obtain ChIP-Seq data from clinical samples
Epigenetic misregulation is now known to contribute to diseases such as cancer. In cancer, mutations in the enzymes that regulate histone modification deposition and removal are mutated at a high frequency and these mutations result in alterations in global histone modification patterns. Understanding changes in global histone modification landscapes can provide clues to cellular origins, disease progression and possibly, patient outcome. In order to fully realize the potential of global histone modification profiling toward advances in disease biology and clinical outcomes, it will be necessary to generate profiles using FFPE preserved patient samples. However, ChIP-Seq, the technique that is used to generate these profiles, is challenging and has traditionally required cell numbers that are much greater than what can be obtained from FFPE sections. To address this limitation, scientists at Active Motif have developed the ability to perform ChIP-Seq from limited amounts of formalin-fixed, paraffin-embedded (FFPE) tissue.
The FFPE ChIP-Seq Service Includes:
- Chromatin isolation from FFPE blocks, slides or sections*.
- Immunoprecipitation using a robust histone modification or TF antibody.
- Library construction for Next-Gen sequencing.
- Next-Gen sequencing using an Illumina sequencer.
- Data Analysis.
*Active Motif will recommend the amount of material to be supplied, which will depend on the tissue type being used. Typically > 5 sections (10µm) per ChIP-Seq experiment are necessary.
FFPE ChIP-Seq Data
Active Motif has performed FFPE ChIP-Seq from clinical samples that have been preserved for more than 10 years. Sample types include tumor and matched normal tissue from human liver, kidney, colon and others. These assays have been performed successfully using robust ChIP-Seq validated antibodies against histone modifications.
Figure 1: FFPE ChIP-Seq performed using 20 year old colon tumor FFPE block and antibodies against H3K4me3 and H3K36me3.
Figure 2: FFPE ChIP-Seq performed using 20 year old colon tumor FFPE block and antibodies against H3K27ac and H3K27me3.
Figure 3: FFPE ChIP-Seq performed using 2 human Glioblastoma biopsies and an antibody against H3K27ac.
Figure 4: FFPE ChIP-Seq performed using 2 human Glioblastoma biopsies and an antibody against H3K27ac.
Figure 5: FFPE ChIP-Seq performed using 2 human Glioblastoma biopsies and an antibody against H3K27ac.
Figure 6: FFPE ChIP-Seq was performed using chromatin from two human tumor biopsies and an antibody against H3K27ac.
Figure 7: FFPE ChIP-Seq performed using a human Glioblastoma biopsy and an antibody against H3K27me3.
Figure 8: FFPE ChIP-Seq performed using a human Glioblastoma biopsy and an antibody against H3K27me3.