Diagenode

ChIPmentation for high-quality and fast ChIP-seq library preparation

Diagenode now offers a unique system that incorporates automation and a ligation-free protocol for chromatin immunoprecipitation coupled with library preparation for high-throughput sequencing (ChIP-seq), ChIPmentation. ChIPmentation is based on tagmentation which enables the integration of the library preparation during the ChIP itself using transposase and sequencing-compatible adaptors. Unlike standard library preparation techniques that require multi-step ligation, ChIPmentation incorporates a much easier and shorter protocol with high efficiency for low input samples. The new ChIPmentation system is available only on the IP-Star Automation System ensuring the highest reproducibility for challenging samples of limited quantities.

Benefits of the ChIPmentation system for optimal ChIP-seq

  • Automate on the IP-Star® to support standardization and reproducibility
  • Save one full day from standard protocols in generating ChIP-seq libraries
  • Enjoy an easier protocol
  • Benefit from the elimination of sequencing adaptor dimers
  • Ensure high quality data on low cell numbers and rare cell types
Diagenode-ChIPmentation

In traditional ChIP-seq library preparation, the ligation of the adaptors is performed after chromatin immunoprecipitation, in three steps. In the Diagenode ChIPmentation workflow, not only are the adaptors directly incorporated during ChIP, but also the main steps are automated on the Diagenode IP-Star®. The combination of direct adaptor incorporation and automation allows for higher sensitivity from low cell numbers and reproducibility 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.

Kit for Auto ChIPmentation - coming soon!

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