A. GENERAL METHODS
Gradient solution preparation (mammalian)
Gradient solution preparation (non-mammalian)
Gradients (discontinuous and continuous)
Gradients (self-generated gradients)
Homogenization of mammalian tissues
Homogenization of mammalian cells
Homogenates, differential centrifugation of
Gradient harvesting
Gradient analysis

B. SUBCELLULAR MEMBRANES (MAMMALIAN)
Caveolae
See “Plasma membrane domains”
Cytoplasmic vesicles
See “Protein localization (membrane versus cytosol)”
Cytosol/membrane vesicle separation
See “Protein localization (membrane versus cytosol)”
Endocytosis analysis
Cultured cells (endosomes/lysosomes/plasma membrane)
Lysosome/late endosome events (rat liver)
Methodological review
Self-generated gradients; buoyant density separation
Lysosome/late endosome analysis using Nycodenz®
Endoplasmic reticulum
See “Membrane trafficking” for resolution of endoplasmic reticulum from other membrane
compartments, e.g. plasma membrane, Golgi, trans-Golgi network, endosomes, ERGIC
Endoplasmic reticulum domains
Lipid droplets
Mitochondria-associated
Perinuclear

Endoplasmic reticulum – rough/smooth fractionation
Cultured cells (continuous gradients)
Self-generated gradients
Separation from Golgi
Endosomes
See “Endocytosis analysis”
See “Membrane trafficking” for resolution of endosomes from other membrane compartments, e.g. endoplasmic reticulum, plasma membrane, Golgi, trans-Golgi network, ERGIC
Exocyst function
Plasma membrane domain targeting
Exocyst vesicle trafficking – methodological summary
Exosomes and other microvesicles (mammalian)
Extracellular vesicles (non-mammalian sources)
GLUT 4 trafficking (self-generated gradient)
Golgi and trans-Golgi network
See “Endoplasmic reticulum – rough/smooth fractionation – separation from Golgi”
See also “Membrane trafficking” for resolution of Golgi (or trans-Golgi network) from other membrane compartments – e.g. endoplasmic reticulum, plasma membrane, endosomes, ERGIC
Intracellular signalling

Light mitochondrial fraction, analysis of
Continuous gradient
Self-generated gradient
See also “Lysosomes”
See also “Mitochondria”
See also “Peroxisomes”
Lipid rafts
See “Plasma membrane domains”
Lysosomes
Discontinuous gradient
Methodological review
See also “Light mitochondrial fraction, analysis of”
See also “Endocytosis analysis/lysosome/late endosome events
Lysosomes (ER/endosomes/plasma membrane)
Continuous gradient
Membrane trafficking (endoplasmic reticulum, plasma
membrane, Golgi, trans-Golgi network, endosomes, ERGIC)
Continuous gradient (short spin)
Continuous gradient (long spin)
Discontinuous gradient (flotation)
Discontinuous gradient (sedimentation)
Sedimentation velocity
Self-generated gradient
Membrane vesicle/cytosol separation
See “Protein localization”
Mitochondria:
Mammalian (discontinuous gradient)
Purification and analysis
See also “Light mitochondrial fraction, analysis of”

Neural tissue organelles
Synaptosomes, synaptoneurosomes, neuromelanin granules
and synaptic vesicles – a methodological survey 
Nuclei
Discontinuous gradients and density barrier
Methodological review
Peroxisomes (mammalian)
Continuous gradient
Discontinuous gradient or density barrier
Self-generated gradient
See also “Light mitochondrial fraction, analysis”
Plasma membrane
See “Membrane trafficking” for resolution of plasma membrane from other membrane compartments, e.g. endoplasmic reticulum, Golgi, trans-Golgi network, endosomes, ERGIC
Cardiac muscle, from
Cationic colloidal silica
Flotation in a discontinuous gradient
Plasma membrane domains
Caco-2 cells (apical/basolateral)
Cationic colloidal silica
Caveolae
Epithelial cells (apical junction complex)
Intestinal mucosa (brush border/basolateral)
Lipid rafts
Detergent strategy
Detergent-free strategy
Renal cortex (brush border/glomeruli/slit diaphragm)
MDCK cells
See “Epithelial cells (apical junction complex)”
NRK cells
“See Epithelial cells (apical junction complex) ”
Plasma membrane domain targeting (exocyst)
Protein localization (large protein complexes)
Protein localization (membrane versus cytosol)
Discontinuous flotation gradient
Self-generated gradient
Retinal rod outer segments
Optical disks
Secretory granules
Eosinophils
Pancreatic cells
Adrenal chromaffin, lymphocytic, neutrophil-derived,
synaptosomal, parotid and platelets
Storage granules (vesicles)
See “Secretory granules”
Trans-Golgi Network (TGN)
See “Membrane trafficking” for resolution of trans-Golgi network from other membrane compartments, e.g. endoplasmic reticulum, endosomes, plasma membrane, Golgi, , ERGIC

C. SUBCELLULAR MEMBRANES (NON-MAMMALIAN)
Algae
Organelles (various)
Amoeba
Organelles (various)
Arabidopsis thaliana
See “Plants”
Bacteria
Extracellular vesicles
Rhodospirillum rubrum:
Organelles, including acidocalcisomes
Chlamydomonas reinhardtii
See “Algae”
Dictyostelium discoideum
See “Protozoa”
Drosophila membranes
Fungi
Extracellular vesicles
Organelles
Yeast spheroplasts
Endosomes, ER, Golgi, TGN, vacuole
Membrane trafficking (vacuole, Cvt vesicles etc.)
Mitochondria 
Peroxisomes
Phytomonas francai
See “Protozoa”
Plant tissues
Organelles
Proteomic analysis of Arabidopsis
Protein processing
Protozoa
Acidocalcisomes
Contractile vacuoles
Other organelles