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
Protocols for Quantification and Qualification of DNA, RNA, and NGS libraries
Tapestation Protocol
Qubit Protocol
PicoGreen Protocol
Bulk RNA-seq and ATAC-seq
Information and Protocols for all Bulk RNAseq and ATACseq library preparations and analysis currently used in the Beiting Lab
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
Bioinformatics for RNAseq/ATACseq
Single-Cell RNA-seq
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.
scRNA-seq FAQs
10X Genomics FAQs
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 Feature Barcoding Kit
FLEX Kit
ATAC Kit
Multiome Kit
Internal Protocols:
10X CITE-seq and Cell Hashing RNAseq (TotalSeq A)
10X RNAseq Library Prep
10X ATACseq
10X Feature Barcoding CITE-Seq with Single-Cell RNAseq (TotalSeq B)
Bioinformatics for Single Cell
Cell Digest for Tissue Samples stored in CryoStore (CS) 10
Cell Culture
Legacy Protocols
Legacy Protocols
Microbial Genomics
Protocols and Information for Microbial Genomics experiments and analysis
Microbiome FAQs
16S Amplicon Seq
Illumina DNA Prep (Nextera Flex)
Hack Flex - Manual
Hack Flex - Zephyr
Colony DNA Extraction for Illumina DNA Prep or HackFlex
16S Sanger Sequencing
Bioinformatics for Microbial Genomics
Extractions
DNA/RNA extraction protocols
ZymoBiomics™ 96 MagBead DNA Extraction
Linux Server
Information for the CHMI Linux Servers
Using the CHMI Linux server
Connecting to our RStudio server
Software we use
Downloading Data from BaseSpace
Portable Detection
Information for field-portable molecular biology tools
Biomeme Portable qPCR - General
Setting up the MinION/MinIT
BioPoo Assay on eDNA
Loading Sequencers
Information for Sequencers within CHMI and available to the Lab
NextSeq 2000
NextSeq 1000/2000 Library Kits (Full View)
MiniSeq
NovaSeq 6000
Illumina Instrument Troubleshooting
Teaching
Lab resources for learning how to analyze high-throughput sequencing data
Metagenomics in the cloud
Transcriptomics in the cloud
Conda for bioinformatics
Using Github Copilot
Bash basics
Git basics