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Chromatin Immunoprecipitation (ChIP) Antibodies

Introduction

The chromatin immunoprecipitation (ChIP) assay is a major tool used to study epigenetic processes and regulatory proteins associated with DNA. Protein-DNA complexes are captured by primary antibodies, and then amplified for known gene or promoter regions. Aviva Systems Biology (ASB) provides a variety of ChIP tested primary antibodies with detailed experimental data and protocols.

Why ChIP?

ChIP can allow elucidating gene function and helping us understand how transcription factors modulate gene expression.

Application of ChIP

  • Selective enrichment of chromatin fraction(s) containing protein(s) that regulates gene expression using antibodies.
  • Antibodies recognizing the protein bound to the chromatin can be used to determine the relative abundance of that protein at one or more locations in the genome in vivo.
  • ChIP assays can also be used to analyze binding of transcription factors, transcription co-factors, DNA replication factors and DNA repair proteins.

Validation of Aviva ChIP antibodies

For validating many antibodies in ChIP, Aviva utilized a microplate-based ChIP (Matrix-ChIP) method where all steps from immunoprecipitation to DNA purification are done in microplate wells without sample transfers. Matrix-ChIP methods are similar to convention ChIP assays, as described in the protocol section, yet it provides much more information due to its high-throughput capabilities. In many cases, antibody validation data contains:

  • Analysis at multiple time points.
  • Comparisons to known transcriptional proteins.
  • Utilization of blocking peptides to confirm specificity.
  • Conducted in duplicate to demonstrate consistency. Click here for Protocol.

References

1. Sukhatme, V. P. et al. A zinc finger-encoding gene coregulated with c-fos during growth and differentiation, and after cellular depolarization. Cell 53, 37–43 (1988). 3127059
2. Svaren, J. et al. EGR1 target genes in prostate carcinoma cells identified by microarray analysis. J. Biol. Chem. 275, 38524–31 (2000). 10984481
3. Koldamova, R. et al. Genome-wide approaches reveal EGR1-controlled regulatory networks associated with neurodegeneration. Neurobiol. Dis. 63, 107–14 (2014). 24269917
4. Gokey, N. G., Lopez-Anido, C., Gillian-Daniel, A. L. & Svaren, J. Early growth response 1 (Egr1) regulates cholesterol biosynthetic gene expression. J. Biol. Chem. 286, 29501–10 (2011). 21712389
5. Arora, S. et al. Egr1 regulates the coordinated expression of numerous EGF receptor target genes as identified by ChIP-on-chip. Genome Biol. 9, R166 (2008). 19032775
6. Flanagin, S., Nelson, J. D., Castner, D. G., Denisenko, O. & Bomsztyk, K. Microplate-based chromatin immunoprecipitation method, Matrix ChIP: a platform to study signaling of complex genomic events. Nucleic Acids Res. 36, e17 (2008). 18203739
7. Yu, J. et al. Microplate-based platform for combined chromatin and DNA methylation immunoprecipitation assays. BMC Mol. Biol. 12, 49 (2011). 22098709

Featured Products

All ChIP Validated Antibodies

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Gene Sku Species Reactivity Application Size Price
ACTL6AOACA02417HumanELISA, WB, IHC, ChIP100 ul$315
AgO2OACA02418HumanELISA, WB, IHC, ChIP100 ug$315
AKT1OACA02419HumanELISA, WB, IHC, ChIP100 ug$315
APEX1OACA02420HumanELISA, WB, IHC, ChIP100 ug$315
BAZ2AOADC00244HumanCHIP, WB100 ul$298
BRD4ARP39076_P050Human, Mouse, RatCHIP, IF, WB100 ul$289
CBFBOADC00013HumanCHIP, ELISA100 ul$298
CBX1OADC00153HumanCHIP, WB, IF50 ug$298
CDC73OADC00018CHIP, IP, CHIP100 ul$298
CDC73OADC00019HumanCHIP, IF, CHIP50 ug$298
CDH1OACA02431HumanELISA, IHC, ChIP100 ul$315
CIITAOADC00027HumanCHIP50 ug$298
CTCFOADC00029HumanCHIP, ELISA, WB50 ug$298
CTCFARP38820_P050Human, Mouse, RatCHIP, WB100 ul$289
CTCFP100757_P050Human, Mouse, RatCHIP, WB100 ul$289
EHMT2ARP32493_P050Human, Mouse, RatWB, CHIP100 ul$289
ESR1OADC00046HumanCHIP, WB, SDS-PAGE, IC, IP, CHIP100 ul$298
ESR1OADC00047HumanCHIP, WB, IC50 ug$298
ESR1OACA02432HumanELISA, IHC, ChIP100 ug$315
EZH1ARP34235_P050Human, Mouse, RatWB, CHIP100 ul$289
EZH2OADC00049HumanCHIP50 ug$298
EZH2OADC00051HumanCHIP, WB, IC50 ug$298
FBXO11ARP43327_P050Human, Mouse, RatWB, CHIP100 ul$289
FOXP1OACA02421HumanELISA, WB, IHC, ChIP100 ug$315
H3K27 (me1)OAAH00063WB, IF, DB, CHIP100 ul$220
H3K36 (me1)OAAH00060WB, IF, DB, CHIP100 ul$220
H3K36 (me2)OAAH00061WB, IF, DB, CHIP100 ul$220
H3K36 (me3)OAAH00062WB, IF, DB, CHIP100 ul$220
H3K4 (me1)OAAH00066WB, IF, DB, CHIP100 ul$220
H3K4 (me2)OAAH00067WB, IF, DB, CHIP100 ul$220
H3K4 (me3)OAAH00068WB, DB, CHIP100 ul$220
H3K79 (me2)OAAH00059WB, IF, DB, CHIP100 ul$220
H3K9 (me3)OAAH00065IF, DB, CHIP100 ul$220
H4K20 (me1)OAAH00057WB, IF, DB, CHIP100 ul$220
H4K20 (me2)OAAH00058WB, IF, DB, CHIP100 ul$220
HDAC1OADC00263HumanCHIP, WB100 ul$415
HDAC1OADC00144HumanCHIP, ELISA, WB, Array, IF50 ug$380
HDAC1OADC00268HumanCHIP, WB, IF50 ug$415
HDAC1OACA02422HumanELISA, WB, IHC, ChIP100 ug$315
HDAC2OADC00146HumanCHIP, WB, IF50 ug$298
HDAC2ARP31931_P050Human, Mouse, RatCHIP, IHC, WB100 ul$289
HDAC2ARP32619_P050Human, Mouse, RatCHIP, WB100 ul$289
HDAC2ARP32619_P050Human, Mouse, RatCHIP, WB100 ul$289
HDAC3OADC00264HumanCHIP100 ul$415
HDAC3OADC00269HumanCHIP, IF50 ug$415
HDAC3OACA02423HumanELISA, WB, IHC, ChIP100 ug$315
Hdac4ARP43602_P050Human, Mouse, RatCHIP, WB100 ul$289
HDAC6ARP31451_P050Human, Mouse, RatCHIP, WB100 ul$289
Hdac6ARP38730_P050Human, Mouse, RatCHIP, WB100 ul$289
HDAC9ARP42788_T100Human, MouseCHIP, IHC, WB100 ul$229
HIST1H1CARP46122_P050Human, Mouse, RatCHIP, WB100 ul$289
HIST1H2AGOACA02424HumanELISA, WB, IHC, ChIP100 ug$315
HIST2H2BFARP56220_P050Human, Mouse, RatCHIP, WB100 ul$289
His-TagOADC00148CHIP, CHIP, IS, IP50 ug$298
Histone H2AOADC00068HumanCHIP, ELISA, DB50 ug$298
Histone H2A (Acetyl-Lys12)OADC00069HumanCHIP, ELISA, DB, WB50 ug$298
Histone H2A (Acetyl-Lys5)OADC00066HumanCHIP, ELISA, DB, WB50 ug$298
Histone H2A (Acetyl-Lys5/7/11)OADC00064HumanCHIP, ELISA, DB, IF50 ug$298
Histone H2A (Acetyl-Lys5/7/11)OADC00260HumanCHIP, ELISA, WB, IF50 ug$415
Histone H2A (Acetyl-Lys5/7/11)OADC00261HumanCHIP, ELISA, DB, WB, IF50 ug$415
Histone H2A (Pan)OADC00062HumanCHIP, ELISA, WB50 ug$298
Histone H2B (Acetyl-Lys15)OADC00070HumanCHIP, ELISA, DB, WB50 ug$298
Histone H3OADC00128HumanCHIP, WB, IF50 ug$298
Histone H3OADC00106HumanCHIP, ELISA, WB, IF50 ug$298
Histone H3 (Acetyle-Lys4)OADC00094HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H3 (Acetyl-Lys18)OADC00076HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H3 (Acetyl-Lys27)OADC00079HumanCHIP, ELISA, WB, IF50 ug$298
Histone H3 (Acetyl-Lys27)OADC00080HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H3 (Acetyl-Lys27)OADC00258HumanCHIP, ELISA, DB, WB, IF50 ug$415
Histone H3 (Acetyl-Lys56)OADC00107HumanCHIP, ELISA, DB50 ug$298
Histone H3 (Acetyl-Lys9)OADC00116HumanCHIP, ELISA, WB, IF50 ug$198
Histone H3 (Acetyl-Lys9)OADC00117HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H3 (Acetyl-Lys9/Phospho-Ser10)OADC00119HumanCHIP, ELISA, DB, WB, IF100 ul$298
Histone H3 (Acetyl-Lys9-14)OADC00115HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H3 (Acetyl-Lys9-14)OADC00259HumanCHIP, WB, IF, CHIP, ELISA50 ug$415
Histone H3 (Asym Di-Methyl-Arg17/Acetyl-Lys18)OADC00130HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H3 (Di/Tri-Methyl-Lys27)OADC00083HumanCHIP, DB, WB, IF50 ug$298
Histone H3 (Di-Methyl-Arg17)OADC00129HumanCHIP, ELISA, DB, WB100 ul$298
Histone H3 (Di-Methyl-Lys27)OADC00082HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H3 (Di-Methyl-Lys36)OADC00090HumanCHIP, ELISA, DB, WB, IF100 ul$298
Histone H3 (Di-Methyl-Lys36)OADC00089HumanCHIP, ELISA, DB, WB50 ug$298
Histone H3 (Di-Methyl-Lys4)OADC00099HumanCHIP, ELISA, DB, WB100 ul$298
Histone H3 (Di-Methyl-Lys4)OADC00098HumanCHIP, ELISA, WB, IF50 ug$298
Histone H3 (Di-Methyl-Lys4)OADC00100HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H3 (Di-Methyl-Lys79)OADC00111HumanCHIP, ELISA, DB, WB100 ul$298
Histone H3 (Di-Methyl-Lys79)OADC00112HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H3 (Di-Methyl-Lys9)OADC00122HumanCHIP, ELISA, WB, IF50 ug$298
Histone H3 (Di-Methyl-Lys9)OADC00123HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H3 (Methyl-Lys27)OADC00081HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H3 (Methyl-Lys36)OADC00088HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H3 (Methyl-Lys4)OADC00096HumanCHIP, ELISA, DB, WB100 ul$298
Histone H3 (Methyl-Lys4)OADC00095HumanCHIP, ELISA, WB, IF50 ug$298
Histone H3 (Methyl-Lys4)OADC00097HumanCHIP, ELISA, DB, WB50 ug$298
Histone H3 (Methyl-Lys4)OADC00256HumanCHIP, ELISA, DB, WB, IF50 ug$415
Histone H3 (Methyl-Lys64)OADC00108HumanCHIP, ELISA, DB, WB50 ug$298
Histone H3 (Methyl-Lys79)OADC00109HumanCHIP, ELISA, DB, WB100 ul$298
Histone H3 (Methyl-Lys79)OADC00110HumanCHIP, ELISA, DB, WB50 ug$298
Histone H3 (Methyl-Lys9)OADC00120HumanCHIP, ELISA, DB, WB, IF100 ul$298
Histone H3 (Methyl-Lys9)OADC00121HumanCHIP, ELISA, DB, WB50 ug$298
Histone H3 (Pan)OADC00073HumanCHIP, ELISA, DB, WB100 ul$298
Histone H3 (Pan)OADC00072HumanCHIP, WB50 ug$298
Histone H3 (Phospho-Ser10)OADC00131HumanCHIP, ELISA, DB, WB, IF, IP100 ul$298
Histone H3 (Phospho-Ser10)OADC00132HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H3 (Tri-Methyl-Lys27)OADC00084HumanCHIP, ELISA, WB, IF50 ug$298
Histone H3 (Tri-Methyl-Lys27)OADC00085HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H3 (Tri-Methyl-Lys27)OADC00257HumanCHIP, ELISA, DB, WB, IF50 ug$415
Histone H3 (Tri-Methyl-Lys27/Phospho-Ser28)OADC00087HumanCHIP, ELISA, DB, WB, IF, IP100 ul$298
Histone H3 (Tri-Methyl-Lys27/Phospho-Ser28)OADC00086HumanCHIP, ELISA, DB, WB50 ug$298
Histone H3 (Tri-Methyl-Lys36)OADC00092HumanCHIP, ELISA, DB, WB100 ul$298
Histone H3 (Tri-Methyl-Lys36)OADC00091HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H3 (Tri-Methyl-Lys36)OADC00093HumanCHIP, ELISA, DB, WB50 ug$298
Histone H3 (Tri-Methyl-Lys36)OADC00254HumanCHIP, ELISA, DB, WB, IF50 ug$415
Histone H3 (Tri-Methyl-Lys4)OADC00102HumanCHIP, ELISA, DB, WB100 ul$298
Histone H3 (Tri-Methyl-Lys4)OADC00101HumanCHIP, ELISA, WB, IF50 ug$298
Histone H3 (Tri-Methyl-Lys4)OADC00277HumanCHIP, ELISA, DB, WB50 ug$415
Histone H3 (Tri-Methyl-Lys79)OADC00114HumanCHIP, ELISA, DB, WB50 ug$298
Histone H3 (Tri-Methyl-Lys9)OADC00265HumanCHIP, DB, WB100 ul$415
Histone H3 (Tri-Methyl-Lys9)OADC00125HumanCHIP, ELISA, DB, WB, IF100 ul$298
Histone H3 (Tri-Methyl-Lys9)OADC00124HumanCHIP, CHIP100 ul$298
Histone H3 (Tri-Methyl-Lys9)OADC00126HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H3 (Tri-Methyl-Lys9)OADC00270HumanCHIP, DB, WB50 ug$415
Histone H3 (Tri-Methyl-Lys9)OADC00272HumanCHIP, ELISA, WB, IF50 ug$415
Histone H3 (Tri-Methyl-Lys9)OADC00255HumanCHIP, ELISA, DB, WB, IF50 ug$415
Histone H3 (Tri-Methyl-Lys9)OADC00278HumanCHIP, IF50 ug$415
Histone H3 (Tri-Methyl-Lys9/Phospho-Ser10)OADC00127HumanCHIP, ELISA, DB, WB, IF100 ul$298
Histone H4OADC00133HumanCHIP, ELISA, DB50 ug$298
Histone H4 (Acetyl-Lys12)OADC00139HumanCHIP, ELISA, WB, IF50 ug$298
Histone H4 (Acetyl-Lys5/8/12/16)OADC00140HumanCHIP, ELISA, DB, WB50 ug$298
Histone H4 (Acetyl-Lys5/8/12/16)OADC00138HumanCHIP, ELISA, DB, IF50 ug$298
Histone H4 (Acetyl-Lys8)OADC00141HumanCHIP, ELISA, DB, WB100 ul$298
Histone H4 (Acetyl-Lys8)OADC00142HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H4 (Methyl-Lys20)OADC00266HumanCHIP, DB, WB100 ul$415
Histone H4 (Methyl-Lys20)OADC00135HumanCHIP, ELISA, DB, WB100 ul$298
Histone H4 (Methyl-Lys20)OADC00134HumanCHIP, ELISA, DB, WB50 ug$298
Histone H4 (Methyl-Lys20)OADC00271HumanCHIP, DB, WB, IF50 ug$415
Histone H4 (Tri-Methyl-Lys20)OADC00267HumanCHIP, WB, IF100 ul$415
Histone H4 (Tri-Methyl-Lys20)OADC00136HumanCHIP, ELISA, DB, WB100 ul$298
Histone H4 (Tri-Methyl-Lys20)OADC00137HumanCHIP, ELISA, DB, WB, IF50 ug$298
Histone H4 (Tri-Methyl-Lys20)OADC00262HumanCHIP, ELISA, DB, WB, IF50 ug$415
JUNP100911_P050Human, Mouse, RatCHIP, WB100 ul$289
KDM1AOADC00167HumanCHIP, ELISA, WB, IF50 ug$298
KDM1AOADC00168HumanCHIP, CHIP50 ug$298
KDM8ARP58120_P050Human, Mouse, RatCHIP, WB100 ul$289
KLF2ARP32760_P050Human, Mouse, RatIHC, WB100 ul$289
MBD1OADC00173HumanCHIP, ELISA, WB50 ug$298
MBD4ARP34797_P050HumanWB, CHIP100 ul$289
MCM3OACA02425HumanELISA, WB, IHC, ChIP100 ul$315
MECP2OADC00178HumanCHIP, ELISA, WB50 ug$298
MED14ARP58139_P050Human, MouseWB, CHIP100 ul$289
MED17ARP34192_P050Human, Mouse, RatIHC, WB, CHIP100 ul$289
MED19ARP55596_P050Human, Mouse, RatWB, CHIP100 ul$289
Med21ARP35728_P050Human, Mouse, RatWB, CHIP100 ul$289
MED25ARP50698_P050Human, Mouse, RatWB, CHIP100 ul$289
MED25ARP50699_P050Human, Mouse, RatWB, CHIP100 ul$289
MED25ARP50699_P050Human, Mouse, RatWB, CHIP100 ul$289
MED31ARP56820_P050Human, Mouse, RatWB, CHIP100 ul$289
MED6ARP34219_P050Human, Mouse, RatWB,CHIP100 ul$289
MED6ARP34220_P050Human, Mouse, RatWB, CHIP100 ul$289
MED7ARP38446_P050Human, Mouse, RatWB, CHIP100 ul$289
NELFBOACA02426HumanELISA, WB, IHC, ChIP100 ug$315
NFKB1OACA02427HumanELISA, WB, IHC, ChIP100 ug$315
NR3C1OADC00056HumanCHIP, ELISA, WB, SDS-PAGE, IC, Flow, IP50 ug$298
p53OADC00188HumanCHIP, ELISA, WB50 ug$298
p53 (Methyl-Lys372)OADC00189HumanCHIP, CHIP50 ug$298
PAF1OADC00193HumanCHIP, CHIP50 ug$298
POLR2AOADC00206HumanCHIP, ELISA, WB, IF50 ug$298
POLR2AOADC00207HumanCHIP, ELISA, WB, IF50 ug$298
POLR2AOADC00205HumanCHIP, ELISA, WB, IF50 ug$298
POLR3AOACA02433HumanELISA, IHC, ChIP100 ug$315
PPARGOADC00208HumanCHIP, ELISA, WB50 ug$298
PRKCGARP56425_P050Human, Mouse, RatWB, CHIP100 ul$289
PRMT2ARP40195_P050Human, RatWB, CHIP100 ul$289
PRMT3ARP40183_P050Human, Mouse, RatWB, CHIP100 ul$289
PRMT6ARP40190_P050Human, Mouse, RatWB, CHIP100 ul$289
RARAOADC00209HumanCHIP, ELISA, WB100 ul$298
RELAOACA02434HumanELISA, IHC, ChIP100 ug$315
RFXAPOADC00212HumanCHIP50 ug$298
RTF1OADC00215CHIP, IF, IP, CHIP100 ul$298
RTF1OADC00216CHIP, IF, IP, CHIP50 ug$298
RUNX1OADC00005HumanCHIP, ELISA, WB100 ul$298
RUNX1T1OADC00048HumanCHIP, ELISA100 ul$298
SAP30OADC00218HumanCHIP, WB50 ug$198
SKI3OADC00227HumanCHIP, IF, CHIP150 ug$298
SMARCA1ARP38215_P050Human, Mouse, RatCHIP, WB100 ul$289
SMARCA1ARP38215_P050Human, Mouse, RatCHIP, WB100 ul$289
SMARCA1ARP37435_T100Mouse, RatCHIP, WB100 ul$229
SMARCA5ARP30031_P050Human, Mouse, RatCHIP, WB100 ul$289
SMARCC2OACA02428HumanELISA, WB, IHC, ChIP100 ul$315
SMYD2ARP50639_P050Human, Mouse, RatWB, CHIP100 ul$289
SMYD3ARP50666_P050Human, Mouse, RatWB, CHIP100 ul$289
SNF2L2OACA02435HumanELISA, IHC, ChIP100 ug$315
SRFP100866_T100Human, Mouse, RatCHIP, WB100 ul$229
STAT5BOACA02429HumanELISA, WB, IHC, ChIP100 ul$315
Suv420h1ARP51247_P050Human, Mouse, RatCHIP, WB100 ul$289
Suv420h1ARP51247_P050Human, Mouse, RatCHIP, WB100 ul$289
SUZ12OADC00238HumanCHIP, CHIP100 ul$298
SUZ12OADC00239HumanCHIP, WB50 ug$298
SUZ12ARP32515_P050Human, Mouse, RatCHIP, IHC, WB100 ul$289
TAF1ARP32472_P050Human, Mouse, RatWB, CHIP100 ul$289
TAF1ARP32473_P050Human, Mouse, RatIHC, WB, CHIP100 ul$289
TAF12P100965_P050Human, Mouse, RatWB, CHIP100 ul$289
TAF2ARP33392_P050Human, Mouse, RatWB, CHIP100 ul$289
TAF4ARP33394_P050Human, MouseWB, CHIP100 ul$289
TAF6ARP38653_P050Human, Mouse, RatWB, CHIP100 ul$289
TAF9ARP34551_P050Human, Mouse, RatIHC, WB, CHIP100 ul$289
TBPOADC00242HumanCHIP100 ug$298
THOC1OACA02430HumanELISA, WB, IHC, ChIP100 ul$315
TY1OADC00245HumanCHIP, WB50 ug$298
WDR61OADC00228CHIP, CHIP150 ug$298

Experimental Methods

Why EGR1?

EGR1 is an important transcriptional regulator and has been described as a “master switch” linking extracellular stimuli to diverse long-term responses including cell growth, proliferation, apoptosis, inflammation, cardiac and pulmonary fibrosis and a variety of roles in the physiology of the central nervous system. In several types of human tumor cells, Egr1 displays tumor suppressor activity via the binding to and transactivation of major tumor suppressor factors, including TGFβ1, p53, p73, and PTEN.

Specificity

Chromatin immunoprecipitation (ChIP) is an invaluable method for studying interactions between specific proteins or modified forms of proteins and a genomic DNA region. One of the major requirements of ChIP is the need for antibodies that recognize the target protein with a high degree of specificity and that efficiently precipitate the protein even after crosslinking.

Antibodies of high quality are extremely important for a successful ChIP experiment. It is important to be aware that antibodies can cross-react with non-specific proteins in ChIP experiments. Therefore the ChIP validated antibodies have to be specific and has to recognize the target protein with no or very low background. Aviva Systems Biology wants to assist researchers in ChIP experiments and has validated many antibodies that are specific for ChIP. To demonstrate specificity, Aviva antibodies are tested in peptide inhibition assay using blocking peptides.

Consistency

In the final step of a ChIP experiment either PCR or real-time PCR is carried out to identify the DNA sequence bound to the protein. To demonstrate experimental consistency of the ChIP experiment the real-time PCR amplification, data acquisition and analysis were run in quadruplicate for each PCR reaction.

Histone Modification Proteins

Histone modifications not only play important roles in regulating chromatin structure and nuclear processes but also can be passed to daughter cells as epigenetic marks. Modifications on histones can directly influence chromatin structure. There are broadly four types of histone-modifying enzymes: Histone acetyltransferases (HATs); Histone deacytylases (HDACs); Histone methyltransferases (HMTs); and Histone demethylases (KDMs). There are many ways to modify histones; HATs add acetyl groups, whereas HDACs remove acetyl groups. HMTs add methyl groups, while KDMs remove methyl groups.

For instance, acetylation on lysine residues by Histone Acetyltransferases (HATs) can reduce the positive charge of histones; thereby weakening their interaction with negatively charged DNA as a result the condensed chromatin is transformed into a more relaxed structure that is associated with greater levels of gene transcription. This relaxation can be reversed by histone deacetylation activity by Histone Deacetylases (HDACs) where the DNA becomes more tightly wrapped around the histone cores, making it harder for transcription factors to bind to the DNA. This leads to decreased levels of gene expression known as gene silencing.

Methylation of histone tails on lysine and arginine residues by histone methyltransferase (HMT) and protein arginine methyltransferase (PRMT) can be associated with either transcriptional repression or activation. The status of methylation (single or multiple) can result in either loosening or encompassing the histone tails, thereby allowing or blocking transcription machinery access to the DNA.

Featured Products

ChIP Validated Antibodies

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Gene SKU Species Reactivity Application Quantity Price
H3K27 (me1) OAAH00063WB, IF, DB, CHIP100 ul$220
H3K36 (me1) OAAH00060WB, IF, DB, CHIP100 ul$220
H3K36 (me2) OAAH00061WB, IF, DB, CHIP100 ul$220
H3K36 (me3) OAAH00062WB, IF, DB, CHIP100 ul$220
H3K4 (me1) OAAH00066WB, IF, DB, CHIP100 ul$220
H3K4 (me2) OAAH00067WB, IF, DB, CHIP100 ul$220
H3K4 (me3) OAAH00068WB, DB, CHIP100 ul$220
H3K79 (me2) OAAH00059WB, IF, DB, CHIP100 ul$220
H3K9 (me3) OAAH00065IF, DB, CHIP100 ul$220
H4K20 (me1) OAAH00057WB, IF, DB, CHIP100 ul$220
H4K20 (me2) OAAH00058WB, IF, DB, CHIP100 ul$220
HIST1H1C ARP46122_P050Human, Mouse, RatCHIP, WB100 ul$289
HIST2H2BF ARP56220_P050Human, Mouse, RatCHIP, WB100 ul$289

Chromatin Modifiers

Chromatin Modifying Proteins

Chromatin associated/modifying proteins modify chromatin by adding certain small molecules such as acetyl and methyl group to lysine and/or arginine residues of histone. These changes regulate chromatin structure and influence gene transcription, and also influence the repair of damaged DNA and the replication of DNA molecules (Kouzarides et al, 2007).

1. Kouzarides, T. Chromatin modifications and their function. Cell 128, 693–705 (2007). PMID: 17320507

Other chromatin modifying proteins

The other chromatin modifying proteins that are recruited to the unraveled chromatin are the non-histone proteins. Thus, depending on the composition of modifications on a given histone, a set of proteins are encouraged to bind or are occluded from chromatin. These proteins carry with them enzymatic activities (e.g., remodeling ATPases) that further modify chromatin. Various processes such as transcription, DNA replication and repair require a distinct type of chromatin-remodeling activity and different set of proteins are recruited for those different mechanisms.

Featured Products

ChIP Validated Antibodies

Scroll Vertically and Horizontally to see entire view
Gene SKU Species Reactivity Application Quantity Price
BRD4 ARP39076_P050Human, Mouse, RatCHIP, IF, WB100 ul$289
EHMT2 ARP32493_P050Human, Mouse, RatWB, CHIP100 ul$289
EZH1 ARP34235_P050Human, Mouse, RatWB, CHIP100 ul$289
FBXO11 ARP43327_P050Human, Mouse, RatWB, CHIP100 ul$289
HDAC2 ARP31931_P050Human, Mouse, RatCHIP, IHC, WB100 ul$289
HDAC2 ARP32619_P050Human, Mouse, RatCHIP, WB100 ul$289
HDAC2 ARP32619_P050Human, Mouse, RatCHIP, WB100 ul$289
HDAC4 ARP43602_P050Human, Mouse, RatCHIP, WB100 ul$289
HDAC6 ARP31451_P050Human, Mouse, RatCHIP, WB100 ul$289
HDAC6 ARP38730_P050Human, Mouse, RatCHIP, WB100 ul$289
HDAC9 ARP42788_T100Human, MouseCHIP, IHC, WB100 ul$229
JMJD5 ARP58120_P050Human, Mouse, RatCHIP, WB100 ul$289
MBD4 ARP34797_P050HumanWB, CHIP100 ul$289
PRMT2 ARP40195_P050Human, RatWB, CHIP100 ul$289
PRMT3 ARP40183_P050Human, Mouse, RatWB, CHIP100 ul$289
PRMT6 ARP40190_P050Human, Mouse, RatWB, CHIP100 ul$289
SMARCA1 ARP37435_T100Mouse, RatCHIP, WB100 ul$229
SMARCA1 ARP38215_P050Human, Mouse, RatCHIP, WB100 ul$289
SMARCA1 ARP38215_P050Human, Mouse, RatCHIP, WB100 ul$289
SMARCA5 ARP30031_P050Human, Mouse, RatCHIP, WB100 ul$289
SMYD2 ARP50639_P050Human, Mouse, RatWB, CHIP100 ul$289
SMYD3 ARP50666_P050Human, Mouse, RatWB, CHIP100 ul$289
SUV420H1 ARP51247_P050Human, Mouse, RatCHIP, WB100 ul$289
Suv420h1 ARP51247_P050Human, Mouse, RatCHIP, WB100 ul$289
SUZ12 ARP32515_P050Human, Mouse, RatCHIP, IHC, WB100 ul$289

Transcription Factors

Proteins that bind to specific DNA sequences (enhancers or promoters) and control the synthesis of mRNA. These proteins contain one or more DNA-binding domains which attach to specific DNA sequences at or adjacent to the genes they regulate. Transcription factors can act at specific genes alone, or as apart of a complex, to recruit or block RNA polymerase from binding and driving transcription.

Mechanisms used by transcription factors to regulate gene expression include, 1) stabilize or block the binding of RNA polymerase to DNA, 2) either directly or indirectly catalyze the acetlyation or deacetylation of histone proteins, 3) recruit coactivator or corepressor proteins to the DNA complex.

Featured Products

ChIP Validated Antibodies

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Gene SKU Species Reactivity Application Quantity Price
CRSP6 ARP34192_P050Human, Mouse, RatIHC, WB, CHIP100 ul$289
CTCF ARP38820_P050Human, Mouse, RatCHIP, WB100 ul$289
CTCF P100757_P050Human, Mouse, RatCHIP, WB100 ul$289
HES1 ARP32372_T100HumanChIP100 ul$229
JUN P100911_P050Human, Mouse, RatCHIP, WB100 ul$289
KLF2 ARP32760_P050Human, Mouse, RatIHC, WB100 ul$289
MED14 ARP58139_P050Human, MouseWB, CHIP100 ul$289
MED19 ARP55596_P050Human, Mouse, RatWB, CHIP100 ul$289
MED21 ARP35728_P050Human, Mouse, RatWB, CHIP100 ul$289
MED25 ARP50698_P050Human, Mouse, RatWB, CHIP100 ul$289
MED25 ARP50699_P050Human, Mouse, RatWB, CHIP100 ul$289
MED31 ARP56820_P050Human, Mouse, RatWB, CHIP100 ul$289
MED6 ARP34219_P050Human, Mouse, RatWB,CHIP100 ul$289
MED6 ARP34220_P050Human, Mouse, RatWB, CHIP100 ul$289
MED7 ARP38446_P050Human, Mouse, RatWB, CHIP100 ul$289
MED7 ARP50699_P050Human, Mouse, RatWB, CHIP100 ul$289
P53 AMM00023HumanChIP100 ul$249
P53 AMM00024HumanChIP100 ul$249
P53 AMM00025HumanChIP100 ul$249
P53 ARP30307_P050HumanChIP100 ul$289
P53 ARP30311_P050HumanChIP100 ul$289
P53 ARP30312_P050HumanChIP100 ul$289
P53 ARP30370_P050HumanChIP100 ul$289
RBPSUH ARP31121_P050HumanChIP100 ul$289
SRF P100866_T100Human, Mouse, RatCHIP, WB100 ul$229
TAF1 ARP32472_P050Human, Mouse, RatWB, CHIP100 ul$289
TAF1 ARP32473_P050Human, Mouse, RatIHC, WB, CHIP100 ul$289
TAF12 P100965_P050Human, Mouse, RatWB, CHIP100 ul$289
TAF2 ARP33392_P050Human, Mouse, RatWB, CHIP100 ul$289
TAF4 ARP33394_P050Human, MouseWB, CHIP100 ul$289
TAF6 ARP38653_P050Human, Mouse, RatWB, CHIP100 ul$289
TAF9 ARP34551_P050Human, Mouse, RatIHC, WB, CHIP100 ul$289

Description of Protocol

Matrix-ChIP utilizes sheared chromatin. Capture antibodies are surface-immobilized via blocked, Protein A coated 96-well plates. Blocking buffer consists of 5% BSA and 100ug/mL sheared salmon sperm DNA in immunoprecipitation (IP) buffer. After washing, sheared chromatin samples are added and the plates are floated in an ultrasonic water bath (Bronson 8510) to accelerate protein-antibody binding. Wells are then washed and DNA eluted with Tris base (pH 9.8) and stored (4C) in the same Matrix ChIP plates for repeated use. Plates are sealed with adhesive film to prevent evaporation and can be stored/re-sealed for months for repeated qPCR.

Real-time PCR is performed with 2X SYBR Green PCR master mix, eluted DNA template and primers in a 2-4uL final volume in a 384-well Optical Reaction Plate. Amplification (three steps, 40 cycles), data acquisition and analysis were run in quadruplicate for each PCR reaction.

Microplate-based chromatin immunoprecipitation method, Matrix-ChIP: a platform to study signaling of complex genomic events.
Flanagin S, Nelson JD, Castner DG, Denisenko O, Bomsztyk K.
Nucleic Acids Res. 2008 Feb;36(3)

Microplate-based platform for combined chromatin and DNA methylation immunoprecipitation assays.
Yu J, Feng Q, Ruan Y, Komers R, Kiviat N, Bomsztyk K.
BMC Mol Biol. 2011 Nov 18;12:49.

Matrix-ChIP FAQ

What is microplate immunoprecipitation (Matrix-ChIP)?

The microplate-based ChIP (Matrix-ChIP) method is a method where all steps from immunoprecipitation to DNA purification are done in microplate wells without sample transfers. This platform has several advantages over the traditional tube-based assay including simplified sample handling, high throughput, improved sensitivity and reproducibility, and potential for automation.

Do Matrix-ChIP validated antibodies work in traditional ChIP?

Yes. Matrix-ChIP has been shown to be more sensitive and reproducible that traditional bead-based ChIP.

Can Matrix ChIP be used for MeDIP?

Yes, but the blocking buffer does not contain salmon sperm DNA (see Yu, et.al. BMC Mol Biol. 2011 Nov 18;12:49). 5-Methylcytosine (Methyl-CpG) mouse monoclonal antibody; clone#: 33D3 (AMM99021)

Can the Matrix platform be used for RNA immunoprecipitations (RIP)?

Yes, with minor modifications as described in Mikula JBC 286, 9763, 2011.

Do you have a list of Matrix-ChIP validated antibodies?

Histone/Histone Modification:
HIST1H1C (ARP46122_P050)
HIST2H2BF (ARP56220_P050)
H3K36(me1) (OAAH00060)
H3K36(me3) (OAAH00062)
H4K20(me2) (OAAH00058)
H3K4(me1) (OAAH00066)
H3K36(me2) (OAAH00061)
H4K20(me1) (OAAH00057)
H3K79(me2) (OAAH00059)
H3K27(me1) (OAAH00063)
H3K9(me3) (OAAH00065)
H3K4(me3) (OAAH00068)
H3K4(me2) (OAAH00067)

Chromatin Associated and/or Modifying Proteins:
BRD4 (ARP39076_P050)
SMARCA1 (ARP37435_T100)
SMARCA1 (ARP38215_P050)
SMARCA5 (ARP30031_P050)
HDAC2 (ARP32619_P050)
HDAC2 (ARP31931_P050)
HDAC4 (ARP43602_P050)
HDAC6 (ARP31451_P050)
HDAC6 (ARP38730_P050)
HDAC9 (ARP42788_T100)
JMJD5 (ARP58120_P050)
SUV420H1 (ARP51247_P050)
SUZ12 (ARP32515_P050)
Suv420h1 (ARP51247_P050)
HDAC2 (ARP32619_P050)
SMARCA1 (ARP38215_P050)
SMYD2 (ARP50639_P050)
SMYD3 (ARP50666_P050)
MBD4 (ARP34797_P050)
PRMT2 (ARP40195_P050)
PRMT3 (ARP40183_P050)
PRMT6 (ARP40190_P050)
FBXO11 (ARP43327_P050)
EZH1 (ARP34235_P050)
EHMT2 (ARP32493_P050)

Transcription Factors:
CTCF (ARP38820_P050)
CTCF (P100757_P050)
JUN (P100911_P050)
SRF (P100866_T100)
KLF2 (ARP32760_P050)
MED6 (ARP34219_P050)
MED6 (ARP34220_P050)
MED7 (ARP38446_P050)
MED7 (ARP50699_P050)
MED14 (ARP58139_P050)
MED19 (ARP55596_P050)
MED21 (ARP35728_P050)
MED25 (ARP50698_P050)
MED25 (ARP50699_P050)
MED31 (ARP56820_P050)
TAF1 (ARP32472_P050)
TAF1 (ARP32473_P050)
TAF2 (ARP33392_P050)
TAF4 (ARP33394_P050)
TAF6 (ARP38653_P050)
TAF9 (ARP34551_P050)
TAF12 (P100965_P050)
CRSP6 (ARP34192_P050)
P53 (AMM00024)
P53 (AMM00025)
P53 (AMM00023)
P53 (ARP30307_P050)
P53 (ARP30311_P050)
P53 (ARP30312_P050)
P53 (ARP30370_P050)
RBPSUH (ARP31121_P050)
HES1 (ARP32372_T100)

Other:
PRKCG (ARP56425_P050)
PAX6 (ARP32741_P050)