Diagenode µChIPmentation for Histones

The Diagenode µChIPmentation Kit for Histones is optimized to perform ChIP-seq on as little as 10.000 cells from cell fixation to purified libraries. To reduce DNA lost the number of sample transfer from tube to tube has been limited: during whole workflow - from cell fixation to library prurification - only 3 tubes per sample are used. Reduced number of steps, reduced number of sample transfer and ChIPmentation technology itself enable for efficient and robust ChIP-seq on limited amount of sample. The kit µChIPmentation for Histones includes all reagents for chromatin preparation, chromatin immunoprecipitation and library preparation using tagmentation. The primer indexes for multiplexing are not included in the kit and have to be purchase separately - read more.

Benefits of the µChIPmentation system for histone ChIP-seq

• Easier and faster than classical ChIP-seq
• Optimized for low input samples: as little as 10,000 cells
• Protocol optimized for FACS-sorted cells
• Validated for various histone marks
• High quality sequencing data

ChIPmentation is based on tagmentation that allows library preparation to be integrated during the ChIP itself using transposase and sequencing-compatible adaptors. Our new improved µChIPmentation protocol combines 3 features for guaranteeing high quality sequencing data on small sample inputs 1) optimized chromatin shearing preparation protocol, 2) reduced number of steps, 3) reduced number of sample transfer from tube to tube - only 3 tubes per sample for the whole process, from cell fixation to purified libraries.

•  Workflow of µChIPmentation for Histones

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Figure 1. Comparison between ChIPmentation and µChIPmentation

ChIPmentation: chromatin preparation has been performed on 7 M K562 cells using the ChIPmentation Kit for Histones (Cat. No. C01011000) and diluted chromatin from 500.000 cells was used for the immunoprecipitation. µChIPmentation: chromatin preparation and immunoprecipitation have been performed on 10.000 K562 cells using the µChIPmentation Kit for Histones (Cat. No. C01011011) and 24 SI for Tagmented libraries (Cat. No. C010111032). The Diagenode antibody targeting H3K27me3 (Cat. No. C15410195) was used.

A. Distribution of the ChIPmentation and µChIPmentation readsets in a representative region of the genome (in duplicates). B. Comparison of the top 40% peaks from µChIPmentation (10.000 cells) with dataset generated with ChIPmentation (500.000 cells).

Figure 2. Sequencing profiles of µChIPmentation libraries

Chromatin preparation and immunoprecipitation have been performed on 10.000 cells using the µChIPmentation Kit for Histones (Cat. No. C01011011) and 24 SI for Tagmented libraries (Cat. No. C010111032) using K562 cells. The Diagenode antibodies targeting H3K4me3 (Cat. No. C15410003), H3K27ac (Cat. No. C15410196), H3K27me3 (Cat. No. C15410195) and H3K9me3 (Cat. No. C15410193) have been used.

Figure 3. Integrative genomics viewer (IGV) visualization of from ChIP-seq experiments using H3K27me3 antibody (Diagenode, Cat. No.  C15410195) and 10.000 cells of K562 cells per immunoprecipitation.