Diagenode

iDeal ChIP-seq kit for Transcription Factors

Catalog Number
Format
Price
C01010054
2 chrom. prep./10 IPs
$575.00
Other format

Diagenode’s iDeal ChIP-seq Kit for Transcription Factors is a highly validated solution for robust transcription factor and other non-histone proteins ChIP-seq results and contains everything you need for start-to-finish ChIP prior to Next-Generation Sequencing. This complete solution contains all buffers and reagents for cell lysis, chromatin shearing, immunoprecipitation, and DNA purification. In addition, unlike competing solutions, the kit contains positive and negative control antibodies (CTCF and IgG, respectively) as well as positive and negative control PCR primers pairs (H19 and Myoglobin exon 2, respectively) for your convenience and a guarantee of optimal results.

The  iDeal ChIP-seq kit for Transcription Factors is compatible for cells or tissues:

Amount per IP
Cells 4,000,000
Tissues 30 mg

The iDeal ChIP-seq kit is the only kit on the market validated for major sequencing systems. Our expertise in ChIP-seq tools allows reproducible and efficient results every time.

TESTIMONIAL

One of our issues was that we could obtain only a limited number of cells, which is not enough for canonical ChIP-seq protocols. To solve this issue, we used the Diagenode ChIPmentation solution composed of iDeal ChIP-seq Kit for Transcription Factor, TAG Kit for ChIPmentation, and 24 SI for ChIPmentation. We performed ChIPmentation with IP-Star automated system for GATA6 in 2 million GATA6-overxpressing iPS cells. The result showed clear signal/noise ratio and was highly reproducible. This solution also worked in vitro differentiated definitive endoderm cells (data not shown).

Region 1

Region 2

Figure 1. ChIPmentation sequencing profiles for Gata6
Chromatin preparation and immunoprecipitation have been performed on hiPSCs (human induced Pluripotent Stem Cells) overexpressing Gata6 using the iDeal ChIP-seq kit for TFs (Cat. No. C01010055). Chromatin from 2,000,000 cells was used for the immunoprecipitation in combination with either anti-GATA6 antibody. The library preparation was performed with the TAG Kit for ChIPmentation (Cat. No. C01011030) and 24 SI for ChIPmentation (Cat. No. C01011031).

Takahiro Suzuki, Ph.D., Senior Research Scientist, Cellular Function Conversion Technology Team, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
  • Characteristics
    • Highly optimized protocol for ChIP-seq from cells and tissues
    • Validated for ChIP-seq with multiple transcription factors and non-histone targets
    • Most complete kit available (covers all steps, including the control antibodies and primers)
    • Magnetic beads make ChIP easy, fast and more reproducible
    • Combination with Diagenode ChIP-seq antibodies provides high yields with excellent specificity and sensitivity
    • Purified DNA suitable for any downstream application
    • Easy-to-follow protocol

     

    ChIP-seq on cells

    CTCF Diagenode

    Figure 1. (A) Chromatin Immunoprecipitation has been performed using chromatin from HeLa cells, the iDeal ChIP-seq kit for Transcription Factors and the Diagenode ChIP-seq-grade CTCF antibody. The IP'd DNA was subsequently analysed on an Illumina® HiSeq. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. This figure shows the peak distribution in a region surrounding the GAPDH positive control gene.

    CTCF Diagenode

    Figure 1B. The ChIP-seq dataset from this experiment has been compared with a reference dataset from the Broad Institute. We observed a perfect match between the top 40% of Diagenode peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.

     

    ChIP-seq figure A

    ChIP-seq figure B

    ChIP-seq figure C

    Figure 2. Chromatin Immunoprecipitation has been performed using chromatin from HeLa cells, the iDeal ChIP-seq kit for Transcription Factors and the Diagenode ChIP-seq-grade HDAC1 (A), LSD1 (B) and p53 antibody (C). The IP'd DNA was subsequently analysed on an Illumina® Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. This figure shows the peak distribution in regions of chromosome 3 (A), chromosome 12 (B) and chromosome 6 (C) respectively.

     

    ChIP-seq on tissue

    ChIP-seq figure A

    Figure 3A. Chromatin Immunoprecipitation has been performed using chromatin from mouse liver tissue, the iDeal ChIP-seq kit for Transcription Factors and the Diagenode ChIP-seq-grade CTCF antibody. The IP'd DNA was subsequently analysed on an Illumina® HiSeq. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. This figure shows the peak distribution in a region surrounding the Vwf positive control gene.

    Match of the Top40 peaks

    Figure 3B. The ChIP-seq dataset from this experiment has been compared with a reference dataset from the Broad Institute. We observed a perfect match between the top 40% of Diagenode peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.

  • Species, cell lines, tissues tested

    The iDeal ChIP-seq Kit for Transcription Factors is compatible with a broad variety of cell lines, tissues and species, as shown below. Other species / cell lines / tissues can be used with this kit.

    Cell lines:

    Human: A549, A673, BT-549, CD4 T, HCC1806, HeLa, HepG2, HFF, HK-GFP-MR, ILC, K562, KYSE-180, LapC4, M14, MCF7, MDA-MB-231, MDA-MB-436, RDES, SKNO1, VCaP, U2-OS, ZR-75-1                     

    Mouse: ESC, NPCs, BZ, GT1-7, acinar cells, HSPCs, Th2 cells, keratinocytes

    Cattle: pbMEC, MAC-T

    Tissues:

    Mouse: kidney, heart, brain, iris, liver, limbs from E10.5 embryos

    Horse: liver, brain, heart, lung, skeletal muscle, lamina, ovary

    ChIP on yeast

    The iDeal ChIP-seq kit for TF is compatible with yeast samples. Check out our Application Note presenting an optimized detailed protocol for ChIP on yeast.

    Did you use the iDeal ChIP-seq for Transcription Factors Kit on other cell line / tissue / species? Let us know!

  •  Testimonials

    We were very happy with the method.  It gave good results in the end, and required much smaller samples than we need to reliably perform conventional ChIP-seq.
    In our view, the main advantages of the ChIPmentation kit compared to our conventional ChIP-seq protocol are (most important first):

    • smaller sample requirement,
    • simpler workflow with less that can go wrong,
    • slightly higher resolution and signal: noise ratio.

    ChIPmentation sequencing profiles for p65. Chromatin preparation and immunoprecipitation have been performed on stimulated NIH3T3 cells using the iDeal ChIP-seq kit for TFs (Cat. No. C01010055). Chromatin from 4,000,000 cells was used for the immunoprecipitation in combination with either anti-p65 antibody or IgG. The library preparation was performed with the TAG Kit for ChIPmentation (Cat. No. C01011030) and 24 SI for ChIPmentation (Cat. No. C01011031).

    Researcher from University of Nice-Sophia Antipolis, Nice, France

    I have been using Diagenode products to perform ChIP-seq during the last three years and I am very satisfied, with the Bioruptor, the kits and the antibodies. I have used the iDeal ChIP-seq kit for Histones and the iDeal ChIP-seq kit for Transcription Factors with very successful and reproducible results. Once I tried to ChIP histones with a home-made protocol and it worked much worse in comparison with Diagenode kits. In other occasion, I tried a non-Diagenode antibody for a transcription factor and I also got much poor results, however with the Diagenode antibody I always got very nice results. I strongly recommend the use of Diagenode products.

    Dr. Francisca Martinez Real - Development and Disease Research Group - Max Planck Institute for Molecular Genetics, Berlin, Germany

    There are so many ChIP-related products on the market, but I feel so lucky that I have been using the ones from Diagenode since I started my CHIP-seq project. I have used their iDeal CHIP-seq Kit for Transcription Factors and MicroPlex Library Prep Kit v2. Both of them are fantastic and very reproducible. With the very-well written protocols, you will just be home and dry. Particularly, I want to thank the technical support, who is very patient, knowledgeable and extremely helpful. I would definitely recommend my colleagues to use the CHIP products from Diagenode.

    Dr Kaiyu Lei, Faculty of Medicine, Department of Surgery & Cancer, Imperial College London
  • Additional solutions compatible with iDeal ChIP-seq kit for Transcription Factors

    The Chromatin shearing optimization kit – Low SDS (iDeal Kit for TFs) is the kit compatible with the iDeal ChIP-seq kit for TF, recommended for the optimization of chromatin shearing, a critical step for ChIP.

    ChIP Cross-link Gold should be used in combination with formaldehyde when working with higher order and/or dynamic interactions, for efficient protein-protein fixation.

    For library preparation of immunoprecipitated samples we recommend to use the  MicroPlex Library Preparation Kit - validated for library preparation from picogram inputs.

    ChIP-seq grade antibodies provide high yields with excellent specificity and sensitivity.

    Check the list of available Primer pairs designed for high specificity to specific genomic regions.

    Plus, for our IP-Star Automation users for automated ChIP, check out our automated version of this kit.

  •  Documents
    iDeal ChIP-seq Kit for Transcription Factors - Manual MANUAL
    Diagenode’s iDeal ChIP-seq Kit for Transcription Factors is a highly specialized solution f...
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    Chromatin Brochure BROCHURE
    Whether you are experienced or new to the field of chromatin immunoprecipitation, Diagenode has e...
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    iDeal ChIP-seq Kit for Transcription Factors -マニュアル マニュアル
    DiagenodeのiDeal ChIP-seq kit for transcription factorsは、強力な転写因子ChIP-seqの結果を得るための高度に特殊化されたソリューションで...
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    Optimize the selection of guide RNA by ChIP to keep CRISPR on-target APPLICATION NOTE
    The mechanisms of target recognition and target specificity of the Cas9 protein is still not comp...
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    Application note - ChIP on yeast APPLICATION NOTE
    The Application Note: "Use of the iDeal® chromatin immunoprecipitation (ChIP) kit for the ide...
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  •  Safety sheets
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  •  Publications

    How to properly cite this product in your work

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    Using our products in your publication? Let us know!

    ThPOK is a critical multifaceted regulator of myeloid lineagedevelopment.
    Basu J. et al.
    The transcription factor ThPOK (encoded by Zbtb7b) is well known for its role as a master regulator of CD4 lineage commitment in the thymus. Here, we report an unexpected and critical role of ThPOK as a multifaceted regulator of myeloid lineage commitment, differentiation and maturation. Using reporter and knockout ...

    Mediator 1 ablation induces enamel-to-hair lineage conversion in micethrough enhancer dynamics.
    Thaler R. et al.
    Postnatal cell fate is postulated to be primarily determined by the local tissue microenvironment. Here, we find that Mediator 1 (Med1) dependent epigenetic mechanisms dictate tissue-specific lineage commitment and progression of dental epithelia. Deletion of Med1, a key component of the Mediator complex linking enh...

    Supraphysiological Androgens Promote the Tumor Suppressive Activity of the Androgen Receptor Through cMYC Repression and Recruitment of the DREAM Complex
    Nyquist M. et al.
    The androgen receptor (AR) pathway regulates key cell survival programs in prostate epithelium. The AR represents a near-universal driver and therapeutic vulnerability in metastatic prostate cancer, and targeting AR has a remarkable therapeutic index. Though most approaches directed toward AR focus on inhibiting AR ...

    In skeletal muscle and neural crest cells, SMCHD1 regulates biologicalpathways relevant for Bosma syndrome and facioscapulohumeral dystrophyphenotype.
    Laberthonnière C. et al.
    Many genetic syndromes are linked to mutations in genes encoding factors that guide chromatin organization. Among them, several distinct rare genetic diseases are linked to mutations in SMCHD1 that encodes the structural maintenance of chromosomes flexible hinge domain containing 1 chromatin-associated factor. In hu...

    Vitamin D Receptor Cross-talk with p63 Signaling PromotesEpidermal Cell Fate.
    Oda Y. et al.
    The vitamin D receptor with its ligand 1,25 dihydroxy vitamin D (1,25D) regulates epidermal stem cell fate, such that VDR removal from Krt14 expressing keratinocytes delays re-epithelialization of epidermis after wound injury in mice. In this study we deleted Vdr from Lrig1 expressing stem cells in the isthmus of th...

    SOX expression in prostate cancer drives resistance to nuclear hormonereceptor signaling inhibition through the WEE1/CDK1 signaling axis.
    Williams A. et al.
    The development of androgen receptor signaling inhibitor (ARSI) drug resistance in prostate cancer (PC) remains therapeutically challenging. Our group has described the role of sex determining region Y-box 2 (SOX2) overexpression in ARSI-resistant PC. Continuing this work, we report that NR3C1, the gene encoding glu...

    Epigenetic silencing of selected hypothalamic neuropeptides in narcolepsywith cataplexy.
    Seifinejad A. et al.
    Narcolepsy with cataplexy is a sleep disorder caused by deficiency in the hypothalamic neuropeptide hypocretin/orexin (HCRT), unanimously believed to result from autoimmune destruction of hypocretin-producing neurons. HCRT deficiency can also occur in secondary forms of narcolepsy and be only temporary, suggest...

    Activation of AKT induces EZH2-mediated β-catenin trimethylation incolorectal cancer.
    Ghobashi A. H. et al.
    Colorectal cancer (CRC) develops in part through the deregulation of different signaling pathways, including activation of the WNT/β-catenin and PI3K/AKT pathways. Enhancer of zeste homolog 2 (EZH2) is a lysine methyltransferase that is involved in regulating stem cell development and differentiation and is ove...

    Low affinity CTCF binding drives transcriptional regulation whereashigh affinity binding encompasses architectural functions
    Marina-Zárate E. et al.
    CTCF is a DNA-binding protein which plays critical roles in chromatin structure organization and transcriptional regulation; however, little is known about the functional determinants of different CTCF-binding sites (CBS). Using a conditional mouse model, we have identified one set of CBSs that are lost upon CTCF de...

    ZEB1 controls a lineage-specific transcriptional program essential formelanoma cell state transitions
    Tang Y. et al.
    Cell plasticity sustains intra-tumor heterogeneity and treatment resistance in melanoma. Deciphering the transcriptional mechanisms governing reversible phenotypic transitions between proliferative/differentiated and invasive/stem-like states is required in order to design novel therapeutic strategies. EMT-inducing ...

    A dataset of definitive endoderm and hepatocyte differentiations fromhuman induced pluripotent stem cells.
    Tanaka Y. et al.
    Hepatocytes are a major parenchymal cell type in the liver and play an essential role in liver function. Hepatocyte-like cells can be differentiated in vitro from induced pluripotent stem cells (iPSCs) via definitive endoderm (DE)-like cells and hepatoblast-like cells. Here, we explored the in vitro differentiation ...

    The mineralocorticoid receptor modulates timing and location of genomicbinding by glucocorticoid receptor in response to synthetic glucocorticoidsin keratinocytes.
    Carceller-Zazo E. et al.
    Glucocorticoids (GCs) exert potent antiproliferative and anti-inflammatory properties, explaining their therapeutic efficacy for skin diseases. GCs act by binding to the GC receptor (GR) and the mineralocorticoid receptor (MR), co-expressed in classical and non-classical targets including keratinocytes. Using knocko...

    In vitro production of cat-restricted Toxoplasma pre-sexual stages byepigenetic reprogramming
    Antunes A. V.et al.
    Sexual reproduction of , which is restricted to the small intestine of felids, is sparsely documented, due to ethical concerns surrounding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cis...

    A Systemic and Integrated Analysis of p63-Driven RegulatoryNetworks in Mouse Oral Squamous Cell Carcinoma.
    Glathar A. R. et al.
    Oral squamous cell carcinoma (OSCC) is the most common malignancy of the oral cavity and is linked to tobacco exposure, alcohol consumption, and human papillomavirus infection. Despite therapeutic advances, a lack of molecular understanding of disease etiology, and delayed diagnoses continue to negatively affect sur...

    The aryl hydrocarbon receptor cell intrinsically promotes resident memoryCD8 T cell differentiation and function.
    Dean J. W. et al.
    The Aryl hydrocarbon receptor (Ahr) regulates the differentiation and function of CD4 T cells; however, its cell-intrinsic role in CD8 T cells remains elusive. Herein we show that Ahr acts as a promoter of resident memory CD8 T cell (T) differentiation and function. Genetic ablation of Ahr in mouse CD...

    Impact of Fetal Exposure to Endocrine Disrupting ChemicalMixtures on FOXA3 Gene and Protein Expression in Adult RatTestes.
    Walker C. et al.
    Perinatal exposure to endocrine disrupting chemicals (EDCs) has been shown to affect male reproductive functions. However, the effects on male reproduction of exposure to EDC mixtures at doses relevant to humans have not been fully characterized. In previous studies, we found that in utero exposure to mixtures of th...

    Expression of RNA polymerase I catalytic core is influenced byRPA12.
    Ford B. L. et al.
    RNA Polymerase I (Pol I) has recently been recognized as a cancer therapeutic target. The activity of this enzyme is essential for ribosome biogenesis and is universally activated in cancers. The enzymatic activity of this multi-subunit complex resides in its catalytic core composed of RPA194, RPA135, and RPA12, a s...

    ΔNp63α facilitates proliferation and migration, and modulates the chromatin landscape in intrahepatic cholangiocarcinoma cells
    Anghui Peng et al.
    p63 plays a crucial role in epithelia-originating tumours; however, its role in intrahepatic cholangiocarcinoma (iCCA) has not been completely explored. Our study revealed the oncogenic properties of p63 in iCCA and identified the major expressed isoform as ΔNp63α. We collected iCCA clinical data from Th...

    Identification of an E3 ligase that targets the catalytic subunit ofRNA polymerase I upon transcription stress.
    Pitts Stephanie et al.
    RNA polymerase I (Pol I) synthesizes ribosomal RNA (rRNA), which is the first and rate-limiting step in ribosome biogenesis. Factors governing the stability of the polymerase complex are not known. Previous studies characterizing the Pol I inhibitor BMH-21 revealed a transcriptional stress-dependent pathway for degr...

    Histone Deacetylases 1 and 2 target gene regulatory networks of nephronprogenitors to control nephrogenesis.
    Liu Hongbing et al.
    Our studies demonstrated the critical role of Histone deacetylases (HDACs) in the regulation of nephrogenesis. To better understand the key pathways regulated by HDAC1/2 in early nephrogenesis, we performed chromatin immunoprecipitation sequencing (ChIP-Seq) of Hdac1/2 on isolated nephron progenitor cells (NPCs) fro...

    Identification of genomic binding sites and direct target genes for thetranscription factor DDIT3/CHOP.
    Osman A. et al.
    DDIT3 is a tightly regulated basic leucine zipper (bZIP) transcription factor and key regulator in cellular stress responses. It is involved in a variety of pathological conditions and may cause cell cycle block and apoptosis. It is also implicated in differentiation of some specialized cell types and as an oncogene...

    Androgen-Induced MIG6 Regulates Phosphorylation ofRetinoblastoma Protein and AKT to Counteract Non-Genomic ARSignaling in Prostate Cancer Cells.
    Schomann T. et al.
    The bipolar androgen therapy (BAT) includes the treatment of prostate cancer (PCa) patients with supraphysiological androgen level (SAL). Interestingly, SAL induces cell senescence in PCa cell lines as well as ex vivo in tumor samples of patients. The SAL-mediated cell senescence was shown to be androgen receptor (A...

    Co-inhibition of ATM and ROCK synergistically improves cellproliferation in replicative senescence by activating FOXM1 and E2F1.
    Yang Eun Jae et al.
    The multifaceted nature of senescent cell cycle arrest necessitates the targeting of multiple factors arresting or promoting the cell cycle. We report that co-inhibition of ATM and ROCK by KU-60019 and Y-27632, respectively, synergistically increases the proliferation of human diploid fibroblasts undergoing replicat...

    Derailed peripheral circadian genes in polycystic ovary syndrome patientsalters peripheral conversion of androgens synthesis.
    Johnson B.S. et al.
    STUDY QUESTION: Do circadian genes exhibit an altered profile in peripheral blood mononuclear cells (PBMCs) of polycystic ovary syndrome (PCOS) patients and do they have a potential role in androgen excess? SUMMARY ANSWER: Our findings revealed that an impaired circadian clock could hamper the regulation of peripher...

    GATA6 is predicted to regulate DNA methylation in an in vitro model ofhuman hepatocyte differentiation.
    Suzuki T. et al.
    Hepatocytes are the dominant cell type in the human liver, with functions in metabolism, detoxification, and producing secreted proteins. Although gene regulation and master transcription factors involved in the hepatocyte differentiation have been extensively investigated, little is known about how the epigenome is...

    A systematic comparison of FOSL1, FOSL2 and BATF-mediatedtranscriptional regulation during early human Th17 differentiation.
    Shetty A. et al.
    Th17 cells are essential for protection against extracellular pathogens, but their aberrant activity can cause autoimmunity. Molecular mechanisms that dictate Th17 cell-differentiation have been extensively studied using mouse models. However, species-specific differences underscore the need to validate these findin...

    An obesogenic feedforward loop involving PPARγ, acyl-CoA bindingprotein and GABA receptor.
    Anagnostopoulos Gerasimos et al.
    Acyl-coenzyme-A-binding protein (ACBP), also known as a diazepam-binding inhibitor (DBI), is a potent stimulator of appetite and lipogenesis. Bioinformatic analyses combined with systematic screens revealed that peroxisome proliferator-activated receptor gamma (PPARγ) is the transcription factor that best expl...

    Transient regulation of focal adhesion via Tensin3 is required fornascent oligodendrocyte differentiation
    Merour E. et al.
    The differentiation of oligodendroglia from oligodendrocyte precursor cells (OPCs) to complex and extensive myelinating oligodendrocytes (OLs) is a multistep process that involves largescale morphological changes with significant strain on the cytoskeleton. While key chromatin and transcriptional regulators of diffe...

    Characteristics of Immediate-Early 2 (IE2) and UL84 Proteins in UL84-Independent Strains of Human Cytomegalovirus (HCMV)
    Salome Manska and Cyprian C Rossetto
    Human cytomegalovirus (HCMV) immediate-early 2 (IE2) protein is the major transactivator for viral gene expression and is required for lytic replication. In addition to transcriptional activation, IE2 is known to mediate transcriptional repression of promoters, including the major immediate-early (MIE) promoter and ...

    Essential role of a ThPOK autoregulatory loop in the maintenance ofmature CD4 T cell identity and function.
    Basu Jayati et al.
    The transcription factor ThPOK (encoded by the Zbtb7b gene) controls homeostasis and differentiation of mature helper T cells, while opposing their differentiation to CD4 intraepithelial lymphocytes (IELs) in the intestinal mucosa. Thus CD4 IEL differentiation requires ThPOK transcriptional repression via reactivati...

    Environmental enrichment preserves a young DNA methylation landscape inthe aged mouse hippocampus
    Zocher S. et al.
    The decline of brain function during aging is associated with epigenetic changes, including DNA methylation. Lifestyle interventions can improve brain function during aging, but their influence on age-related epigenetic changes is unknown. Using genome-wide DNA methylation sequencing, we here show that experiencing ...

    Sarcomere function activates a p53-dependent DNA damage response that promotes polyploidization and limits in vivo cell engraftment.
    Pettinato, Anthony M. et al.
    Human cardiac regeneration is limited by low cardiomyocyte replicative rates and progressive polyploidization by uncle