Diagenode

Auto ChIPmentation for Histones

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Catalog Number
Format
Price
C01011000
24 rxns
$2,320.00

This product must be used with the IP-Star Compact Automated System.

Difficult and challenging histone ChIP-seq is now solved. Diagenode’s latest technology for histone ChIP-seq, ChIPmentation, incorporates automation with an ligation-free protocol that integrates chromatin immunoprecipitation with NGS library preparation. Using histone ChIPmentation, you can avoid the multi-step ligation required for traditional histone ChIP-seq protocols, providing an easier protocol, faster time to results, and unmatched efficiency and reproducibility for histone ChIP-seq from challenging and low input samples.

  • Characteristics

    ChIPmentation is based on tagmentation that allows library preparation to be integrated during the ChIP itself using transposase and sequencing-compatible adaptors. ChIPmentation involves much easier and shorter protocol with high efficiency for low input samples using optimized ChIP and NGS sample preparation reagents on the IP-Star Compact Automated System. The IP-Star Compact Automated System ensures the highest reproducibility for challenging samples from limited input amounts.

    Benefits of the ChIPmentation system for histone ChIP-seq

    • Automates ChIP-seq of histones on the IP-Star® for highest reproducibility
    • Ensures best quality data on low cell numbers and rare cell types
    • Provides results faster than traditional protocols by one full day
    • Eliminates sequencing adaptor dimers for higher specificity of results

    ChIPmentation - Highest reliability for even the lowest inputs

    The new Auto ChIPmentation technology has been tested on histone marks and compared to available datasets from the ENCODE project (Figure 1). ChIPmentation generated high quality data with low background. In addition, more than 99% of the top 40% peaks obtained with auto-ChIPmentation overlap with ENCODE datasets, which shows that ChIP-seq data obtained with ChIPmentation are highly reliable.

    A.
    Diagenode-Auto-ChIPmentation

    B. Match of the Top40 peaks of Auto-ChIPmentation
    • Figure 1

      Comparison of ChIPmentation sequencing results and reference ChIP-seq data.
      ChIPmentation has been performed using chromatin from 100,000 K562 cells, the Auto ChIPmentation for Histones Kit, and the Diagenode antibody targeting H3K4me3 (Cat. no. C15410003). The experiment was performed on the IP-Star® Compact Automated System. A. Distribution of the ChIPmentation and ENCODE readsets in a representative region of the genome. B. Comparison of the top 40% peaks from ChIPmentation dataset to the ENCODE dataset.

    As ChIPmentation is a ligation-free protocol and requires fewer steps than a classical workflow, it allows the generation of excellent ChIP-seq data from reduced starting amounts. The sequencing data generated from 5,000 and 10,000 cells are very similar to those obtained with 100,000 cells, showing more than 98% overlap of the top 40% peaks (Figure 2).

    A.
    Diagenode-ChIPmentation-sequencing
    B. Match of the Top40 peaks of ChIPmentation from 10.000 cells
    C. Match of the Top40 peaks of ChIPmentation from 5.000 cells
    • Figure 2

      ChIPmentation sequencing results obtained from decreasing starting amounts of cells.
      ChIPmentation has been performed using chromatin from 100.000, 10.000 and 5.000 K562 cells, the Auto ChIPmentation for Histones kit and the Diagenode antibody targeting H3K4me3 (Cat. no. C15410003). The experiments were performed on the IP-Star® Compact Automated System. A. Distribution of the ChIPmentation readsets in a representative region of the genome. B. and C. Comparison of the top 40% peaks from 10.000 (B.) and 5.000 (C.) cells with dataset generated from 100.000 cells.

    Moreover, in order to check the reproducibility of data generated with low cell amounts, correlation between replicates for 10.000 and 5.000 starting cells was performed (Figure 3). The data show very high correlations with Pearson’s coefficients of 0.96 for both conditions.

    A. Auto ChIPmentation on 10.000 cells
    B. Auto ChIPmentation on 5.000 cells
    • Figure 3

      Correlation of replicates of auto-ChIPmentation experiments. ChIPmentation has been performed using chromatin from 10.000 and 5.000 K562 cells, Auto ChIPmentation for Histones Kit and the Diagenode antibody targeting H3K4me3 (Cat. no. C15410003). The experiments were performed on the IP-Star® Compact Automated System.The scatterplots show the correlation between the enrichments between two replicates. The green line represents an ideal case where the two replicates are identical, while the red curve fitted on the data points by a LOESS regression shows the actual trend. A. Correlation analysis between two replicates of auto-ChIPmentation experiments starting from 10.000 cells. B. Correlation analysis between two replicates of auto-ChIPmentation experiments starting from 5.000 cells.

    The Auto-ChIPmentation workflow is easy and fast, producing high-quality ChIP-seq data even on low starting amounts.

    • Figure 4

      ChIPmentation sequencing results for four histone marks. ChIPmentation has been performed using chromatin from K562 cells, the Auto ChIPmentation for histones and the Diagenode antibodies targeting H3K4me1 (Cat. no. C15410194), H3K27me3 (Cat. no. C15410195) and H3K27ac (Cat. no. C15410196), IgG (Cat. no. C15410206). The experiment was performed on the IP-Star® Compact Automated System.

  • Applications
    ChIP-seq
    Chromatin Immunoprecipitation (ChIP) coupled with high-throughput massively parallel sequencing as a detection method (ChIP-seq) has become one of the primary methods for epigenomics researchers, namely to investigate protein-DNA interaction on ... Read more
  • Documents
    Auto ChIPmentation for Histones MANUAL
    Manual of the Auto ChIPmentation for Histones
    Download
  • Publications

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