Protocols and troubleshooting tips

Protocols - by application

Antibody conjugation and purification (2)+

• Sodium Azide removal protocol

• Biotin conjugation

Cell culture (8)+

• Aseptic technique video protocol
• Cell culturing summary
• Counting cells using a haemocytometer
• Cryopreservation of mammalian cell lines
• Dealing with cell culture contamination
• Differentiation of Human Embryonic Stem Cells to Hepatic Endoderm
• Mammalian cell tissue culture techniques
• Stimulating MMP-9 expression protocol

Cell isolation (2)+

• Murine endothelial cell isolation

• T cell purification from splenocytes

ChIP (7)+

• Discussion of ChIP protocol and technique

• ChIP troubleshooting tips
• ChIP using plant samples - Arabidopsis
• Chromatin preparation from tissues for chromatin immunoprecipitation (ChIP)
• Cross-linking chromatin immunoprecipitation (X-ChIP) protocol
• Native chromatin immunoprecipitation protocol
• X-ChIP protocol summary

Dot blot (1)+

• Dot blot protocol

ELISA (12)+

• Calculating & evaluating ELISA data
• Control samples required for ELISA
• Direct ELISA using fluorescent substrate protocol
• Direct ELISA using primary antibody protocol
• ELISA sample preparation guide
• ELISA troubleshooting tips
• In Cell ELISA (ICE)
• Indirect ELISA protocol
• Indirect ELISA protocol summary
• Non-denaturing extraction for ELISA and dipstick activity assays
• Sandwich ELISA protocol
• Sandwich ELISA protocol summary

ELISPOT (4)+

• Dual ELISPOT protocol: Detection of two secreted targets per sample
• ELISPOT protocol
• ELISPOT sample preparation guide
• ELISPOT troubleshooting tips

Flow cytometry / FACS (13)+

• Direct flow cytometry (FACS) protocol
• Flow cytometry - recommended controls
• Flow cytometry immunophenotyping
• Flow cytometry intracellular staining protocol
• Flow cytometry membrane staining protocol summary
• Flow cytometry troubleshooting tips
• Fluorescence activated cell sorting of live cells
• Fluorescence compensation in flow cytometry
• Indirect flow cytometry (FACS) protocol
• Intracellular flow cytometry protocol summary
• Introduction to flow cytometry
• Propidium iodide staining of cells to assess DNA cell cycle
• Red blood cell lysis protocol

Immunoprecipitation (6)+

• Crosslinking the antibody to the beads protocol
• Immunoprecipitation protocol
• IP troubleshooting tips
• RNA Immunoprecipitation (RIP)
• Using IgM antibodies for IP
• UV Cross-Linking and Immunoprecipitation (CLIP)

Immunostaining (20)+

• BrdU immunostaining procedure for cell cultures and tissue sections.

• GMA (Glycol methacrylate) embedding for immmunohistochemistry protocol

• ICC/IF Immunocytochemistry and immuofluorescence protocol

• IHC and ICC fixation and permeabilization protocol 

• IHC-FoFr Immunohistochemistry perfusion fixation protocol

• IHC-FoFr Perfusion fixation troubleshooting tips

• IHC-Fr frozen sections staining protocol

• IHC-FrFl Immunohistochemistry on free floating brain sections

• IHC-P Immunohistochemistry protocol

• IHC-P paraffin staining protocol - detailed guide

• Immunostaining protocol summary - flow diagram

• ISH - In situ hybridization protocol

• Mouse on Mouse (MOM) staining procedure

• Validating phospho-specificity of antibodies (WB, IHC) protocol

• IHC for paraffin-embedded sections video protocol
• IHC troubleshooting tips
• Immunohistochemistry - Methods Express Book Series
• Recommended controls for IHC/ICC
• Sectioning of paraffin-embedded tissue video protocol
• Whole mount staining protocols

siRNA  (1)+

• Recommended checks and controls for siRNA experiments

Toxin neutralization (2)+

• Cell culture preparation and plating protocol

• Toxin neutralization assay

Western blot (15)+

• Western blotting - a detailed guide

• Blocking with immunizing peptide protocol
• Blue native electrophoresis protocol
• Buffers and stock solutions
• Histone blotting protocol
• Histone extraction protocol for Western blot
• Mitochondrial purification protocol for Western blot samples
• Peptide competition assay (peptide blocking)
• Procedure for detection of phosphorylated proteins in Western blot
• Recommended controls for Western blotting
• Soluble (S-100) mitochondrial fractionation protocol for Western blot
• Western blot membrane stripping for restaining protocol
• Western blot protocol
• Western blot short step by step diagram
• Western blot troubleshooting tips

Protocols - by research area

Apoptosis protocols (5)+

• Annexin V detection protocol for apoptosis
• Apoptosis DNA fragmentation analysis protocol
• Caspase apoptosis detection protocol
• Introduction to apoptosis
• Protocols for biological and chemical induction of apoptosis in cells

Cardiovascular protocols (3)+

• Cardiomyocyte immunofluorescence protocol
• Isolation of human platelets from whole blood
• Mouse adipocyte glucose uptake assay

Molecular biology protocols (6)+

• Calcium phosphate transfection protocol
• Gelatin zymography protocol
• Measuring activity of gelatinase enzymes
• RNA isolation protocol: cells in culture
• Subcellular fractionation protocol
• Transforming competent cells and isolating plasmid DNA

Neuroscience protocols (13)+

• Amyloid Beta Uptake by Glia Cells
• Antibody staining of whole mount Drosophila embryos
• Bielschowsky’s Silver Stain for Axons
• Brain Synaptosomal Preparation
• BrdU protocol
• CLARITY protocol
• DEA Extraction of [soluble] Amyloid beta from Mouse Brain
• FA Extraction of [insoluble] Amyloid beta from Mouse Brain
• IF protocol for perfusion fixed tissue
• IHC Protocol for Free Floating Brain Sections
• Nuclear enrichment
• Primary Cultures for IHC – Viability Assays
• SWITCH protocol

Stem cells protocols (3)+

• Differentiation of 3T3-L1 cells into adipocyte-like cells
• Hepatocyte differentiation protocol
• Mouse embryonic stem cells to macrophage-like cells

Protocol guides and diagrams

Detailed application guides (4)+

• MitoTox™ : Mitochondrial toxicity application guide

• Cell culture guidelines
• IHC paraffin staining guide
• Western blotting guide

Protocol diagrams (8)+

• ELISPOT protocol summary
• Flow cytometry membrane staining protocol summary
• IHC protocol summary
• Indirect ELISA protocol summary
• Intracellular flow cytometry protocol summary
• Sandwich ELISA protocol summary
• Western blot protocol summary
• X-ChIP protocol summary

General help

Frequently asked questions (7)+

• Enzymatic assay Kits FAQ

• ChIP FAQ
• ELISA FAQ
• Flow cytometry FAQ
• Immunohistochemistry FAQ
• Immunoprecipitation FAQ
• Western blot FAQ

Product guides (6)+

• Antibody arrays - specific protein profiling tool

• ELISA, ELIPAIR, ELISPOT & FLUOROSPOT Kits
• Fluorescent ligand binding - frequently asked questions
• Immunohistochemistry (IHC) reagents | IHC protocols
• Recombinant and native proteins
• Secondary antibodies

Secondary antibody and fluorescence guides (6)+

• Conjugate guide | Biotin, HRP, AP and Fluorochrome
• DyLight® Fluorochrome conjugated secondary antibodies
• Fluorescence guide
• Fluorophore table
• The complete guide to secondary antibody selection
• Understanding secondary antibodies

Troubleshooting tips (8)+

• Troubleshooting tips for enzymatic assay kits

• ChIP troubleshooting tips
• ELISA troubleshooting tips
• ELISPOT troubleshooting tips
• Flow cytometry troubleshooting tips
• IHC troubleshooting tips
• IP troubleshooting tips
• Western blot troubleshooting tips