- What is the difference between tagmentation and ChIPmentation?
Tagmentation is a reaction where an enzyme (a transposase) cleaves DNA and incorporates sequencing adaptors at the ends of the fragments in one step. In our ChIPmentation technology we combine chromatin immunoprecipitation and tagmentation in one streamlined workflow where the tagmentation step occurs directly on chromatin. - What is the expected concentration of ChIPmentation libraries?
The concentration of libraries that you need to reach will depend on the sensitivity of the machine and kits that you will use to perform the quality control and the sequencing of your libraries. Usually a concentration of 4-8 ng/μl is enough for a quality control using the Qubit High Sensitivity assay (ThermoFischer Scientific) and the High Sensitivity chip for BioAnalyzer (Agilent) and for sequencing on Illumina HiSeq3000/4000. - Does the ChIPmentation approach work on plants?
Our ChIPmentation solution has been validated on human cells and we do not have any data on plants. It should be compatible. We would recommend using our Universal Plant ChIP Kit in combination with the TAG Kit for ChIPmentation and the 24 SI for ChIPmentation. - What is the size of the fragments after the tagmentation?
The size of the fragments at the end of the ChIPmentation protocol can vary depending on many parameters like the shearing efficiency, the antibody used or the tagmentation time. However, with our standard protocol we usually obtain a library peak which is around 200-300 bp (see example of results at the end of the manual). If many fragments larger than 500 bp are present , the best would be to contact your sequencing provider to ask what their requirements are, because it can vary depending on the sequencer. If you want to remove the large fragments you can use the size selection protocol described in the manual. - What is the size of the adapters?
The sum of the adapters is 128 bp.
TAG Kit for ChIPmentation
Catalog Number
Format
Price
C01011030
24 rxns
$1,075.00
The TAG Kit for ChIPmentation offers an optimized ChIP-seq library preparation solution based on tagmentation. This kit includes reagents for tagmentation-based library preparation integrated in the IP and is compatible with any ChIP protocol based on magnetic beads. The primer indexes for multiplexing must be purchased separately and are available as a reference:
24 UDI for Tagmented libraries - Set I, Cat. No. C0101134
24 UDI for Tagmented libraries - Set II, Cat. No. C0101136
24 UDI for Tagmented libraries - Set III, Cat. No. C0101137
Alternatively, for histone marks, Hologic Diagenode proposes the complete solution (including all buffers for ChIP, tagmentation and multiplexing): ChIPmentation for Histones and µChIPmentation for Histones.
Features
- Sample: chromatin-antibody-magnetic beads complexes
- Input: chromatin from 5 K – 4 M cells
- Easy and fast protocol
- Compatible with any ChIP protocol based on magnetic beads
- No adapter dimers
- Sequencing technology: Illumina
TESTIMONIALOne 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).
- Characteristics
Comparing to classical ChIP-seq, ChIPmentation enables:
- An easier protocol
- Faster time to results
- Flexibility – the TAG Kit for ChIPmentation allows you to perform ChIPmentation with any ChIP protocol (based on magnetic beads)
ChIPmentation on histone marks using TAG KIT for ChIPmentation
ChIPmentation sequencing results for four histone marks. Chromatin preparation has been performed on 7M K562 cells using the Auto iDeal ChIP-seq Kit for Histones (Cat. No. C01010057), TAG Kit for ChIPmentation (Cat. No. C01011030) and 24 SI for ChIPmentation (Cat. No. C01011031)*. Diluted chromatin from 1,000,000 cells was used for the immunoprecipitation with the Diagenode antibodies targeting H3K4me1 (Cat. No. C15410194), H3K27me3 (Cat. No. C15410195), H3K27ac (Cat. No. C15410196) and IgG (Cat. No. C15410206). The experiment was performed on the IP-Star® Compact Automated System.
*The Auto iDeal ChIP-seq for Histones (C01010057), TAG Kit for ChIPmentation (C01011030) and 24 SI for ChIPmentation (C01011031) form together the Auto ChIPmentation Kit for Histones* (C01011000).
ChIPmentation on non-histone proteins using TAG Kit for ChIPmentation
ChIPmentation sequencing results for two non histone factors. Chromatin preparation has been performed on 25M K562 cells using the iDeal ChIP-seq kit for TFs (Cat. No. C01010055). Diluted chromatin from 1,000,000 or 4,000,000 cells was used for the immunoprecipitation with the Diagenode antibodies targeting CTCF (Cat. No. C15410210) and RNA PolII (Cat. No. C15100055 ) respectively. The library preparation was performed with the TAG Kit for ChIPmentation (Cat. No. C01011030) and 24 SI for ChIPmentation (Cat. No. C01011031).
- 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.
Researcher from University of Nice-Sophia Antipolis, Nice, FranceChIPmentation 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).
- Publications
How to properly cite our product/service in your work
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Using our products or services in your publication? Let us know!
Neurons undergo IFNγ-driven persistent epigenetic shifts and synaptopathy in encephalitis
Shammas, Ghazal et al.
In infectious and autoimmune disorders of the central nervous system, neurons can become cognate immunological targets of cytotoxic T cells, leading to persistent functional and synaptic impairments. However, the molecular underpinnings of such irreversible alterations remain unclear. Using a cytotoxic T cell-driv...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 ...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... - Related products
