Links to Nature Protocols and other papers with procedures for antibody related experiments are given below. To suggest literature or resources for this page, please email us at

Western blotting

Metabolic labeling of glycans with azido sugars and subsequent glycan-profiling and visualization via Staudinger ligation.
Laughlin ST, Bertozzi CR
Nature protocols 2007;2(11):2930-44

A simple slot blot for the detection of virtually all subtypes of the influenza A viral hemagglutinins using universal antibodies targeting the fusion peptide.
Li C, Jaentschke B, Song Y, Wang J, Cyr TD, Van Domselaar G, He R, Li X
Nature protocols 2010;5(1):14-9

Automated microfluidic protein immunoblotting.
He M, Herr AE
Nature protocols 2010;5(11):1844-56

Colony filtration blotting for screening soluble expression in Escherichia coli.
Dahlroth SL, Nordlund P, Cornvik T
Nature protocols 2006;1(1):253-8

Generation of cell-free extracts of Xenopus eggs and demembranated sperm chromatin for the assembly and isolation of in vitro-formed nuclei for Western blotting and scanning electron microscopy (SEM).
Allen TD, Rutherford SA, Murray S, Sanderson HS, Gardiner F, Kiseleva E, Goldberg MW, Drummond SP
Nature protocols 2007;2(5):1173-9

Separation and detection of large phosphoproteins using Phos-tag SDS-PAGE.
Kinoshita E, Kinoshita-Kikuta E, Koike T
Nature protocols 2009;4(10):1513-21

Western blot analysis of sub-cellular fractionated samples using the Odyssey Infrared Imaging System
Misawa Y, Li Y, Rekosh D, Hammarskjold M
Protocol Exchange 2006 September

Phos-tag Western blotting for detecting stoichiometric protein phosphorylation in cells
Kosako H
Protocol Exchange 2009 September

TH17 cells contribute to uveitis and scleritis and are inhibited by IL-27/STAT1 in the retina. (3) Western Blot Analysis
Egwuagu C, Yu C, Amadi-Obi A, Liu X, Mahdi R, Lee Y
Protocol Exchange 2007 August

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Chromatin immunoprecipitation, RNA immunoprecipitation protocols

Chromatin immunoprecipitation and microarray-based analysis of protein location.
Lee TI, Johnstone SE, Young RA
Nature protocols 2006;1(2):729-48

Analysis of epigenetic modifications of chromatin at specific gene loci by native chromatin immunoprecipitation of nucleosomes isolated using hydroxyapatite chromatography.
Brand M, Rampalli S, Chaturvedi CP, Dilworth FJ
Nature protocols 2008;3(3):398-409

A rapid micro chromatin immunoprecipitation assay (microChIP).
Dahl JA, Collas P
Nature protocols 2008;3(6):1032-45

Protocol for the fast chromatin immunoprecipitation (ChIP) method.
Nelson JD, Denisenko O, Bomsztyk K
Nature protocols 2006;1(1):179-85

Serial analysis of binding elements for human transcription factors.
Chen J
Nature protocols 2006;1(3):1481-93

Detection of in vivo protein-DNA interactions using DamID in mammalian cells.
Vogel MJ, Peric-Hupkes D, van Steensel B
Nature protocols 2007;2(6):1467-78

Use of in vivo biotinylation to study protein-protein and protein-DNA interactions in mouse embryonic stem cells.
Kim J, Cantor AB, Orkin SH, Wang J
Nature protocols 2009;4(4):506-17

An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in Arabidopsis plants.
Saleh A, Alvarez-Venegas R, Avramova Z
Nature protocols 2008;3(6):1018-25

The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana.
Deal RB, Henikoff S
Nature protocols 2011 Jan;6(1):56-68

Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP).
Kaufmann K, Muiño JM, Østerås M, Farinelli L, Krajewski P, Angenent GC
Nature protocols 2010;5(3):457-72

Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans.
Mukhopadhyay A, Deplancke B, Walhout AJ, Tissenbaum HA
Nature protocols 2008;3(4):698-709

'Calling Cards' method for high-throughput identification of targets of yeast DNA-binding proteins.
Wang H, Heinz ME, Crosby SD, Johnston M, Mitra RD
Nature protocols 2008;3(10):1569-77

ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos.
Sandmann T, Jakobsen JS, Furlong EE
Nature protocols 2006;1(6):2839-55

RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts.
Keene JD, Komisarow JM, Friedersdorf MB
Nature protocols 2006;1(1):302-7

Immunoprecipitation of mRNA-protein complexes.
Peritz T, Zeng F, Kannanayakal TJ, Kilk K, Eiríksdóttir E, Langel U, Eberwine J
Nature protocols 2006;1(2):577-80

Methylome analysis using MeDIP-seq with low DNA concentrations.
Taiwo O, Wilson GA, Morris T, Seisenberger S, Reik W, Pearce D, Beck S, Butcher LM
Nature protocols 2012 Mar 8;7(4):617-36

Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq.
Adli M, Bernstein BE
Nature protocols 2011 Sep 29;6(10):1656-68

Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue.
Fanelli M, Amatori S, Barozzi I, Minucci S
Nature protocols 2011 Nov 10;6(12):1905-19

Chromatin immunoprecipitation (ChIP) assay
Ni Z, Ng D, Liu J, Chen Z
Protocol Exchange 2009 January

Chromatin immunoprecipitation from C. elegans embryos
Ercan S, Whittle C, Lieb J
Protocol Exchange 2007 February

Chromatin preparation and ChIP from Drosophila brain and discs tissues
Richter C, Richter C, Oktaba K, Mueller J, Knoblich J
Protocol Exchange 2011 June

TH17 cells contribute to uveitis and scleritis and are inhibited by IL-27/STAT1 in the retina. (5) Chromatin immunoprecipitation
Egwuagu C, Yu C, Amadi-Obi A, Liu X, Mahdi R, Lee Y
Protocol Exchange 2007 August

Ubp-M knockdown, RT-PCR and ChIP assays
Wang H
Protocol Exchange 2007 October

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Protein immunoprecipitation protocols

Optimization of immunoprecipitation-western blot analysis in detecting GW182-associated components of GW/P bodies.
Moser JJ, Chan EK, Fritzler MJ
Nature protocols 2009;4(5):674-85

One-step analysis of protein complexes in microliters of cell lysate using indirect immunolabeling & fluorescence cross-correlation spectroscopy.
Stoevesandt O, Brock R
Nature protocols 2006;1(1):223-9

A differential proteome screening system for post-translational modification-dependent transcription factor interactions.
Pless O, Kowenz-Leutz E, Dittmar G, Leutz A
Nature protocols 2011 Mar;6(3):359-64

Detecting protein-protein interactions by Far western blotting.
Wu Y, Li Q, Chen XZ
Nature protocols 2007;2(12):3278-84

Purification of a protein complex that associates with chromatin
Okada M, Fukagawa T
Protocol Exchange 2006 December

Immunoprecipitation of endogenous MEKK1 and kinase assay
Gallagher E, Enzler T, Matsuzawa A, Karin M
Protocol Exchange 2007 January

Immunoprecipitation (IP) of Homer 1a, injection of virions and in situ hybridization in the spinal cord
Kuner R
Protocol Exchange 2006 June

Co-immunoprecipitation of Platelet Factor 4 and RANTES from human platelets
Koenen R, Weber C
Protocol Exchange 2009 June

Co-immunoprecipitation of human mitochondrial proteases AFG3L2 and paraplegin heterologously expressed in yeast cells
Fracasso V, Lazzaro F, Muzi-Falconi M
Protocol Exchange 2010 March

Detection of in vivo ubiquitinated protein
Gallagher E, Enzler T, Matsuzawa A, Karin M
Protocol Exchange 2007 January

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Microscopy protocols

A protocol for phenotypic detection and characterization of vascular cells of different origins in a lung neovascularization model in rodents.
Jones RC, Capen DE, Cohen KS, Munn LL, Jain RK, Duda DG
Nature protocols 2008;3(3):388-97

Immunogold quantification of amino acids and proteins in complex subcellular compartments.
Bergersen LH, Storm-Mathisen J, Gundersen V
Nature protocols 2008;3(1):144-52

Cryosectioning and immunolabeling.
Slot JW, Geuze HJ
Nature protocols 2007;2(10):2480-91

A protocol for isolating Xenopus oocyte nuclear envelope for visualization and characterization by scanning electron microscopy (SEM) or transmission electron microscopy (TEM).
Allen TD, Rutherford SA, Murray S, Sanderson HS, Gardiner F, Kiseleva E, Goldberg MW, Drummond SP
Nature protocols 2007;2(5):1166-72

Visualization of the nucleus and nuclear envelope in situ by SEM in tissue culture cells.
Allen TD, Rutherford SA, Murray S, Gardiner F, Kiseleva E, Goldberg MW, Drummond SP
Nature protocols 2007;2(5):1180-4

ISH-IEM: a sensitive method to detect endogenous mRNAs at the ultrastructural level.
Herpers B, Xanthakis D, Rabouille C
Nature protocols 2010;5(4):678-87

Immunofluorescence microscopy and immunogold EM for investigating fungal infection of plants.
Thornton CR, Talbot NJ
Nature protocols 2006;1(5):2506-11

High-contrast en bloc staining of neuronal tissue for field emission scanning electron microscopy.
Tapia JC, Kasthuri N, Hayworth KJ, Schalek R, Lichtman JW, Smith SJ, Buchanan J
Nature protocols 2012 Jan 12;7(2):193-206

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Protocols for antibody independent applications of electron microscopy

Processing tissue and cells for transmission electron microscopy in diagnostic pathology and research.
Graham L, Orenstein JM
Nature protocols 2007;2(10):2439-50

Preparation of cells for assessing ultrastructural localization of nanoparticles with transmission electron microscopy.
Schrand AM, Schlager JJ, Dai L, Hussain SM
Nature protocols 2010;5(4):744-57

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Histological/cytological technique protocols

Immunocytochemistry and quantification of protein colocalization in cultured neurons.
Glynn MW, McAllister AK
Nature protocols 2006;1(3):1287-96

A protocol for preparing GFP-labeled neurons previously imaged in vivo and in slice preparations for light and electron microscopic analysis.
Knott GW, Holtmaat A, Trachtenberg JT, Svoboda K, Welker E
Nature protocols 2009;4(8):1145-56

The morphological and molecular features of the epithelial-to-mesenchymal transition.
Moreno-Bueno G, Peinado H, Molina P, Olmeda D, Cubillo E, Santos V, Palacios J, Portillo F, Cano A
Nature protocols 2009;4(11):1591-613

Combining patch-clamping of cells in brain slices with immunocytochemical labeling to define cell type and developmental stage.
Káradóttir R, Attwell D
Nature protocols 2006;1(4):1977-86

Immunofluorescence in brain sections: simultaneous detection of presynaptic and postsynaptic proteins in identified neurons.
Schneider Gasser EM, Straub CJ, Panzanelli P, Weinmann O, Sassoè-Pognetto M, Fritschy JM
Nature protocols 2006;1(4):1887-97

Adult mouse hematopoietic stem cells: purification and single-cell assays.
Ema H, Morita Y, Yamazaki S, Matsubara A, Seita J, Tadokoro Y, Kondo H, Takano H, Nakauchi H
Nature protocols 2006;1(6):2979-87

A light microscope-based double retrograde tracer strategy to chart central neuronal connections.
Ruigrok TJ, Apps R
Nature protocols 2007;2(8):1869-78

Staining protocol for organotypic hippocampal slice cultures.
Gogolla N, Galimberti I, DePaola V, Caroni P
Nature protocols 2006;1(5):2452-6

Fluorescent microsphere technique to measure cerebral blood flow in the rat.
De Visscher G, Haseldonckx M, Flameng W
Nature protocols 2006;1(4):2162-70

Immunohistochemical staining of post-mortem adult human brain sections.
Waldvogel HJ, Curtis MA, Baer K, Rees MI, Faull RL
Nature protocols 2006;1(6):2719-32

Bioconjugated quantum dots for multiplexed and quantitative immunohistochemistry.
Xing Y, Chaudry Q, Shen C, Kong KY, Zhau HE, Chung LW, Petros JA, O'Regan RM, Yezhelyev MV, Simons JW, Wang MD, Nie S
Nature protocols 2007;2(5):1152-65

Whole-mount three-dimensional imaging of internally localized immunostained cells within mouse embryos.
Yokomizo T, Yamada-Inagawa T, Yzaguirre AD, Chen MJ, Speck NA, Dzierzak E
Nature protocols 2012 Feb 9;7(3):421-31

Dendritic spines observed by extracellular DiI dye and immunolabeling under confocal microscopy
Rasia-Filho A
Protocol Exchange 2010

Optimized immunofluorescence staining protocol to detect the nucleoporin Nup98 in different subcellular compartments
Kodiha M, Umar R, Stochaj U
Protocol Exchange 2009 January

Double-label immunofluorescent staining of CD38 and oxytocin in the mouse hypothalamus
Noda M, A. Kido M, Fujita K, Seike T, Tanaka T, Higashida H
Protocol Exchange 2007 March

Immunofluorescent staining for the laser microdissection of individual cells.
Anthony R, Gause W
Protocol Exchange 2006 August

Indirect immunofluorescence with preextraction (in situ cell fractionation)
Di Micco R, d'Adda di Fagagna F
Protocol Exchange 2006 December

Immunostaining of DDR proteins in senescent cells
Di Micco R, Fumagalli M, d'Adda di Fagagna F
Protocol Exchange 2006 December

Immunohistochemistry protocol for γH2AX detection (formalin-fixed paraffin-embedded sections)
Luise C, Nuciforo P
Protocol Exchange 2006 December

Immunohistochemistry analysis
Mandelboim O
Protocol Exchange 2006 August

Immunohistochemistry and in situ hybridization protocols
Hunsberger J, Newton S
Protocol Exchange 2007 December

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Histological/ cytological technique protocols for non-mammalian systems

Immunocytochemical technique for protein localization in sections of plant tissues.
Paciorek T, Sauer M, Balla J, Wisniewska J, Friml J
Nature protocols 2006;1(1):104-7

Immunocytochemical techniques for whole-mount in situ protein localization in plants.
Sauer M, Paciorek T, Benková E, Friml J
Nature protocols 2006;1(1):98-103

A protocol for dissecting Drosophila melanogaster brains for live imaging or immunostaining.
Wu JS, Luo L
Nature protocols 2006;1(4):2110-5

Immunofluorescent staining and imaging of the pupal and adult Drosophila visual system.
Walther RF, Pichaud F
Nature protocols 2006;1(6):2635-42

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Protein array protocols

Reverse-phase protein lysate microarrays for cell signaling analysis.
Spurrier B, Ramalingam S, Nishizuka S
Nature protocols 2008;3(11):1796-808

The 'reverse capture' autoantibody microarray: a native antigen-based platform for autoantibody profiling.
Ehrlich JR, Qin S, Liu BC
Nature protocols 2006;1(1):452-60

An antigen microarray immunoassay for multiplex screening of mouse monoclonal antibodies.
Di Cristina M, Nunziangeli L, Giubilei MA, Capuccini B, d'Episcopo L, Mazzoleni G, Baldracchini F, Spaccapelo R, Crisanti A
Nature protocols 2010 Dec;5(12):1932-44

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors.
Berger MF, Bulyk ML
Nature protocols 2009;4(3):393-411

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EMSA/ antibody supershift protocols

Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions.
Hellman LM, Fried MG
Nature protocols 2007;2(8):1849-61

Alpha 4, the major regulatory protein of herpes simplex virus type 1, is stably and specifically associated with promoter-regulatory domains of alpha genes and of selected other viral genes.
Kristie TM, Roizman B
Proceedings of the National Academy of Sciences of the United States of America 1986 May;83(10):3218-22

Two-dimensional gel electrophoresis for identifying proteins that bind DNA or RNA.
Stead JA, McDowall KJ
Nature protocols 2007;2(8):1839-48

Southwestern blotting in investigating transcriptional regulation.
Siu FK, Lee LT, Chow BK
Nature protocols 2008;3(1):51-8

The electrophoretic mobility shift assay (EMSA)
Lackey E, Chen Z
Protocol Exchange 2009 January

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General protocols

Schägger H
Nature protocols 2006;1(1):16-22

Blue native PAGE.
Wittig I, Braun HP, Schägger H
Nature protocols 2006;1(1):418-28

State-of-the-art two-dimensional gel electrophoresis: a key tool of proteomics research.
Carrette O, Burkhard PR, Sanchez JC, Hochstrasser DF
Nature protocols 2006;1(2):812-23

Two-dimensional fluorescence difference gel electrophoresis for comparative proteomics profiling.
Tannu NS, Hemby SE
Nature protocols 2006;1(4):1732-42

Application of highly sensitive fluorescent dyes (CyDye DIGE Fluor saturation dyes) to laser microdissection and two-dimensional difference gel electrophoresis (2D-DIGE) for cancer proteomics.
Kondo T, Hirohashi S
Nature protocols 2006;1(6):2940-56

Highly selective enrichment of phosphorylated peptides using titanium dioxide.
Thingholm TE, Jørgensen TJ, Jensen ON, Larsen MR
Nature protocols 2006;1(4):1929-35

Recombinant protein purification by self-cleaving aggregation tag.
Wu WY, Mee C, Califano F, Banki R, Wood DW
Nature protocols 2006;1(5):2257-62

Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomics.
Cox B, Emili A
Nature protocols 2006;1(4):1872-8

In-gel stable isotope labeling for relative quantification using mass spectrometry.
Asara JM, Zhang X, Zheng B, Maroney LA, Christofk HR, Wu N, Cantley LC
Nature protocols 2006;1(1):46-51

Labeling of immune cells for in vivo imaging using magnetofluorescent nanoparticles.
Pittet MJ, Swirski FK, Reynolds F, Josephson L, Weissleder R
Nature protocols 2006;1(1):73-9

Rapid generation of fully human monoclonal antibodies specific to a vaccinating antigen.
Smith K, Garman L, Wrammert J, Zheng NY, Capra JD, Ahmed R, Wilson PC
Nature protocols 2009;4(3):372-84

Labeling of biotin antibodies with horseradish peroxidase using cyanuric chloride.
Abuknesha RA, Jeganathan F, Wu J, Baalawy Z
Nature protocols 2009;4(4):452-60

Directional conjugation of antibodies to nanoparticles for synthesis of multiplexed optical contrast agents with both delivery and targeting moieties.
Kumar S, Aaron J, Sokolov K
Nature protocols 2008;3(2):314-20

Selection of human antibody fragments by phage display.
Lee CM, Iorno N, Sierro F, Christ D
Nature protocols 2007;2(11):3001-8

Subtractive single-chain antibody (scFv) phage-display: tailoring phage-display for high specificity against function-specific conformations of cell membrane molecules.
Eisenhardt SU, Schwarz M, Bassler N, Peter K
Nature protocols 2007;2(12):3063-73

Selection of antibodies against a single rare cell present in a heterogeneous population using phage display.
Sørensen MD, Kristensen P
Nature protocols 2011 Apr;6(4):509-22

E-clonal antibodies: selection of full-length IgG antibodies using bacterial periplasmic display.
Mazor Y, Van Blarcom T, Iverson BL, Georgiou G
Nature protocols 2008;3(11):1766-77

Isolating and engineering human antibodies using yeast surface display.
Chao G, Lau WL, Hackel BJ, Sazinsky SL, Lippow SM, Wittrup KD
Nature protocols 2006;1(2):755-68

Production of a site- and phosphorylation state-specific antibody.
Goto H, Inagaki M
Nature protocols 2007;2(10):2574-81

Tunable pharmacokinetics: modifying the in vivo half-life of antibodies by directed mutagenesis of the Fc fragment.
Olafsen T, Kenanova VE, Wu AM
Nature protocols 2006;1(4):2048-60

Protocol for the selection of single-domain antibody fragments by third generation intracellular antibody capture.
Tanaka T, Rabbitts TH
Nature protocols 2010;5(1):67-92

Generation of acetyllysine antibodies and affinity enrichment of acetylated peptides.
Guan KL, Yu W, Lin Y, Xiong Y, Zhao S
Nature protocols 2010 Sep;5(9):1583-95

Screening individual hybridomas by microengraving to discover monoclonal antibodies.
Ogunniyi AO, Story CM, Papa E, Guillen E, Love JC
Nature protocols 2009;4(5):767-82

Development of DNA aptamers using Cell-SELEX.
Sefah K, Shangguan D, Xiong X, O'Donoghue MB, Tan W
Nature protocols 2010;5(6):1169-85

Fluorescence-activated cell sorting for aptamer SELEX with cell mixtures.
Mayer G, Ahmed MS, Dolf A, Endl E, Knolle PA, Famulok M
Nature protocols 2010 Dec;5(12):1993-2004

Mouse corneal lymphangiogenesis model.
Cao R, Lim S, Ji H, Zhang Y, Yang Y, Honek J, Hedlund EM, Cao Y
Nature protocols 2011 Jun;6(6):817-26

Ex vivo T cell-based HIV suppression assay to evaluate HIV-specific CD8+ T-cell responses.
Sáez-Cirión A, Shin SY, Versmisse P, Barré-Sinoussi F, Pancino G
Nature protocols 2010;5(6):1033-41

Coupling surface plasmon resonance to mass spectrometry to discover novel protein-protein interactions.
Madeira A, Ohman E, Nilsson A, Sjögren B, Andrén PE, Svenningsson P
Nature protocols 2009;4(7):1023-37

Extraction, purification and analysis of histones.
Shechter D, Dormann HL, Allis CD, Hake SB
Nature protocols 2007;2(6):1445-57

Locating proteins in the cell using TargetP, SignalP and related tools.
Emanuelsson O, Brunak S, von Heijne G, Nielsen H
Nature protocols 2007;2(4):953-71

GFP-based optimization scheme for the overexpression and purification of eukaryotic membrane proteins in Saccharomyces cerevisiae.
Drew D, Newstead S, Sonoda Y, Kim H, von Heijne G, Iwata S
Nature protocols 2008;3(5):784-98

Site-specific protein labeling by Sfp phosphopantetheinyl transferase.
Yin J, Lin