Immunology
BioGPS is a great source for find tissue-specific gene expression
Immuno-Navigator A database for gene coexpression in the immune system
The Biolgend web is an outstanding for all things immunology
CD molecules (Biolegend)
Cell markers (Biolegend)
Maturation markers (Biolegend)
Flow cytometry buffers (Biolegend)
Fluorescence spectra analyzer (Biolegend)
Landscape of Immuno-Oncology Drug Development interactive tool for keeping up with the development of anti-cancer drugs.
Cell Culture
Cell Counting with a Hemocytometer (BitesizeBio) – Click here to download PDF
Useful Numbers for Cell Culture (Thermo Scientific)
Microbiology and molecular biology links
Interactive molecular biology tools (NEB)
Molecular biology protocols (NEB)
Plasmid guide (Addgene) – very useful for cloning questions
Making LB agar plate – protocol Making LB agar plate – video (Addgene)
Making glycerol stocks (Addgene)
Antibiotic concentrations spreadsheet (Addgene, InvivoGen)
Antibiotic concentrations (Thermo Fisher)
How to verify your plasmid (Addgene)
Plasmids 101: The promotor region (Addgene) Download PDF
Better Plasmid Midipreps Part II: What Causes Low Yields? (BitesizeBio)
Protein analysis and prediction
Predict Eukaryotic Linear Motifs (ELM) (e.g. ITIM, ITSM, ITAM)
Predict protein structure and features: SMART (e.g. IG domains, signal peptides)
Predict protein domains and signal peptides: Phobius
Predict protein domains: TMHMM server
Predict signal peptides: SignalP
Predict molecular weight and other good stuff: Protparam ProtPI
Predict non-classically secreted proteins: SecretomeP
Calculate multi-protein percent identity: Clustal Omega
Predict nuclear localization signals: cNLS mapper
Find potential restriction sites in a DNA sequence by introducing silent mutations that do not change the protein sequence: Webcutter
Amino acid properties and consequences of substitutions: Russel Lab
Software
Excellent software for plasmid construction, sequence analysis and general purpose DNA work: SnapGene
Protein alignments and general protein and DNA analysis: CLC Sequence Viewer (free version)
Free software environment for statistical computing and graphics: R-project, RStudio
Free image editing software: GNU Image Manipulation Program (GIMP)
Free software to design degenerate primers: HYDEN
Recipes
Buffer preparation calculator from @AATBioquest
Protocols
- CHO cell adaption to serum-free media
- Hybridoma production
- Hyrbidoma screening ELISA
- Protein A purification
- Plasmid construction protocol for recombinant DNA
- Cell culture protocol and notes
Working with animals
Procedures with care – tutorial videos for animal techniques
Working with genetically-modified organisms
What Dealings With GMOs are Classified as Exempt Dealings?
What are Notifiable Low Risk Dealings (NLRDs)?
Types of Dealings with GMOs classified as Notifiable Low Risk Dealings (NLRDs)
Useful flow chart for using genetically-modified organisms
Guidance Notes for the Containment of Exempt Dealings