DNA Repair ChIP PCR Array
|DNA Repair ChIP PCR Array
|The Mouse DNA Repair EpiTect Chip qPCR Array profiles the histone modification status or “histone code” of 84
key genes encoding the enzymes that repair damaged DNA. Histone modifications regulate chromatin structure,
genome integrity, chromosome stabilization, DNA repair and transcriptional activity. Daily exposure to environmental
agents (such as reactive oxygen species, methylating agents, UV light and other ionizing radiation) and even normal
physiological processes (like replication and recombination) all damage DNA. Cells must repair DNA damage to
prevent mutations from accumulating and to maintain genome integrity and stability. Inherited and acquired defects
in DNA repair lead to accelerated aging and increased predisposition to cancer. Epigenetic dysregulation, also often
occurring in cancer, affects DNA repair by altering the expression levels of relevant genes. For example, the BRCA1
promoter carries the H3K4me3 histone mark consistent with its active transcription in normal breast tissues.
However, the BRCA1 promoter in breast cancers exhibits transcriptional repression, due to loss of H3K4me3 and
gain of H3K9me2 histone marks. This array represents genes involved in the base-excision, nucleotide excision,
mismatch, double-strand break, and other repair processes. Using chromatin immunoprecipitation and this real-time
PCR Array, you can easily and reliably analyze the histone modification patterns associated with a focused gene
panel involved in DNA Repair.
The EpiTect Chip qPCR Arrays are intended for molecular biology applications. This product is not
intended for the diagnosis, prevention, or treatment of a disease.
Base Excision Repair (BER): Apex1, Apex2, Ccnu (Ccno), Lig3, Mpg, Mutyh, Neil1, Neil2, Neil3, Nthl1, Ogg1, Parp1, Parp2, Parp3, Polb, Smug1, Tdg, Ung, Xrcc1.
Nucleotide Excision Repair (NER): Atxn3, Brip1, Ccnh, Cdk7, Ddb1, Ddb2, Ercc1, Ercc2, Ercc3, Ercc4, Ercc5, Ercc6, Ercc8, Lig1, Mms19l (Mms19), Pnkp, Poll, Rad23a, Rad23b, Rpa1, Rpa3, Slk, Xab2, Xpa, Xpc.
Mismatch Repair (MMR): Mlh1, Mlh3, Msh2, Msh3, Msh4, Msh5, Msh6, Pms1, Pms2, Pold3, Trex1, Trex2.
Double-Strand Break (DSB) Repair: Brca1, Brca2, Dmc1, Fen1, Lig4, Mre11a, Prkdc, Rad21, Rad50, Rad51, Rad51c, Rad51l1, Rad51l3, Rad52, Rad54l, Xrcc2, Xrcc3, Xrcc4, Xrcc5, Xrcc6.
Other Genes Related to DNA Repair: Atm, Exo1, Mgmt, Rad18, Rfc1, Top3a, Top3b, Xrcc6bp1.
EpiTect Chip qPCR Arrays provide a reliable tool for the analysis of a
panel of ChIP-enriched genomic sequences associated with transcription
factors and co-regulators, modified and unmodified histones, and other
DNA-binding proteins. The ChIP PCR Arrays can be used for research on stem
cells, cancer, immunology, stem cells, toxicology, biomarker discovery and
How it Works
The ChIP PCR array is a set of optimized real-time PCR primer assays on 96-well
or 384-well plates for pathway or disease focused analysis of in vivo
protein-DNA interactions. The ChIP PCR array performs ChIP DNA analysis with
real-time PCR sensitivity and the multi-genomic loci profiling capability of a
ChIP-on-chip. Simply mix your ChIP DNA samples with the appropriate ready-to-use
PCR master mix, aliquot equal volumes to each well of the same plate, and then
run the real-time PCR cycling program. (Download user manual)
What ChIP PCR Array Offers?
- Function or Disease Focused: Arrays represent a panel of
genomic regions relevant to a biological function or disease state.
- Reliable & Sensitive: Arrays can analyze multiple genomic regions
simultaneously with Real-Time PCR precision and sensitivity.
- Easy to Use Data Analysis: Download an easy-to-use Excel-based data
analysis template [here]. Data analysis is based on the ΔΔCt method with
normalization of the specific antibody and control IgG raw data to input
Layout and Controls: The PCR Arrays are available in both 96- and
384-well plates and are used to monitor the expression of 84 genes related to a
disease state or pathway plus five housekeeping genes. Controls are also
included on each array for ChIP DNA quality controls and general PCR
You can easily perform a ChIP PCR Array experiment in your own laboratory, or
send your samples to us and take advantage of our PCR
EpiTect Chip qPCR Arrays provide the high sensitivity, specificity and
reproducibility using SYBR-based real-time PCR technology.
Together with our easy and fast One-Day ChIP kit, ChIP-Grade Antibody Kits, one
million cells per assay as starting material provides 100% effective call rates.
|Percent Distribution of Ct
Table 1. ChIP PCR Arrays Analyze the Enrichment of 84 Genomic Sites with
as Little as One Million Cells. P19 mouse embryonic carcinoma cells were
prepared for ChIP Assay using the EpiTect Chip One-Day Kit and anti-H3K4me3
Antibody Kit. One million cells were used as starting material for each ChIP
Assay. The purified ChIP DNA samples were characterized using Mouse Stem Cell
Transcription Factor ChIP PCR Array with 1/100th of the ChIP DNA as template in
each well. The Real-Time PCR results demonstrate 100 % effective call rates for
the Input Fraction (Ct < 30). The difference of Ct value between the
anti-H3K4me3 antibody and the control IgG fractions indicates the specific
enrichment of the antibody, whereas the high Ct value of the control IgG
fraction indicates the low background of the assay.
The complete ChIP PCR Array System demonstrates a high degree of
reproducibility across technical replicates, lots, instruments, and different
handling, insuring reliable detection of differences in genomic DNA enrichment
among biological samples.
Figure 5. Consistent Performance within the Same Plate or across Different
Plates. Sonicated chromatin from HeLa cells (20 µg) was immunoprecipitated
with 2 µg of anti-H3ac antibody or control IgG for 2 hours using the
EpiTect Chip One-Day Kit. The obtained ChIP DNA samples were characterized in
triplicates with EpiTect Chip qPCR primers specific for the active genes (GAPDH,
RPL30, ALDOA), inactive genes (MYOD1, SERPINA), repetitive sequence (SAT2, SATa),
and an ORF-free region (IGX1A) either within the same array plate or among
different array plates in order to evaluate the intra- and inter-plate
consistency. The anti-H3ac antibody enriched genomic DNA at active gene promoter
regions with a high signal-to-noise ratio and a low co-efficiency of variation
(less than 2.02%), irrespective of the type of assay (intra or inter-plate)
Figure 6. Consistent Performance with Various Amount of DNA Samples,
Instruments or Handling Conditions. All experiments were performed in
triplicates. Cells from MCF-7 (1 million per sample) were subjected to ChIP
assay with anti-RNA Polymerase II (Pol 2) antibody followed by qPCR analysis of
the proximal promoter of GAPDH, and an ORF-free region (IGX1A). Researcher A
& B performed the PCR assays either in 96-well plate or 384-well plate
format, on a Stratagene MX 3005 or an ABI 7900 Real-Time PCR instrument
respectively. The same ChIP DNA samples were used which were stored for extended
periods of time as indicated. The results demonstrate high reproducibility of
PCR performance across technical replicates, lots, instruments, and differential
Specific and Accurate ChIP-qPCR Detection
One prerequisite for ChIP PCR Array technology is the uniform and high
PCR amplification efficiency allowing a reciprocal comparison of ChIP enrichment
among all genomic loci analyzed. The unique combination of SABiosciences'
proprietary ChIP-qPCR primer design algorithm, rigorous validation of every
ChIP-qPCR primer assay, and high performance SYBR Green master mix guarantees
superior performance of EpiTect Chip qPCR Arrays.
Figure 7. Uniform Amplification Efficiency and Specific PCR Detection.
96 ChIP-qPCR primers were randomly picked from our genome-wide primer pool and
analyzed for their performance. (A) All assays exhibit an average amplification
efficiency of 99% with a 104.5% confidence interval between 102.5-105.2%, the
uniform high amplification efficiency ensures accurate analysis of multiple
genomic loci simultaneously using ΔΔCt method. (B) Each ChIP-qPCR primer assay
is experimentally validated using dissociation (melt) curve analysis and agarose
gel verification. Each pair of primers on PCR Array produces a single specific
product as indicated by a single Dissociation Curve peak at a melting
temperature (Tm) greater than 75 ºC, and PCR product was further validated
on agarose gel for a single product of the predicted size without secondary
products such as primer dimers
EpiTect Chip qPCR Arrays provide streamlined approaches to 1) Study biology or
disease-focused gene regulation through histone modification and transcriptional
regulatory network; 2) Monitor the dynamics of chromatin structure in the
screening of function-specific epigenetic patterns; 3) Validate ChIP-on-chip or
ChIP-seq results. The EpiTect Chip qPCR Arrays are also powerful tools for
studying the mechanism contributing to gene expression changes observed by RT²
Profiler PCR Arrays.
Below are listed a few examples of application data
generated by our R&D group. To see the research using ChIP PCR Arrays
published by the scientific community, please see our Publication List: http://www.sabiosciences.com/support_publication.php
Stem Cell Research
Stem cell differentiation into specific tissues involves the complex yet
coordinated action of many transcription factors regulating not only
tissue-specific genes, but also genes essential for differentiation itself.
Histone modifications at the promoters of transcription factors are key
mechanism regulating their expression. We used EpiTect Chip qPCR Arrays and RT²
PCR Arrays to monitor the dynamic coordination of epigenetic modification and
gene expression during retinoic acid (RA) induced differentiation of P19 mouse
embryonic carcinoma cells (Figure 1). This RA treatment differentiates
pluripotent P19 cells into somatic cells (Figure 2). The EpiTect Chip qPCR Array
data showed that both gene expression and histone modifications on key
transcription factors were changed in a dynamic manner through the course of P19
cell differentiation (Figure 3).
Figure 1. Schematic Representation of Pluripotency-Associated Gene
Dynamics throughout Stem Cell Differentiation
Figure 2. Retinoic Acid (RA) Differentiation of Mouse Embryonic Carcinoma
Figure 3. Dynamic Epigenetic Alternations and Gene Expression
Changes during RA-Induced P19 Differentiation. ChIP PCR Arrays and RT² PCR
Arrays were used to monitor the changes in gene expression levels and histone
modification marks (H3Ac, H3K4me3, H3K27me3, and H3K9me3). The promoter region
and expression levels of 84 key stem cell transcription factors were
simultaneously analyzed during RA-induced neurogenesis of P19 cells at various
time points (day 0, 4, and 8). Primer sets for the +1kb region downstream of the
transcription start sites of the 84 genes and 12 control regions were preloaded
on the ChIP PCR Array. Cluster analysis (http://www.sabiosciences.com/chippcrarray_data_analysis.php)
of histone marks and mRNA level changes for the 84 genes were visualized as a
heat map to represent the fold-differences during the RA-induced differentiation
at the specified time points.
Characterize the Pattern of Histone Modifications
EpiTect Chip qPCR Arrays can be used to monitoring differential
histone modifications across a gene.
Figure 4. The Custom EpiTect Chip 30Kb Tiling Array Quickly
Maps Histone Modifications Surrounding the Transcription Start Site (TSS) of
CDKN1A Gene. EpiTect Chip Antibodies against modified histones (H3Ac,
H3K4me2, H3K27me3), or NIS were used to precipitate chromatin from one million
HeLa cells. Each ChIP DNA fraction was analyzed with Custom EpiTect Chip 30Kb
Tiling Array representing 30 one-kb tile intervals across the promoter region of
the CDKN1A gene. The results indicate the enrichment of histone markers for
actively transcribed genes (H3Ac and H3K4me2) but not marks for transcriptional
inactive genes (H3K27me3) in the genomic region surrounding the TSS of CDNK1A.
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The complete EpiTect Chip qPCR Array System insures that you will
get high-quality results from your ChIP analysis the first time, and
every time guaranteed.
The Complete EpiTect Chip qPCR Array System Includes:
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