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
Tapestation ProtocolQubit ProtocolPicoGreen ProtocolBulk RNA-seq and ATAC-seq
Information and Protocols for all Bulk RNAseq and ATACseq library preparations and analysis currently used in the Beiting LabRNA-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 PrepSorting cells for RNA-seqBioinformatics for RNAseq/ATACseq
Illumina Stranded mRNA-seqIllumina Stranded Total RNA-seqTakara Low Input RNA-seqTakara Low Input Degraded Total RNA-seq (Pico v3/FFPE-seq)Illumina miRNA-seqIllumina ATAC-seq Library PrepSorting cells for RNA-seqBioinformatics for RNAseq/ATACseqSingle-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 FAQs10X Genomics FAQsSign Up: 10X Chromium Controller and Deep Well Thermocycler
3’ Kit v3.1 Kit
3’ Kit v3.1 Feature Barcoding Kit
FLEX Kit
ATAC Kit
Multiome Kit
Mucosal cell isolation for scRNA-seq
10X Feature Barcoding CITE-Seq (TotalSeq B)
10X CITE-seq and Cell Hashing RNAseq (TotalSeq A)
10X RNAseq Library Prep
10X ATACseqBioinformatics for Single Cell Cell Digest for Tissue Samples stored in CryoStore (CS) 10
Chromium Next GEM Single-Cell Official Protocols (recommended):
3’ Kit v3.1 Kit3’ Kit v3.1 Feature Barcoding KitFLEX KitATAC KitMultiome KitMucosal cell isolation for scRNA-seq10X Feature Barcoding CITE-Seq (TotalSeq B)Internal Protocols:
10X CITE-seq and Cell Hashing RNAseq (TotalSeq A)10X RNAseq Library Prep10X ATACseqBioinformatics for Single Cell Cell Digest for Tissue Samples stored in CryoStore (CS) 10Spatial transcriptomics
Information and Protocols for spatial
Intestinal Swiss Rolls
Intestinal Swiss RollsCell Culture
Information and Protocols for Cell Culture3D 'organotypic' cultureMicroscopy for 3D cultures
Legacy Protocols
Legacy ProtocolsMicrobial Genomics
Protocols and Information for Microbial Genomics experiments and analysisMicrobiome FAQs
16S Amplicon Seq
Illumina DNA Prep (Nextera Flex)
Hack Flex - ManualHack Flex - ZephyrColony DNA Extraction for Illumina DNA Prep or HackFlex
16S Sanger SequencingBioinformatics for Microbial Genomics
16S Amplicon SeqIllumina DNA Prep (Nextera Flex)Hack Flex - ManualHack Flex - ZephyrColony DNA Extraction for Illumina DNA Prep or HackFlex16S Sanger SequencingBioinformatics for Microbial GenomicsExtractions
DNA/RNA extraction protocolsZymoBiomics™ 96 MagBead DNA Extraction
Linux Server
Information for the CHMI Linux ServersUsing the CHMI Linux server
Connecting to our RStudio serverSoftware we useDownloading from BaseSpace
Connecting to our RStudio serverSoftware we useDownloading from BaseSpacePortable Detection
Information for field-portable molecular biology tools
Biomeme Portable qPCR - General
Setting up the MinION/MinITBioPoo Assay on eDNA
Biomeme Portable qPCR - GeneralSetting up the MinION/MinITBioPoo Assay on eDNALoading Sequencers
Information for Sequencers within CHMI and available to the Lab
NextSeq 2000Untitled
MiniSeq
NovaSeq 6000
Illumina Instrument Troubleshooting
NextSeq 2000UntitledMiniSeqNovaSeq 6000Illumina Instrument TroubleshootingTeaching
Lab resources for learning how to analyze high-throughput sequencing data
Transcriptomics in the cloud
Conda for bioinformatics
Using Github Copilot
Bash basics
Git basics
DIYtranscriptomics: a full semester, virtual course on RNA-seq data analysis in R
Metagenomics in the cloudTranscriptomics in the cloudConda for bioinformaticsUsing Github CopilotBash basicsGit basics