Internal Protocols:

10X CITE-seq and Cell Hashing RNAseq (TotalSeq A)
10X CITE-seq and Cell Hashing RNAseq (TotalSeq A)
10X RNAseq Library Prep
10X RNAseq Library Prep
10X ATACseq
10X ATACseq
10X Feature Barcoding CITE-Seq with Single-Cell RNAseq (TotalSeq B)
10X Feature Barcoding CITE-Seq with Single-Cell RNAseq (TotalSeq B)
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Bioinformatics for Single Cell

Cell Culture

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Legacy Protocols

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Legacy Protocols