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/Quality Control
Tapestation Protocol
Qubit Protocol
Bulk RNA-seq and ATAC-seq
RNA-seq FAQS
Stranded mRNA-seq
Stranded Total RNA-seq
Low input RNA-seq
Low input degraded total RNA-seq (Pico v3/FFPE-seq)
miRNA-seq
Sorting cells for RNA-seq
ATAC-seq library prep
Bioinformatics for RNAseq/ATACseq
Legacy RNA-seq protocols
Single cell genomics
scRNA-seq FAQs
10X Genomics FAQs
Chromium Next GEM Single Cell 3’ Kit v3.1
Chromium Next GEM Single Cell 3’ Kit v3.1 (Feature Barcoding)
Chromium Next GEM Single Cell FLEX
Chromium Next GEM Single Cell ATAC Kit
Chromium Next GEM Single Cell Multiome Kit
Single cell RNA-seq library prep (10X)
CITE-seq and Cell Hashing with 10x single cell RNAseq (TotalSeq A)
10x single cell ATACseq
Feature Barcoding CITE-Seq with 10x single cell RNAseq (TotalSeq B)
Bioinformatics for single cell genomics
10X Chromium Controller and Deep Well Thermocycler Sign Up
Legacy single cell protocols
Cell culture
3D 'organotypic' culture
Microscopy for 3D cultures
Teaching
Metagenomics in the cloud
Transcriptomics in the cloud
Conda for bioinformatics
Bash basics
Linux server
Using the CHMI Linux server
Connecting to our RStudio server
Software we use
Humann: How to Set up / Run on Paired Files
Sunbeam: How to Set-up / Run
Portable detection
Biomeme portable QPCR - general
Setting up minION/minIT portable sequencing
BioPoo assay on eDNA
Loading Sequencers
NextSeq 2000
NextSeq 1000/2000 Library Kits (Full View)
NextSeq 500
MiniSeq
NovaSeq 6000