iDeal ChIP-seq kit for Transcription Factors

• 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

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.

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.

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

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.

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.

The iDeal ChIP-seq Kit for Transcription Factors is compatible with a broad variety of cell lines, tissues and species - some examples are 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

Other cell lines / species: compatible, not tested

Tissues:

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

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

Other tissues: compatible, not tested

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!

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

I have been doing ChIPs for a very long time and have tried many kits from different sources like Active Motif, Millipore/Upstate, and homemade reagents. The reproducibility and binding efficacy were never optimal for these until a colleague recommended the iDeal ChIP-seq Kit for Transcription Factors from Diagenode. I have done more than one hundred samples of ChIPs and ChIP-seq using this kit. The results are very consistent and the binding efficacy is higher than with all the other methods. I would definitely recommend this ChIP kit from Diagenode to anyone who is trying to do ChIP or ChIP-seq.

Researcher at Johns Hopkins University, School of Medicine

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

The new Bioruptor^® Pico machine has reduced the amount of time spent sonicating Chromatin by a massive amount. Some protocols require quite harsh fixing conditions which meant fragmenting DNA on the old machine was taking many rounds and several times. With the new Bioruptor^® Pico machine these sonications were taking just one round of 10 cycles thereby reducing the fragmentation time substantially. Following sonication, I have used the new IDeal ChIP-seq kit. This is a nice straight forward kit that if followed with an appropriate chip validated antibody gave amazing chip-seq results that worked time and again with several different transcription factors. I would recommend both kits for good, consistant chromatin work.

Dr. Karen Dawson, RNA Biology Group, Cancer Research UK Manchester Institute at the University of Manchester